_dictionary.title cifdic.m94
_dictionary.version 0.7.1
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
0.1.1
1993-02-11
;
Highlighted all notes with # %%%%% surrounds.
;
0.1.2
1993-02-11
;
Started moving examples to *_appendix data items.
;
0.1.3
1993-02-11
;
Started moving core data names to the *_appendix data items
;
0.1.4
1993-02-11
;
Added example for _symmetry_
;
0.1.5
1993-03-24
;
Finished moving examples to *_appendix data items
;
0.1.6
1993-03-24
;
Dealt with many issues raised by SR Hall.
Some were merely typographical.
Changed temp to B_iso
Changed occ to occupancy
Changed special_details to details.
Changed asl to label everywhere.
Shuffled data names in _struct_conf_ and _struct_conn_
;
0.1.7
1993-03-24
;
Tested for Cyclops compliance - most problems are names that
are too long.
Changed crystal_prepration to crystal_prep
Changed d_resolution to d_res
Many other such changes
;
0.1.8
1993-03-25
;
Still testing for Cyclops compliance - reveal many additional
syntax problems
Also verified with new tool by RG Ball - still more errors fixed
Dealt with issue raised by PE Bourne - amongst changes
Rewrote _database_ section completely
Changed _audit_contact_author_ to
_audit_contact_author_name
_audit_contact_author_address
;
0.1.9
1993-03-26
;
Removed _struct_topol_ section until it gets straightened out
;
0.1.10
1993-03-28
;
Filled in examples for several data categories
;
0.1.11
1993-04-03
;
Syntax checked using tools of Peter Murray-Rust - many problems fixed
;
0.1.12
1993-04-06
;
More syntax problems fixed a la Peter Murray-Rust
;
0.1.13
1993-04-07
;
Introduced _exptl_crystal_grow_ data names
;
0.1.14
1993-04-07
;
Experiment with refers_to, category and part_of_key in
entity_conn_atom_ and entity_conn_bond_ sections.
Discovered horror show with nonconcurrent versions on different
computers - not yet resolved.
;
0.1.15
1993-05-09
;
Reconciled nonconcurrent versions
Removed trailing blanks
Made corrections based on email suggestions from P. Bourne
;
0.1.16
1993-05-10
;
Made corrections based on written comments from K. Watenpaugh
Made corrections/additions based on discussions at Rutgers
;
0.1.17
1993-05-11
;
Changed _atom_site_label_component_? to new nomenclature
Introduced category DDL throughout
Introduced refers_to DDL throughout
Introduced part_of_key DDL throughout
Mandated that _list must be in each data definition
Standardized 'need not be unique' statements
Standardized example headers
;
1.1.18
1993-05-12
;
Looped out authors and editors in citation list
Verified with RGB tools
Some style consistency imposed
Fleshed out category definitions and imposed style
Updated "sets of data item" at beginning of document
Checked alphabetical order of data names - moved id's
;
0.2.1
1993-05-13
;
Major rethinking of _entity_ data based following discussions
of 1993-05-10 meeting
;
0.2.2
1993-05-18
;
Style consistency and proof reading changes throughout
Make page numbers general to articles and chapters in citation
Added *_method to all phasing categories
Looped out keywords from _struct_site_ list
Added _atom_site_label_ definitions as per H. Berman
Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne
Added _atom_sites_alt_ data items to formally handle alternative
conformations
Verified with Cyclops and RGB tools
;
0.2.3
1993-05-19
;
Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon
;
0.2.4
1993-05-20
;
DDL adjustment from down under ):-(>
;
0.2.5
1993-05-20
;
A general merging of updates from PMR, BMcM and SRH
Fixed typographical and stylistic problems a la BMcM
;
0.2.6
1993-06-02
;
Fixed _atom_site_ example (_entity_poly_seq_num)
Removed _list_link_parent from _entity_mon_atom_atom_id a
_entity_nonp_atom_atom_id
Added real APS coordinates to _atom_site_ example
Rewrote _atom_sites_footnote_ example
;
0.2.7
1993-08-01
;
Redesigned phasing_MIR definitions
;
0.2.8
1993-08-03
;
More work on phasing_MIR
Created phasing_MIR_der and phasing_MIR_der_shell categories
;
0.3.1
1993-08-08
;
Began implementing DDL v0.7
;
0.3.2
1993-08-11
;
Cleaning up of stray notes
;
0.3.3
1993-08-12
;
Syntax and consistency checks - SRH
Added _type of null for appendix items.
;
0.3.4
1993-09-01
;
Added _struct_conn_ptnr1_label_alt_id and
_struct_conn_ptnr2_label_alt_id
Corrected definitions for _struct_conn_ptnr2_ items
Added _struct_site_gen_label_alt_id
Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis
Change _database_PDB_rev_ example to _loop construction
Added _PDB_remark category (data items _PDB_remark_num and
_PDB_remark_text)
Added 'obsolete' to enumeration list for _database_PDB_rev_status
Added _database_PDB_rev_replaces data item
;
0.3.5
1993-09-08
;
Added missing _diffrn_orient_matrix_UB_33 (in appendix)
Added missing _phasing_MIR_der_shell_der_id to appropriate example
;
0.3.6
1993-10-10
;
Changed *_appendix to *_[mm] throughout
Removed 'Need example here' from _chemical_[mm]
Removed 'Need example here' from _chemical_conn_atom_[mm]
Removed 'Need example here' from _chemical_conn_bond_[mm]
Moved _PDB to end of all relevant data names (except _[mm])
Added _database_rev_record_details_PDB data name
Changed _refine_occupancy_limit_high to _refine_occupancy_max
Changed _refine_occupancy_limit_low to _refine_occupancy_min
Changed _refine_B_iso_limit_high to _refine_B_iso_max
Changed _refine_B_iso_limit_low to _refine_B_iso_min
Changed all definitions and examles in _refine_iso_B_ category
to _refine_B_iso_ equivalents
;
0.3.7
1993-11-16
;
Changed form of dates in _update_history to CIF style
Changed ? to . in examples, where appropriate
Added _example_detail to _refine_ls_restr_type
Expanded definition of _refine_ls_restr_type
;
0.3.8
1993-11-30
;
Moved _audit_author_, _citation_ categories to CIF core
Definitions and small-molecule examples removed from *_[mm]
sections that don't extend core categories - BMcM
;
0.3.9
1993-12-02
;
Deleted section summarizing categories - PMDF
Returned definitions for most *_[mm] sections - PMDF
Added _list and _list_level to global - PMDF
Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF
Checked lists of data items in core, fixing some problems
with missing names and alphabetization - PMDF
Resorted some categories to correct alphabetization - PMDF
Changed form and definitions of _database_remark_num_PDB and
_database_remark_text_PDB - PMDF
Added data item _database_rev_replaced_by_PDB - PMDF
Reordered data items in _citation example - PMDF
Added data item _exptl_crystal_density_%_sol - PMDF
;
0.3.10
1993-12-15
;
Various changes following suggestions from BMcM
Refined definition of _atoms_site_label_atom_id - PMDF
Removed _atom_sites_fract_tran (moved to core) - PMDF
Changed _diffrn_crystal_physical_device to
_diffrn_crystal_support - PMDF
Changed _diffrn_measure_device_part to
_diffrn_measure_device_specific - PMDF
Changed _diffrn_rad_detector_part to
_diffrn_rad_detector_specific - PMDF
Changed _diffrn_rad_source_part to
_diffrn_rad_source_specific - PMDF
Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF
Fixed several occurrences of \&A instead of \%A - PMDF
;
0.3.11
1993-12-22
;
Made a number of fixes relayed by PEB from MS AND RH
_type of _atom_site_footnote_id (numb->char) - PMDF
_type of _database_rev_record_rev_num_PDB (char->numb) - PMDF
_type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF
save_atom_sites_fract_tran_matrx to _matrix - PMDF
_type of _phasing_MIR_site_details (numb->char) - PMDF
_example of _struct_conf_type_reference - PMDF
;
0.3.12
1993-12-23
;
Broke out examples from intro sections to loop_ _item_examples.case
_example_detail construction - BMcM
;
0.3.13
1994-01-13
;
Rationalisation of categories between mm and core dicts - BMcM
Deleted _diffrn_crystal_environment (same as core
_diffrn_ambient_environment) and moved other _diffrn_crystal
items to core - BMcM
Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM
Some re-alphabetization - BMcM
;
0.3.14
1994-01-26
;
Lots more re-alphabetization - PMDF
Changed non_s to nstd throughout - PMDF
Changed nonp to npol throughout - PMDF
Removed all multiple spaces - PMDF
Fixed a couple of alignment problems - PMDF
;
0.4.1
1994-02-04
;
Major modifications of _entity_ subcategories - PMDF
Added angles, planes, torsion angles and chiral centers to
_entity_mon_ and _entity_npol_
Added many missing definitions
Added many missing examples
;
0.4.2
1994-02-25
;
Corrected spelling errors found by BMcM - PMDF
;
0.4.3
1994-03-28
;
Various changes following suggestions by IDB - PMDF
Changed _entity_mon_angle_value to
_entity_mon_angle_value_angle in example
Changed save_entity_npol_bond_value to
save_entity_npol_bond_value_dist
Changed nonp to npol in _entity_npol_tor_value category
Reworded angle _enumeration_details in _refine_ls_restr_type
Reworded defintions in _struct_asym_[mm] and _struct_biol_[mm]
Reworded definitions of _struct_conn_symmetry_*
_struct_site_gen_symmetry
_struct_biol_gen_symmetry
Split _struct_conn_symmetry_* into
_struct_conn_ptnr1_symmetry and
_struct_conn_ptnr2_symmetry
Split _struct_conn_role_* into
_struct_conn_ptnr1_role and
_struct_conn_ptnr2_role
Removed _list_link_child from _struct_conn_conn_type_id
Added _list_link_child to _struct_conn_type_id
;
0.5.1
1994-10-10
;
Implementation of Treaty of Brussels - PMDF
Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary
dated 1994-05-20.
The history records for the core dictionary are included here
to identify the version of the core that was merged:
_dictionary_name cifdic.c94
_dictionary_version 2.0
_dictionary_update 1994-03-01
_dictionary_history
1991-05-27 Created from CIF Dictionary text. SRH
1991-05-30 Validated with CYCLOPS & CIF ms. SRH
1991-06-03 Adjustments to some definitions. SRH
1991-06-06 Adjustments a la B. McMahon. SRH
1991-06-18 Additions & some redefinitions. SRH
1991-07-04 Corrected 90:0 in *_detect_slit_. SRH
1991-09-20 Additions & some redefinitions. SRH
1991-09-20 Final published version. IUCr
1991-11-12 Add _diffrn_ambient_environment. SRH
1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH
1993-02-23 Apply global_ and 'unknown' -> '?' SRH
1993-03-05 Changes resulting from MM dictionary. SRH
1993-05-20 Changes arising from new DDL commands. SRH
1993-08-05 Additional finetuning pre-Beijing. SRH
1993-12-22 Introductory sections added to categories. BMcM
1993-12-22 Additional categories from mm work: _audit_author,
_citation, _atom_sites_fract_tran_matrix. BMcM
1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM
1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM
1994-03-01 Add 'atom_site_aniso_ratio'. BMcM
--------------
Removed all mm sections that enumeration items present in core
but not present in mm dictionary.
Fixed errors with missing trailing _'s in some category headers
Also unbalanced ##'s in same place
Removed "End of Example" statement everywhere
Standardized syntax for missing examples
Standardized syntax and style for category _definition data
items. Added a bunch of ending dashed lines where they were missing.
Merged [] and [mm] category explanation sections. Made HIV
example always example 1, moved examples from core (where
they were different from the HIV example) to higher numbers.
Changed data_ to save_ everywhere
Changed _name to _item.name everywhere
Added _item.mandatory_code everywhere
Added save_ everywhere
Moved _description to top of _save frame everywhere
Changed _example to _item_examples.case everywhere
Changed _example_detail to _item_examples.detail everywhere
Changed _description to _item.description.description
everywhere
Removed _list yes everywhere
Removed _list_reference everywhere
Changed _enumeration_range to enumeration_limit.minimum and
enumeration_limit.maximum everywhere
;
0.5.4
1994-11-14
;
Implementation of DDL 2.0.7 dictionary wide - PMDF
Changed _enumeration to _enumeration.code
Changed _enumeration_detail to _enumberation.code_detail
Changed _enumeration_default to _enumeration_default.code
Put .'s in item names (incomplete)
Moved _PDB back to appropriate place in item names in the
_database_remark_PDB_ and _database_rev_PDB_ and
_database_rev_record_PDB_ categories
Changed database_rev_PDB to database_PDB_rev
Changed database_remark_PDB to database_PDB_remark
Changed database_rev_record_PDB to database_PDB_rev_record
Changed category items from item to category
Began getting rid of *_whatever construction in category
and item descriptions
;
0.5.5
1994-11-15
;
Implementation of DDL 2.0.7 dictionary wide - PMDF
Finished putting .'s in itme names
Changed _diffrn_measure_ to _diffrn_measurement.
Changed _diffrn_rad_ to _diffrn_radiation.
Implemented category and id pointers for entity category.
Found all sorts of errors while doing this, and attempted
to fix them consistently. Did not remove child data
Items, even though they don't have to be specified - they
should help keep all of this straight during the transition.
Some silly reformatting to ensure that data values always
have the first alphabetic character in column 33.
More silly reformatting to put each example in an example
loop on a separate line.
;
0.6.1
1994-11-21
;
Changes (JDW):
+ Converted dictionary and dictionary_history categories.
Incorporated core dictionary history list into the new
history list in the revision 0.5.1 where the dictionary
merger is firsted discussed.
;
0.6.2
1994-11-28
;
Changes (PMDF):
+ Made loop_ _item.name data items into separate data items
This involved rewriting the definitions of most of them.
In doing so I continued to eliminate the a.b_* construction.
Added unit type of degrees.
Added unit type of minutes.
Added unit type of electrons.
;
0.6.2
1994-11-30
;
Changes (PMDF):
+ Finished conversion of units data items
Added a number of unit types to the table
Conversation table still need to be fleshed out
Removed _list_mandatory and changed _item_mandatory.code to yes for
those data items
;
0.6.3
1994-12-01
;
Changes (PMDF):
+ Began conversion of _list_link_parent items to appropriate new DDL
relationships
;
0.6.4
1994-12-02
;
Changes (PMDF):
+ Began implementation of new scheme for relationships in the entity
category
All entities will be treates as polymers - non-polymers will have
a number of monomers of 1
All data items in ENTITY_NPOL categories are elminated
All data items in ENTITY_POLY category are moved to ENTITY
;
0.6.5
1994-12-06
;
Changes (PMDF):
+ Finished conversion of _list_link_parent items to appropriate new DDL
relationships
Filled out category_key.id items in each category
Had to add diffrn_refln.id item, as cannot use h k l in that category
(perfectly valid to measure same relfection more than once).
Used _diffrn_standard_refln.code in that category - this may cause a
problem with old files, as example file did not give this data item
Moved _entity_poly items back to _entity category
Moved _entity_poly.formula_weight to entity.formula_weight
Used _exptl_crystal.id in that category - this may cause a
problem with old files, as example file did not give this data item
Added _exptl_crystal_grow.crystal_id in that category
Added _symmetry_equiv.id in that category - this may cause a
problem with old files, as this is a new data item
;
0.6.6
1994-12-07
;
Changes (PMDF):
+ Created DATABASE_NEW category to solve logical problems with old DATABASE
category. Need to think some more about how old data items are handled.
Added aliases for remaining c91 data items
Changed geom_angle to geom_angle.value (aliased to original name)
Changed geom_torsion to geom_torsion.value (aliased to original name)
Returned ATOM_SITE items taken out during ATOM_SITE_MM transition
;
0.6.7
1994-12-08
;
Changes (PMDF):
+ Created ATOM_SITE_ANISOTROP category to provide for ability to have
aniostropic data is a separate loop, if desired.
Checked and fixed a bunch of style things
Added item_units.code of degrees in data items with degrees in the
description but not in the ddl
Added item_units.code of kelvin in data items with kelvin in the
description but not in the ddl (and added 'in degrees kelvin' to the
description of those with item_units.code of kelvin but no corresponding
phrase in the description)
Added item_units.code of microseconds to _diffrn_radiation.detector_dtime
(added to units list at same time)
Added 'in minutes' to description of _diffrn_refln.elapsed_time
Added 'in kilopascals' to to the description of those with item_units.code
of kilopascals but no corresponding phrase in the description
Added BLOCK category
Added appopriate pointers (in category key, and with a data item pointing
to _block.id) in all categories that needed them
;
0.6.8
1994-12-09
;
Changes (PMDF):
+ Added _esd data items where needed
Rationalized descriptions for all of the coordinate data items
;
0.6.9
1994-12-13
;
Changes (PMDF):
+ Established check-list for unfinished tasks and began dealing with them
Added enumeration limits of 0 and 1 and enumeration default of 1.0 to
occupancy data items
Left heavy-atom maximum with an enumeration of ?
Added enumeration default of 1_555 to all _symmetry data items where it was
missing
Changed 'connect type' to 'interaction' in _struct_conn_type data items.
Filled out sub_category ddl items for cartesian coordinates, fractional
coordinates, cartesian coordinates esds, and Miller indices.
;
0.6.10
1994-12-14
;
Changes (PMDF):
+ Fixed R-Kraut reference
Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all
Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs
Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol
Included full formula for this calculation in description
Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal
Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target
Improved wording of all definitions in REFINE_LS_RESTR
Explained sums in _reflns_shell.Rmerge_I_obs and related data items
;
0.6.11
1994-12-15
;
Changes (PMDF):
+ Changed _enumeration_default.code to _item_default.value
Changed _enumeration_default.value to _item_default.value
Changed _enumeration.code to _item_enumeration.value
Changed _enumeration.detail to _item_enumeration.detail
Changed _enumeration.case to _item_enumeration.value
Changed _enumeration_limit.maximum to _item_range.maximum
Changed _enumeration_limit.minimum to _item_range.minimum
Checked that matrix were properly labelled as either rw_rowwise or just
plan rowwise.
Reworded matrix descriptions for consistency.
Got rid of the last of the a.b_* constructions in descriptions
Added cell_length, cell_length_esd, cell_angle and cell_angle_esd
subcategories
Changed special_details to details for core items - original names retained
in aliases
Added atom_site.id
Added mm_atom_site_label subcategory
Commented out _atom_site.label_component until it can be dealt with
properly
Changed 'SIF' to 'data block' in a number of descriptions.
;
0.6.12
1994-12-16
;
Changes (PMDF):
+ Added data item _refln.R_free_status
Added data item _reflns.R_free_details
Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs
Added _refine_ls_shell.number_R_free
Added _refine_ls_shell.number_all
Added _refine_ls_shell.R_factor_R_free
Added _refine_ls_shell.wR_factor_R_free
Tidied up the count and R-factor descriptions in REFINE_LS_SHELL
Added appropriate item_related names to the R-factors in REFINE_LS_SHELL
Changed 'count' to 'number' in several data names
Changed _reflns.number_total to _reflns.number_all
Changed _reflns.number_observed to _reflns.number.obs
Added _refine.ls_R_factor_R_free
Added _refine.ls_wR_factor_R_free
Edited descriptions of the other R-factor data items in the REFINE
category to conform to the style in REFINE_LS_SHELL
Re-alphabetized the things I changed yesterday from special_details to
details - I had forgotten to do that yesterday
;
0.6.13
1994-12-19
;
Changes (PMDF):
+ Changed refine.ls_number_reflns to refine.ls_number_reflns_obs
Added refine.ls_number_reflns_all
Added refine.ls_number_reflns_R_free
Changed _refln.observed_status to refln.status
Expanded enumeration list to include resolution limits and R-free flag
Rewrote definition
Eliminated refln.R_free_status
Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all
Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs
Changed _refine_ls_shell.number_R_free to
_refine_ls_shell.number_reflns_R_free
Added PHASING category
Filled in and reformatted units conversion table
;
0.7.1
1994-12-19
;
Changes (JDW):
+ First pass through SIFLIB checking tools. Corrected syntax errors and
missing parent references.
;
0.7.2
1994-12-20
;
Changes (PMDF):
+ Merged JDW changes with version 0.6.12
Changed _item_type.code of numb to either int or float
Changed _item_description.descrption to category.description where
appropriate
Fixed a bunch of pure syntax errors
Removed 'refln_scale_group' from list of category groups.
Changed _refln_scale_group_code to _refln.scale_group_code somewhere
Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere
Reformatted CATEGORY_GROUP_LIST items to match style of other
header categories
Ensures that all _category data items obey they rule of first
alphabetic character is column 34 (most didn't before this check)
Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the
rest) data items, and added wording to description that these
items are only there for compliance via the alias (but left in
the one _item_related thing that made the matrix element data item
alternate exclusive to the full matrix data item
Added language about compliance to _atom_sites.cartn.tran.matrix
Added language about compliance to _diffrn_orient_matrix.UB
Added language about compliance to _diffrn_reflns.transf_matrix
Removed matrix element data items for _atom_sites.fract.tran.matrix -
this wasn't in c91 and so doesn't need aliasing
;
0.7.3
1994-12-22
;
Changes (PMDF):
+ Fixed things turned up by JDW checking of 0.7.2
Couple of small typos
Added angstroms_cubed to units list and conversion tables
Added _phasing_MIR_site.atom_type_symbol and added this reference to the
table until _atom_type.symbol
Added _entity_mon_atom.substruct_code
Began adding STRUCT_MON_PROT, but this is not yet complete
;
0.7.4
1995-01-12
;
Changes (PMDF):
+ Finished working on STRUCT_MON_PROT category
Added STRUCT_MON_DETAILS category
Added STRUCT_MON_PROT_CIS category
Added STRUCT_NCS_ENS category
Added STRUCT_NCS_ENS_OPER category
Added STRUCT_NCS_DOM category
Added STRUCT_NCS_DOM_GEN category
Added equations to definitions of _phasing_MIR_der_shell.fom and
_phasing_MIR_shell.fom
Added REFINE_HIST category
;
0.7.5
1995-01-13
;
Changes (PMDF):
+ Provided for sequence microheterogenity by making _entity_poly_seq.mon_id
part of the category key and by adding the data item
_entity_poly_seq.hetero as a flag
Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer
in referenced data items.
Added _entity_mon_atom.alt_atom_id.
Added COMP_PROG category
Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR)
;
0.7.6
1995-01-17
;
Changes (PMDF):
+ Added ENTITY_SRC_NAT category
Added ENTITY_SRC_GEN category
Added ENTITY_NAM_COM category
Added ENTITY_NAM_SYS category
Added _entity.src_method data item
Moved other entity data items to new categories as appropriate
;
0.7.7
1995-01-18
;
Changes (PMDF):
+ Added PHASING_MIR_REFLN category
;
0.7.8
1995-01-25
;
Changes (PMDF):
+ Added _entity_mon.type, _entity_mon.number_atoms_all,
_entity_mon.number_atoms_nh, _entity_mon.one_letter_code
Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd,
_entity_mon_bond.value_dist_esd
Added _entity_mon_atom.type_energy, but since this is intended to be a
pointer to a category (_atom_type_energy) that doesn't exist yet, have
left it commented out
Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and
_entity_mon_chir.volume_flag
Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh
Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh
Added _entity_mon_chir_atom.dev
Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd
Added ENTITY_LINK category
Added ENTITY_LINK_ANGLE category
Added ENTITY_LINK_BOND category
Changes (HB et al.):
+ Added STRUCT_MON_NUCL category
Changes (PMDF):
+ Added label links from STRUCT_MON_NUCL to rest of dictionary
Added label links from STRUCT_MON_PROT as well (forget them initially)
;
loop_
_sub_category.id
_sub_category.description
'cartesian_coordinate'
;
The collection of x, y, and z components of a position specified
with references to a Cartesian (orthonal Angstrom) coordinate
system.
;
'cartesian_coordinate_esd'
;
The collection of estimated standard deviations of the x, y, and
z components of a position specified with references to a
Cartesian (orthogonal Angstrom) coordinate system.
;
'fractional_coordinate'
;
The collection of x, y, and z components of a position specified
with references to unit cell directions.
;
'fractional_coordinate_esd'
;
The collection of estimated standard deviations of the x, y, and
z components of a position specified with references to unit cell
directions.
;
'miller_index'
;
The collection of h, k, and l components of a the Miller index of
a reflection.
;
'cell_length'
;
The collection of a, b, and c axis lengths of a unit cell.
;
'cell_length_esd'
;
The collection of estimated standard deviations of the a, b, and
c axis lengths of a unit cell.
;
'cell_angle'
;
The collection of alpha, beta, and gamma angles of a unit cell.
;
'cell_angle_esd'
;
The collection of estimated standard deviations of the alpha,
beta, and gamma angles of a unit cell.
;
'mm_atom_site_label'
;
The collection of alt id, asym id, atom id, res id and seq id
components of the label for a macrmomolecular atom site.
;
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.description
code
char
'[A-Za-z0-9,.;:"&<>/\{}`~!@#$%]*'
;
code item types ...
;
char
char
'[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% ]*'
;
char item types ...
;
text
char
'[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% \n]*'
;
text item types ...
;
int
numb
'[0-9]+'
;
int item types are the subset of numbers that are the negative or
positive integeters.
;
float
numb
'-?(([0-9]+)|([0-9]*\.[0-9]+)([eE][-+]?[0-9]+)?)'
;
int item types are the subset of numbers that are the floating
numbers.
;
name
uchar
'_[A-Za-z0-9_]+\.[A-Za-z0-9_]+'
;
name item types take the form...
;
idname
uchar
'[A-Za-z0-9_]+'
;
idname item types take the form...
;
any
char
'[A-Za-z0-9,.;:"&<>?/\{}`~!@#$% \n]*'
;
idname item types take the form...
;
date
char
;
{_dictionary_history.update_year}-
{_dictionary_history.update_month}-
{_dictionary_history.update_day}
;
;
date item types take the form...
;
symop
char
'[1-192]\_[1-9][1-9][1-9]'
;
symop item types takes the form n_mmm, where 'n' is the value of
_symmetry_equiv.id that corresponds to the relevant value of
_symmetry_equiv.pos_as_xyz and 'mmm' are the concatenated cell
translations along x, y, z with respect to the base number 555.
The symmetry transformation is applied to the fractional
coordinates in the ATOM_SITE category identified by
_atom_site_label. If there are no cell translations the
translation number may be omitted.
;
loop_
_item_structure_list.code
_item_structure_list.index
_item_structure_list.dimension
'matrix3x3'
0
3
'matrix3x3'
1
3
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group'
.
;
Categories that belong to the macromolecular dictionary.
;
'atom_group'
'inclusive_group'
;
Categories that describe the properties of atoms.
;
'audit_group'
'inclusive_group'
;
Categories that describe dictionary maintenance and
identification.
;
'block_group'
'inclusive_group'
;
Categories that pertain to the entire data block
;
'cell_group'
'inclusive_group'
;
Categories that describe the unit cell.
;
'chemical_group'
'inclusive_group'
;
Categories that describe chemical properties and nomenclature.
;
'citation_group'
'inclusive_group'
;
Categories that provide bibliographic references
;
'computing_group'
'inclusive_group'
;
Categories that describe the computational details of the
experiment.
;
'compliance_group'
'inclusive_group'
;
Categories that are included in this dictionary specifically to
comply with previous dictionaries.
;
'database_group'
'inclusive_group'
;
Categories that hold references to other databases with related
information.
;
'diffrn_group'
'inclusive_group'
;
Categories that describe details of the diffraction experiment.
;
'entity_group'
'inclusive_group'
;
Categories that describe chemical entities
;
'exptl_group'
'inclusive_group'
;
Categories which hold details of the experimental conditions.
;
'geom_group'
'inclusive_group'
;
Categories which hold internal coordinates.
;
'journal_group'
'inclusive_group'
;
Categories which are used for internal processing by the
publication staff.
;
'phasing_group'
'inclusive_group'
;
Categories that describe phasing.
;
'publ_group'
'inclusive_group'
;
Categories that describe manuscript submission.
;
'refine_group'
'inclusive_group'
;
Categories that describe refinement.
;
'refln_group'
'inclusive_group'
;
Categories that describe the details of reflection measurements.
;
'struct_group'
'inclusive_group'
;
Categories that contain details about the crystallographic
structure.
;
'symmetry_group'
'inclusive_group'
;
Categories that describe symmetry information.
;
loop_
_item_units_list.code
_item_units_list.detail
'centimetres'
'centimetres (meters * 10^( -2))'
'millimetres'
'millimetres (meters * 10^( -3))'
'nanometres'
nanometres
(meters
*
10^(
-9))
'angstroms'
'angstroms (meters * 10^(-10))'
'picometres'
'picometres (meters * 10^(-12))'
'reciprocal_centimetres'
'reciprocal centimetres (meters * 10^( -2)^-1)'
'reciprocal_millimetres'
'reciprocal millimetres (meters * 10^( -3)^-1)'
'reciprocal_nanometres'
'reciprocal nanometres (meters * 10^( -9)^-1)'
'reciprocal_angstroms'
'reciprocal angstroms (meters * 10^(-10)^-1)'
'reciprocal_picometres'
'reciprocal picometres (meters * 10^(-12)^-1)'
'nanometres_squared'
'nanometres squared (meters * 10^( -9))^2'
'angstroms_squared'
'angstroms squared (meters * 10^(-10))^2'
'picometres_squared'
'picometres squared (meters * 10^(-12))^2'
'nanometres_cubed'
'nanometres cubed (meters * 10^( -9))^3'
'angstroms_cubed'
'angstroms cubed (meters * 10^(-10))^3'
'picometres_cubed'
'picometres cubed (meters * 10^(-12))^3'
'kilopascals'
'kilopascals'
'gigapascals'
'gigapascals'
'hours'
'hours'
'minutes'
'minutes'
'seconds'
'seconds'
'microseconds'
'microseconds'
'degrees'
'degrees (of arc)'
'celsius'
'degrees (of temperature) Celsius'
'kelvin'
'degrees (of temperature) Kelvin'
'electrons'
'electrons'
'electrons_squared'
'electrons squared'
'electrons_per_nanometres_cubed'
;
electrons per nanometres cubed (meters * 10^( -9))^3
;
'electrons_per_angstroms_cubed'
;
electrons per angstroms cubed (meters * 10^(-10))^3
;
'electrons_per_picometres_cubed'
;
electrons per picometres cubed (meters * 10^(-12))^3
;
loop_
_units_conversion.from_code
_units_conversion.to_code
_units_conversion.operator
_units_conversion.factor
'centimetres'
'millimetres'
'*'
1.0E+01
'centimetres'
'nanometres'
'*'
1.0E+07
'centimetres'
'angstroms'
'*'
1.0E+08
'centimetres'
'picometres'
'*'
1.0E+10
'millimetres'
'centimetres'
'*'
1.0E-01
'millimetres'
'nanometres'
'*'
1.0E+06
'millimetres'
'angstroms'
'*'
1.0E+07
'millimetres'
'picometres'
'*'
1.0E+09
'nanometres'
'centimetres'
'*'
1.0E-07
'nanometres'
'millimetres'
'*'
1.0E-06
'nanometres'
'angstroms'
'*'
1.0E+01
'nanometres'
'picometres'
'*'
1.0E+03
'angstroms'
'centimetres'
'*'
1.0E-08
'angstroms'
'millimetres'
'*'
1.0E-07
'angstroms'
'nanometres'
'*'
1.0E-01
'angstroms'
'picometres'
'*'
1.0E+02
'picometres'
'centimetres'
'*'
1.0E-10
'picometres'
'millimetres'
'*'
1.0E-09
'picometres'
'nanometres'
'*'
1.0E-03
'picometres'
'angstroms'
'*'
1.0E-02
'reciprocal_centimetres'
'reciprocal_millimetres'
'*'
1.0E-01
'reciprocal_centimetres'
'reciprocal_nanometres'
'*'
1.0E-07
'reciprocal_centimetres'
'reciprocal_angstroms'
'*'
1.0E-08
'reciprocal_centimetres'
'reciprocal_picometres'
'*'
1.0E-10
'reciprocal_millimetres'
'reciprocal_centimetres'
'*'
1.0E+01
'reciprocal_millimetres'
'reciprocal_nanometres'
'*'
1.0E-06
'reciprocal_millimetres'
'reciprocal_angstroms'
'*'
1.0E-07
'reciprocal_millimetres'
'reciprocal_picometres'
'*'
1.0E-09
'reciprocal_nanometres'
'reciprocal_centimetres'
'*'
1.0E+07
'reciprocal_nanometres'
'reciprocal_millimetres'
'*'
1.0E+06
'reciprocal_nanometres'
'reciprocal_angstroms'
'*'
1.0E-01
'reciprocal_nanometres'
'reciprocal_picometres'
'*'
1.0E-03
'reciprocal_angstroms'
'reciprocal_centimetres'
'*'
1.0E+08
'reciprocal_angstroms'
'reciprocal_millimetres'
'*'
1.0E+07
'reciprocal_angstroms'
'reciprocal_nanometres'
'*'
1.0E+01
'reciprocal_angstroms'
'reciprocal_picometres'
'*'
1.0E-02
'reciprocal_picometres'
'reciprocal_centimetres'
'*'
1.0E+10
'reciprocal_picometres'
'reciprocal_millimetres'
'*'
1.0E+09
'reciprocal_picometres'
'reciprocal_nanometres'
'*'
1.0E+03
'reciprocal_picometres'
'reciprocal_angstroms'
'*'
1.0E+01
'nanometres_squared'
'angstroms_squared'
'*'
1.0E+02
'nanometres_squared'
'picometres_squared'
'*'
1.0E+06
'angstroms_squared'
'nanometres_squared'
'*'
1.0E-02
'angstroms_squared'
'picometres_squared'
'*'
1.0E+04
'picometres_squared'
'nanometres_squared'
'*'
1.0E-06
'picometres_squared'
'angstroms_squared'
'*'
1.0E-04
'nanometres_cubed'
'angstroms_cubed'
'*'
1.0E+03
'nanometres_cubed'
'picometres_cubed'
'*'
1.0E+09
'angstroms_cubed'
'nanometres_cubed'
'*'
1.0E-03
'angstroms_cubed'
'picometres_cubed'
'*'
1.0E+06
'picometres_cubed'
'nanometres_cubed'
'*'
1.0E-09
'picometres_cubed'
'angstroms_cubed'
'*'
1.0E-06
'kilopascals'
'gigapascals'
'*'
1.0E-06
'gigapascals'
'kilopascals'
'*'
1.0E+06
'hours'
'minutes'
'*'
6.0E+01
'hours'
'seconds'
'*'
3.6E+03
'hours'
'microseconds'
'*'
3.6E+09
'minutes'
'hours'
'/'
6.0E+01
'minutes'
'seconds'
'*'
6.0E+01
'minutes'
'microseconds'
'*'
6.0E+07
'seconds'
'hours'
'/'
3.6E+03
'seconds'
'minutes'
'/'
6.0E+01
'seconds'
'microseconds'
'*'
1.0E+06
'microseconds'
'hours'
'/'
3.6E+09
'microseconds'
'minutes'
'/'
6.0E+07
'microseconds'
'seconds'
'/'
1.0E+06
'celsius'
'kelvin '
'-'
273.0
'kelvin'
'celsius'
'+'
273.0
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed'
'*'
1.0E-03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed'
'*'
1.0E-09
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed'
'*'
1.0E+03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed'
'*'
1.0E-06
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed'
'*'
1.0E+09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed'
'*'
1.0E+06
save_ATOM_SITE
save_atom_site.aniso_B
save_atom_site.aniso_B_esd
save_atom_site.aniso_ratio
save_atom_site.aniso_U
save_atom_site.aniso_U_esd
save_atom_site.aniso_U[1][1]
save_atom_site.aniso_U[1][2]
save_atom_site.aniso_U[2][2]
save_atom_site.aniso_U[1][3]
save_atom_site.aniso_U[2][3]
save_atom_site.aniso_U[3][3]
save_atom_site.attached_hydrogens
save_atom_site.B_iso_or_equiv
save_atom_site.B_iso_or_equiv_esd
save_atom_site.calc_attached_atom
save_atom_site.calc_flag
save_atom_site.cartn_x
save_atom_site.cartn_x_esd
save_atom_site.cartn_y
save_atom_site.cartn_y_esd
save_atom_site.cartn_z
save_atom_site.cartn_z_esd
save_atom_site.chemical_conn_number
save_atom_site.constraints
save_atom_site.description
save_atom_site.disorder_group
save_atom_site.entity_id
save_atom_site.entity_seq_num
save_atom_site.footnote_id
save_atom_site.fract_x
save_atom_site.fract_x_esd
save_atom_site.fract_y
save_atom_site.fract_y_esd
save_atom_site.fract_z
save_atom_site.fract_z_esd
save_atom_site.group_PDB
save_atom_site.id
save_atom_site.label
save_atom_site.label_alt_id
save_atom_site.label_asym_id
save_atom_site.label_atom_id
save_atom_site.label_res_id
save_atom_site.label_seq_id
save_atom_site.occupancy
save_atom_site.occupancy_esd
save_atom_site.refinement_flags
save_atom_site.restraints
save_atom_site.symmetry_multiplicity
save_atom_site.thermal_displace_type
save_atom_site.type_symbol
save_atom_site.U_iso_or_equiv
save_atom_site.U_iso_or_equiv_esd
save_atom_site.Wyckoff_symbol
save_ATOM_SITE_ANISOTROP
save_atom_site_anisotrop.B
save_atom_site_anisotrop.B_esd
save_atom_site_anisotrop.label
save_atom_site_anisotrop.ratio
save_atom_site_anisotrop.type_symbol
save_atom_site_anisotrop.U
save_atom_site_anisotrop.U_esd
save_ATOM_SITES
save_atom_sites.block_id
save_atom_sites.cartn_tran_matrix
save_atom_sites.cartn_tran_matrix[1][1]
save_atom_sites.cartn_tran_matrix[1][2]
save_atom_sites.cartn_tran_matrix[1][3]
save_atom_sites.cartn_tran_matrix[2][1]
save_atom_sites.cartn_tran_matrix[2][2]
save_atom_sites.cartn_tran_matrix[2][3]
save_atom_sites.cartn_tran_matrix[3][1]
save_atom_sites.cartn_tran_matrix[3][2]
save_atom_sites.cartn_tran_matrix[3][3]
save_atom_sites.cartn_transform_axes
save_atom_sites.frac_tran_matrix
save_atom_sites.solution_primary
save_atom_sites.solution_secondary
save_atom_sites.solution_hydrogens
save_ATOM_SITES_ALT
save_atom_sites_alt.details
save_atom_sites_alt.id
save_ATOM_SITES_ALT_ENS
save_atom_sites_alt_ens.details
save_atom_sites_alt_ens.id
save_ATOM_SITES_ALT_GEN
save_atom_sites_alt_gen.alt_id
save_atom_sites_alt_gen.ens_id
save_ATOM_SITES_FOOTNOTE
save_atom_sites_footnote.id
save_atom_sites_footnote.text
save_ATOM_TYPE
save_atom_type.analytical_mass_
save_atom_type.description
save_atom_type.number_in_cell
save_atom_type.oxidation_number
save_atom_type.radius_bond
save_atom_type.radius_contact
save_atom_type.scat_Cromer_Mann_a1
save_atom_type.scat_Cromer_Mann_a2
save_atom_type.scat_Cromer_Mann_a3
save_atom_type.scat_Cromer_Mann_a4
save_atom_type.scat_Cromer_Mann_b1
save_atom_type.scat_Cromer_Mann_b2
save_atom_type.scat_Cromer_Mann_b3
save_atom_type.scat_Cromer_Mann_b4
save_atom_type.scat_Cromer_Mann_c
save_atom_type.scat_dispersion_imag
save_atom_type.scat_dispersion_real
save_atom_type.scat_source
save_atom_type.scat_versus_stol_list
save_atom_type.symbol
save_AUDIT
save_audit.creation_date
save_audit.creation_method
save_audit.revision_id
save_audit.update_record
save_AUDIT_AUTHOR
save_audit_author.address
save_audit_author.name
save_AUDIT_CONTACT_AUTHOR
save_audit_contact_author.address
save_audit_contact_author.email
save_audit_contact_author.fax
save_audit_contact_author.name
save_audit_contact_author.phone
save_BLOCK
save_block.id
save_CELL
save_cell.angle_alpha
save_cell.angle_alpha_esd
save_cell.angle_beta
save_cell.angle_beta_esd
save_cell.angle_gamma
save_cell.angle_gamma_esd
save_cell.block_id
save_cell.details
save_cell.formula_units_Z
save_cell.length_a
save_cell.length_a_esd
save_cell.length_b
save_cell.length_b_esd
save_cell.length_c
save_cell.length_c_esd
save_cell.volume
save_cell.volume_esd
save_CELL_MEASUREMENT
save_cell_measurement.block_id
save_cell_measurement.pressure
save_cell_measurement.pressure_esd
save_cell_measurement.radiation
save_cell_measurement.reflns_used
save_cell_measurement.temperature
save_cell_measurement.temperature_esd
save_cell_measurement.theta_max
save_cell_measurement.theta_min
save_cell_measurement.wavelength
save_CELL_MEASUREMENT_REFLN
save_cell_measurement_refln.index_h
save_cell_measurement_refln.index_k
save_cell_measurement_refln.index_l
save_cell_measurement_refln.theta
save_CHEMICAL
save_chemical.block_id
save_chemical.compound_source
save_chemical.melting_point
save_chemical.name_common
save_chemical.name_mineral
save_chemical.name_structure_type
save_chemical.name_systematic
save_CHEMICAL_CONN_ATOM
save_chemical_conn_atom.charge
save_chemical_conn_atom.display_x
save_chemical_conn_atom.display_y
save_chemical_conn_atom.NCA
save_chemical_conn_atom.NH
save_chemical_conn_atom.number
save_chemical_conn_atom.type_symbol
save_CHEMICAL_CONN_BOND
save_chemical_conn_bond.atom_1
save_chemical_conn_bond.atom_2
save_chemical_conn_bond.type
save_CHEMICAL_FORMULA
save_chemical_formula.analytical
save_chemical_formula.block_id
save_chemical_formula.moiety
save_chemical_formula.structural
save_chemical_formula.sum
save_chemical_formula.weight
save_chemical_formula.weight_meas
save_CITATION
save_citation.abstract
save_citation.book_coden_ISBN
save_citation.book_publisher
save_citation.book_title
save_citation.coordinate_linkage
save_citation.country
save_citation.details
save_citation.id
save_citation.journal_abbrev
save_citation.journal_coden_ASTM
save_citation.journal_coden_ISSN
save_citation.journal_coden_PDB
save_citation.journal_full
save_citation.journal_issue
save_citation.journal_volume
save_citation.language
save_citation.Medline_AN
save_citation.page_first
save_citation.page_last
save_citation.title
save_citation.year
save_CITATION_AUTHOR
save_citation_author.citation_id
save_citation_author.name
save_CITATION_EDITOR
save_citation_editor.citation_id
save_citation_editor.name
save_COMP_PROG
save_comp_prog.citation_id
save_comp_prog.name
save_comp_prog.task
save_comp_prog.version
save_COMPUTING
save_computing.block_id
save_computing.cell_refinement
save_computing.data_collection
save_computing.data_reduction
save_computing.molecular_graphics
save_computing.publication_material
save_computing.structure_refinement
save_computing.structure_solution
save_DATABASE
save_database.block_id
save_database.code_CAS
save_database.code_CSD
save_database.code_ICSD
save_database.code_MDF
save_database.code_NBS
save_database.code_PDF
save_database.journal_ASTM
save_database.journal_CSD
save_DATABASE_NEW
save_database_new.database_id
save_database_new.database_code
save_DATABASE_PDB_REMARK
save_database_PDB_remark.num
save_database_PDB_remark.text
save_DATABASE_PDB_REV
save_database_PDB_rev.author_name
save_database_PDB_rev.date
save_database_PDB_rev.date_original
save_database_PDB_rev.mod_type
save_database_PDB_rev.num
save_database_PDB_rev.replaced_by
save_database_PDB_rev.replaces
save_database_PDB_rev.status
save_DATABASE_PDB_REV_RECORD
save_database_PDB_rev_record.details
save_database_PDB_rev_record.rev_num
save_database_PDB_rev_record.type
save_DIFFRN
save_diffrn.ambient_environment
save_diffrn.ambient_pressure
save_diffrn.ambient_pressure_esd
save_diffrn.ambient_temperature
save_diffrn.ambient_temperature_esd
save_diffrn.block_id
save_diffrn.crystal_support
save_diffrn.crystal_treatment
save_diffrn.details
save_DIFFRN_ATTENUATOR
save_diffrn_attenuator.code
save_diffrn_attenuator.scale
save_DIFFRN_MEASUREMENT
save_diffrn_measurement.block_id
save_diffrn_measurement.details
save_diffrn_measurement.device
save_diffrn_measurement.device_details
save_diffrn_measurement.device_specific
save_diffrn_measurement.device_type
save_diffrn_measurement.method
save_DIFFRN_ORIENT_MATRIX
save_diffrn_orient_matrix.block_id
save_diffrn_orient_matrix.type
save_diffrn_orient_matrix.UB
save_diffrn_orient_matrix.UB[1][1]
save_diffrn_orient_matrix.UB[1][2]
save_diffrn_orient_matrix.UB[1][3]
save_diffrn_orient_matrix.UB[2][1]
save_diffrn_orient_matrix.UB[2][2]
save_diffrn_orient_matrix.UB[2][3]
save_diffrn_orient_matrix.UB[3][1]
save_diffrn_orient_matrix.UB[3][2]
save_diffrn_orient_matrix.UB[3][3]
save_DIFFRN_ORIENT_REFLN
save_diffrn_orient_refln.angle_chi
save_diffrn_orient_refln.angle_kappa
save_diffrn_orient_refln.angle_phi
save_diffrn_orient_refln.angle_psi
save_diffrn_orient_refln.index_h
save_diffrn_orient_refln.index_k
save_diffrn_orient_refln.index_l
save_DIFFRN_RADIATION
save_diffrn_radiation.block_id
save_diffrn_radiation.collimation
save_diffrn_radiation.detector
save_diffrn_radiation_detector_details
save_diffrn_radiation.detector_dtime
save_diffrn_radiation.detector_specific
save_diffrn_radiation.detector_type
save_diffrn_radiation.filter_edge
save_diffrn_radiation.inhomogeneity
save_diffrn_radiation.monochromator
save_diffrn_radiation.polarisn_norm
save_diffrn_radiation.polarisn_ratio
save_diffrn_radiation.source
save_diffrn_radiation.source_details
save_diffrn_radiation.source_power
save_diffrn_radiation.source_specific
save_diffrn_radiation.source_target
save_diffrn_radiation.source_type
save_diffrn_radiation.type
save_diffrn_radiation.wavelength
save_diffrn_radiation.wavelength_id
save_diffrn_radiation.wavelength_wt
save_DIFFRN_REFLN
save_diffrn_refln.angle_chi
save_diffrn_refln.angle_kappa
save_diffrn_refln.angle_omega
save_diffrn_refln.angle_phi
save_diffrn_refln.angle_psi
save_diffrn_refln.angle_theta
save_diffrn_refln.attenuator_code
save_diffrn_refln.counts_bg_1
save_diffrn_refln.counts_bg_2
save_diffrn_refln.counts_net
save_diffrn_refln.counts_peak
save_diffrn_refln.counts_total
save_diffrn_refln.crystal_id
save_diffrn_refln.detect_slit_horiz
save_diffrn_refln.detect_slit_vert
save_diffrn_refln.elapsed_time
save_diffrn_refln.id
save_diffrn_refln.index_h
save_diffrn_refln.index_k
save_diffrn_refln.index_l
save_diffrn_refln.intensity_net
save_diffrn_refln.intensity_sigma
save_diffrn_refln.scale_group_code
save_diffrn_refln.scan_mode
save_diffrn_refln.scan_mode_backgd
save_diffrn_refln.scan_width
save_diffrn_refln.sint/lambda
save_diffrn_refln.standard_code
save_diffrn_refln.wavelength
save_diffrn_refln.wavelength_id
save_DIFFRN_REFLNS
save_diffrn_reflns.av_R_equivalents
save_diffrn_reflns.av_sigmaI/netI
save_diffrn_reflns.block_id
save_diffrn_reflns.limit_h_max
save_diffrn_reflns.limit_h_min
save_diffrn_reflns.limit_k_max
save_diffrn_reflns.limit_k_min
save_diffrn_reflns.limit_l_max
save_diffrn_reflns.limit_l_min
save_diffrn_reflns.number
save_diffrn_reflns.reduction_process
save_diffrn_reflns.theta_max
save_diffrn_reflns.theta_min
save_diffrn_reflns.transf_matrix
save_diffrn_reflns.transf_matrix[1][1]
save_diffrn_reflns.transf_matrix[1][2]
save_diffrn_reflns.transf_matrix[1][3]
save_diffrn_reflns.transf_matrix[2][1]
save_diffrn_reflns.transf_matrix[2][2]
save_diffrn_reflns.transf_matrix[2][3]
save_diffrn_reflns.transf_matrix[3][1]
save_diffrn_reflns.transf_matrix[3][2]
save_diffrn_reflns.transf_matrix[3][3]
save_DIFFRN_SCALE_GROUP
save_diffrn_scale_group.code
save_diffrn_scale_group.I_net
save_DIFFRN_STANDARD_REFLN
save_diffrn_standard_refln.code
save_diffrn_standard_refln.index_h
save_diffrn_standard_refln.index_k
save_diffrn_standard_refln.index_l
save_DIFFRN_STANDARDS
save_diffrn_standards.block_id
save_diffrn_standards.decay_
save_diffrn_standards.interval_count
save_diffrn_standards.interval_time
save_diffrn_standards.number
save_diffrn_standards.scale_sigma
save_ENTITY
save_entity.details
save_entity.formula_weight
save_entity.id
save_entity.src_method
save_entity.type
save_ENTITY_KEYWORDS
save_entity_keywords.entity_id
save_entity_keywords.text
save_ENTITY_LINK
save_entity_link.id
save_entity_link.details
save_entity_link.type_mon_1
save_entity_link.type_mon_2
save_ENTITY_LINK_ANGLE
save_entity_link_angle.atom_1_atom_id
save_entity_link_angle.atom_1_mon_id
save_entity_link_angle.atom_2_atom_id
save_entity_link_angle.atom_2_mon_id
save_entity_link_angle.atom_3_atom_id
save_entity_link_angle.atom_3_mon_id
save_entity_link_angle.value_angle
save_entity_link_angle.value_angle_esd
save_entity_link_angle.value_dist
save_entity_link_angle.value_dist_esd
save_ENTITY_LINK_BOND
save_entity_link_bond.atom_1_atom_id
save_entity_link_bond.atom_1_mon_id
save_entity_link_bond.atom_2_atom_id
save_entity_link_bond.atom_2_mon_id
save_entity_link_bond.value_order
save_entity_link_bond.value_dist
save_entity_link_bond.value_dist_esd
save_ENTITY_MON
save_entity_mon.id
save_entity_mon.model_details
save_entity_mon.model_erf
save_entity_mon.model_source
save_entity_mon.name
save_entity_mon.nstd_class
save_entity_mon.nstd_details
save_entity_mon.nstd_flag
save_entity_mon.nstd_parent
save_entity_mon.number_atoms_all
save_entity_mon.number_atoms_nh
save_entity_mon.one_letter_code
save_entity_mon.type
save_ENTITY_MON_ANGLE
save_entity_mon_angle.atom_id_1
save_entity_mon_angle.atom_id_2
save_entity_mon_angle.atom_id_3
save_entity_mon_angle.mon_id
save_entity_mon_angle.value_angle
save_entity_mon_angle.value_angle_esd
save_entity_mon_angle.value_dist
save_entity_mon_angle.value_dist_esd
save_ENTITY_MON_ATOM
save_entity_mon_atom.alt_atom_id
save_entity_mon_atom.atom_id
save_entity_mon_atom.charge
save_entity_mon_atom.model_cartn_x
save_entity_mon_atom.model_cartn_x_esd
save_entity_mon_atom.model_cartn_y
save_entity_mon_atom.model_cartn_y_esd
save_entity_mon_atom.model_cartn_z
save_entity_mon_atom.model_cartn_z_esd
save_entity_mon_atom.mon_id
save_entity_mon_atom.substruct_code
save_entity_mon_atom.type_symbol
save_ENTITY_MON_BOND
save_entity_mon_bond.atom_id_1
save_entity_mon_bond.atom_id_2
save_entity_mon_bond.mon_id
save_entity_mon_bond.value_order
save_entity_mon_bond.value_dist
save_entity_mon_bond.value_dist_esd
save_ENTITY_MON_CHIR
save_entity_mon_chir.atom_id
save_entity_mon_chir.id
save_entity_mon_chir.mon_id
save_entity_mon_chir.number_atoms_all
save_entity_mon_chir.number_atoms_nh
save_entity_mon_chir.volume_flag
save_entity_mon_chir.volume_three
save_entity_mon_chir.volume_three_esd
save_ENTITY_MON_CHIR_ATOM
save_entity_mon_chir_atom.atom_id
save_entity_mon_chir_atom.chir_id
save_entity_mon_chir_atom.dev
save_ENTITY_MON_PLANE
save_entity_mon_plane.id
save_entity_mon_plane.mon_id
save_entity_mon_plane.number_atoms_all
save_entity_mon_plane.number_atoms_nh
save_ENTITY_MON_PLANE_ATOM
save_entity_mon_plane_atom.atom_id
save_entity_mon_plane_atom.plane_id
save_ENTITY_MON_TOR
save_entity_mon_tor.atom_id_1
save_entity_mon_tor.atom_id_2
save_entity_mon_tor.atom_id_3
save_entity_mon_tor.atom_id_4
save_entity_mon_tor.id
save_entity_mon_tor.mon_id
save_ENTITY_MON_TOR_VALUE
save_entity_mon_tor_value.tor_id
save_entity_mon_tor_value.angle
save_entity_mon_tor_value.angle_esd
save_entity_mon_tor_value.dist
save_entity_mon_tor_value.dist_esd
save_ENTITY_NAME_COM
save_entity_name_com.entity_id
save_entity_name_com.name
save_ENTITY_NAME_SYS
save_entity_name_sys.entity_id
save_entity_name_sys.name
save_entity_name_sys.system
save_ENTITY_POLY
save_entity_poly.entity_id
save_entity_poly.nstd_chirality
save_entity_poly.nstd_linkage
save_entity_poly.nstd_monomer
save_entity_poly.number_of_monomers
save_entity_poly.type
save_entity_poly.type_details
save_ENTITY_POLY_SEQ
save_entity_poly_seq.entity_id
save_entity_poly_seq.hetero
save_entity_poly_seq.mon_id
save_entity_poly_seq.num
save_ENTITY_POLY_SEQ_DIF
save_entity_poly_seq_dif.db_mon_id
save_entity_poly_seq_dif.db_code
save_entity_poly_seq_dif.db_name
save_entity_poly_seq_dif.details
save_entity_poly_seq_dif.entity_id
save_entity_poly_seq_dif.mon_id
save_entity_poly_seq_dif.seq_num
save_ENTITY_REFERENCE
save_entity_reference.database_code
save_entity_reference.database_name
save_entity_reference.details
save_entity_reference.entity_id
save_ENTITY_SRC_GEN
save_entity_src_gen.entity_id
save_entity_src_gen.gene_src_common_name
save_entity_src_gen.gene_src_details
save_entity_src_gen.gene_src_genus
save_entity_src_gen.gene_src_species
save_entity_src_gen.gene_src_strain
save_entity_src_gen.gene_src_tissue
save_entity_src_gen.gene_src_tissue_fraction
save_entity_src_gen.host_org_common_name
save_entity_src_gen.host_org_details
save_entity_src_gen.host_org_genus
save_entity_src_gen.host_org_species
save_entity_src_gen.host_org_strain
save_entity_src_gen.plasmid_details
save_entity_src_gen.plasmid_name
save_ENTITY_SRC_NAT
save_entity_src_nat.common_name
save_entity_src_nat.details
save_entity_src_nat.entity_id
save_entity_src_nat.genus
save_entity_src_nat.species
save_entity_src_nat.strain
save_entity_src_nat.tissue
save_entity_src_nat.tissue_fraction
save_EXPTL
save_exptl.absorpt_coefficient_mu
save_exptl.absorpt_correction_T_max
save_exptl.absorpt_correction_T_min
save_exptl.absorpt_correction_type
save_exptl.absorpt_process_details
save_exptl.block_id
save_exptl.crystals_number
save_exptl.details
save_EXPTL_CRYSTAL
save_exptl_crystal.colour
save_exptl_crystal.density_diffrn
save_exptl_crystal.density_meas
save_exptl_crystal.density_meas_temp
save_exptl_crystal.density_method
save_exptl_crystal.density_percent_sol
save_exptl_crystal.description
save_exptl_crystal.F_000
save_exptl_crystal.id
save_exptl_crystal.preparation
save_exptl_crystal.size_max
save_exptl_crystal.size_mid
save_exptl_crystal.size_min
save_exptl_crystal.size_rad
save_EXPTL_CRYSTAL_FACE
save_exptl_crystal_face.diffr_chi
save_exptl_crystal_face.diffr_kappa
save_exptl_crystal_face.diffr_phi
save_exptl_crystal_face.diffr_psi
save_exptl_crystal_face.index_h
save_exptl_crystal_face.index_k
save_exptl_crystal_face.index_l
save_exptl_crystal_face.perp_dist
save_EXPTL_CRYSTAL_GROW
save_exptl_crystal_grow.apparatus
save_exptl_crystal_grow.atmosphere
save_exptl_crystal_grow.crystal_id
save_exptl_crystal_grow.details
save_exptl_crystal_grow.method
save_exptl_crystal_grow.method_ref
save_exptl_crystal_grow.pH
save_exptl_crystal_grow.pressure
save_exptl_crystal_grow.pressure_esd
save_exptl_crystal_grow.seeding
save_exptl_crystal_grow.seeding_ref
save_exptl_crystal_grow.temp
save_exptl_crystal_grow.temp_esd
save_exptl_crystal_grow.time
save_EXPTL_CRYSTAL_GROW_COMP
save_exptl_crystal_grow_comp.conc
save_exptl_crystal_grow_comp.details
save_exptl_crystal_grow_comp.id
save_exptl_crystal_grow_comp.name
save_exptl_crystal_grow_comp.sol_id
save_exptl_crystal_grow_comp.volume
save_GEOM
save_geom.block_id
save_geom.details
save_GEOM_ANGLE
save_geom_angle.value
save_geom_angle.value_esd
save_geom_angle.atom_site_label_1
save_geom_angle.atom_site_label_2
save_geom_angle.atom_site_label_3
save_geom_angle.publ_flag
save_geom_angle.site_symmetry_1
save_geom_angle.site_symmetry_2
save_geom_angle.site_symmetry_3
save_GEOM_BOND
save_geom_bond.atom_site_label_1
save_geom_bond.atom_site_label_2
save_geom_bond.distance
save_geom_bond.distance_esd
save_geom_bond.publ_flag
save_geom_bond.site_symmetry_1
save_geom_bond.site_symmetry_2
save_GEOM_CONTACT
save_geom_contact.atom_site_label_1
save_geom_contact.atom_site_label_2
save_geom_contact.distance
save_geom_contact.distance
save_geom_contact.publ_flag
save_geom_contact.site_symmetry_1
save_geom_contact.site_symmetry_2
save_GEOM_TORSION
save_geom_torsion.value
save_geom_torsion.value_esd
save_geom_torsion.atom_site_label_1
save_geom_torsion.atom_site_label_2
save_geom_torsion.atom_site_label_3
save_geom_torsion.atom_site_label_4
save_geom_torsion.publ_flag
save_geom_torsion.site_symmetry_1
save_geom_torsion.site_symmetry_2
save_geom_torsion.site_symmetry_3
save_geom_torsion.site_symmetry_4
save_JOURNAL
save_journal.block_id
save_journal.coden_ASTM
save_journal.coden_Cambridge
save_journal.coeditor_address
save_journal.coeditor_code
save_journal.coeditor_email
save_journal.coeditor_fax
save_journal.coeditor_name
save_journal.coeditor_notes
save_journal.coeditor_phone
save_journal.date_accepted
save_journal.date_from_coeditor
save_journal.date_to_coeditor
save_journal.date_printers_final
save_journal.date_printers_first
save_journal.date_proofs_in
save_journal.date_proofs_out
save_journal.date_recd_copyright
save_journal.date_recd_electronic
save_journal.date_recd_hard_copy
save_journal.issue
save_journal.name_full
save_journal.page_first
save_journal.page_last
save_journal.suppl_publ_number
save_journal.suppl_publ_pages
save_journal.techeditor_address
save_journal.techeditor_code
save_journal.techeditor_email
save_journal.techeditor_fax
save_journal.techeditor_name
save_journal.techeditor_notes
save_journal.techeditor_phone
save_journal.volume
save_journal.year
save_PHASING
save_phasing.method
save_PHASING_AVERAGING
save_phasing_averaging.block_id
save_phasing_averaging.details
save_phasing_averaging.method
save_PHASING_ISOMORPHOUS
save_phasing_isomorphous.block_id
save_phasing_isomorphous.details
save_phasing_isomorphous.method
save_phasing_isomorphous.parent
save_PHASING_MAD
save_phasing_MAD.block_id
save_phasing_MAD.details
save_phasing_MAD.method
save_PHASING_MIR
save_phasing_MIR.block_id
save_phasing_MIR.details
save_phasing_MIR.method
save_PHASING_MIR_DER
save_phasing_MIR_der.details
save_phasing_MIR_der.id
save_phasing_MIR_der.number_of_sites
save_phasing_MIR_der.reflns_criteria
save_PHASING_MIR_DER_SHELL
save_phasing_MIR_der_shell.d_res_high
save_phasing_MIR_der_shell.d_res_low
save_phasing_MIR_der_shell.der_id
save_phasing_MIR_der_shell.fom
save_phasing_MIR_der_shell.ha_ampl
save_phasing_MIR_der_shell.loc
save_phasing_MIR_der_shell.phase
save_phasing_MIR_der_shell.power
save_phasing_MIR_der_shell.R_Cullis
save_phasing_MIR_der_shell.R_Kraut
save_phasing_MIR_der_shell.reflns
save_PHASING_MIR_REFLN
save_phasing_MIR_refln.A_calc
save_phasing_MIR_refln.A_meas
save_phasing_MIR_refln.B_calc
save_phasing_MIR_refln.B_meas
save_phasing_MIR_refln.der_id
save_phasing_MIR_refln.F_calc
save_phasing_MIR_refln.F_meas
save_phasing_MIR_refln.F_sigma
save_phasing_MIR_refln.HL_A_iso
save_phasing_MIR_refln.HL_B_iso
save_phasing_MIR_refln.HL_C_iso
save_phasing_MIR_refln.HL_D_iso
save_phasing_MIR_refln.index_h
save_phasing_MIR_refln.index_k
save_phasing_MIR_refln.index_l
save_phasing_MIR_refln.phase_calc
save_phasing_MIR_refln.phase_meas
save_PHASING_MIR_SHELL
save_phasing_MIR_shell.d_res_high
save_phasing_MIR_shell.d_res_low
save_phasing_MIR_shell.fom
save_phasing_MIR_shell.loc
save_phasing_MIR_shell.mean_phase
save_phasing_MIR_shell.power
save_phasing_MIR_shell.R_Cullis
save_phasing_MIR_shell.R_Kraut
save_phasing_MIR_shell.reflns
save_PHASING_MIR_SITE
save_phasing_MIR_site.atom_type_symbol
save_phasing_MIR_site.B_iso
save_phasing_MIR_site.B_iso_esd
save_phasing_MIR_site.cartn_x
save_phasing_MIR_site.cartn_x_esd
save_phasing_MIR_site.cartn_y
save_phasing_MIR_site.cartn_y_esd
save_phasing_MIR_site.cartn_z
save_phasing_MIR_site.cartn_z_esd
save_phasing_MIR_site.der_id
save_phasing_MIR_site.details
save_phasing_MIR_site.fract_x
save_phasing_MIR_site.fract_x_esd
save_phasing_MIR_site.fract_y
save_phasing_MIR_site.fract_y_esd
save_phasing_MIR_site.fract_z
save_phasing_MIR_site.fract_z_esd
save_phasing_MIR_site.id
save_phasing_MIR_site.occupancy
save_PHASING_MR
save_phasing_MR.block_id
save_phasing_MR.method
save_PUBL
save_publ.block_id
save_publ.contact_author
save_publ.contact_author_email
save_publ.contact_author_fax
save_publ.contact_author_phone
save_publ.contact_letter
save_publ.manuscript_creation
save_publ.manuscript_processed
save_publ.manuscript_text
save_publ.requested_coeditor_name
save_publ.requested_journal
save_publ.section_abstract
save_publ.section_acknowledgements
save_publ.section_comment
save_publ.section_discussion
save_publ.section_experimental
save_publ.section_exptl_prep
save_publ.section_exptl_refinement
save_publ.section_figure_captions
save_publ.section_introduction
save_publ.section_references
save_publ.section_table_legends
save_publ.section_title
save_PUBL_AUTHOR
save_publ_author.address
save_publ_author.name
save_PUBL_MANUSCRIPT_INCL
save_publ_manuscript_incl.block_id
save_publ_manuscript_incl.extra_item
save_publ_manuscript_incl.extra_info
save_publ_manuscript_incl.extra_defn
save_REFINE_HIST
save_refine_hist.cycle_id
save_refine_hist.details
save_refine_hist.d_res_high
save_refine_hist.d_res_low
save_refine_hist.number_atoms_solvent
save_refine_hist.number_atoms_total
save_refine_hist.number_reflns_obs
save_refine_hist.R_factor_obs
save_REFINE
save_refine.block_id
save_refine.details
save_refine.diff_density_max
save_refine.diff_density_max_esd
save_refine.diff_density_min
save_refine.diff_density_min_esd
save_refine.diff_density_rms
save_refine.diff_density_rms_esd
save_refine.B_iso_max
save_refine.B_iso_min
save_refine.ls_abs_structure_details
save_refine.ls_abs_structure_Flack
save_refine.ls_abs_structure_Flack_esd
save_refine.ls_abs_structure_Rogers
save_refine.ls_abs_structure_Rogers_esd
save_refine.ls_extinction_coef
save_refine.ls_extinction_coef_esd
save_refine.ls_extinction_expression
save_refine.ls_extinction_method
save_refine.ls_goodness_of_fit_all
save_refine.ls_goodness_of_fit_all_esd
save_refine.ls_goodness_of_fit_obs
save_refine.ls_goodness_of_fit_obs_esd
save_refine.ls_hydrogen_treatment
save_refine.ls_matrix_type
save_refine.ls_number_constraints
save_refine.ls_number_parameters
save_refine.ls_number_reflns_all
save_refine.ls_number_reflns_obs
save_refine_ls.number_reflns_R_free
save_refine.ls_number_restraints
save_refine.ls_R_factor_all
save_refine.ls_R_factor_obs
save_refine.ls_R_factor_R_free
save_refine.ls_restrained_S_all
save_refine.ls_restrained_S_obs
save_refine.ls_shift/esd_max
save_refine.ls_shift/esd_mean
save_refine.ls_structure_factor_coef
save_refine.ls_weighting_details
save_refine.ls_weighting_scheme
save_refine.ls_wR_factor_all
save_refine.ls_wR_factor_obs
save_refine.ls_wR_factor_R_free
save_refine.occupancy_max
save_refine.occupancy_min
save_REFINE_B_ISO
save_refine_b_iso.class
save_refine_b_iso.details
save_refine_b_iso.treatment
save_refine_b_iso.value
save_REFINE_LS_RESTR
save_refine_ls_restr.criterion
save_refine_ls_restr.dev_ideal
save_refine_ls_restr.number
save_refine_ls_restr.rejects
save_refine_ls_restr.dev_ideal_target
save_refine_ls_restr.type
save_REFINE_LS_SHELL
save_refine_ls_shell.number_reflns_all
save_refine_ls_shell.number_reflns_obs
save_refine_ls_shell.number_reflns_R_free
save_refine_ls_shell.d_res_high
save_refine_ls_shell.d_res_low
save_refine_ls_shell.R_factor_all
save_refine_ls_shell.R_factor_obs
save_refine_ls_shell.R_factor_R_free
save_refine_ls_shell.wR_factor_all
save_refine_ls_shell.wR_factor_obs
save_refine_ls_shell.wR_factor_R_free
save_REFINE_OCCUPANCY
save_refine_occupancy.class
save_refine_occupancy.details
save_refine_occupancy.treatment
save_refine_occupancy.value
save_REFLN
save_refln.A_calc
save_refln.A_meas
save_refln.B_calc
save_refln.B_meas
save_refln.crystal_id
save_refln.F_calc
save_refln.F_meas
save_refln.F_sigma
save_refln.F_squared_calc
save_refln.F_squared_meas
save_refln.F_squared_sigma
save_refln.HL_coeff_A
save_refln.index_h
save_refln.index_k
save_refln.index_l
save_refln.intensity_calc
save_refln.intensity_meas
save_refln.intensity_sigma
save_refln.mean_path_length_tbar
save_refln.status
save_refln.phase_calc
save_refln.phase_meas
save_refln.refinement_status
save_refln.scale_group_code
save_refln.sint/lambda
save_refln.symmetry_epsilon
save_refln.symmetry_multiplicity
save_refln.wavelength
save_refln.wavelength_id
save_REFLNS
save_reflns.block_id
save_reflns.data_reduction_details
save_reflns.data_reduction_method
save_reflns.d_resolution_high
save_reflns.d_resolution_low
save_reflns.details
save_reflns.limit_h_max
save_reflns.limit_h_min
save_reflns.limit_k_max
save_reflns.limit_k_min
save_reflns.limit_l_max
save_reflns.limit_l_min
save_reflns.number_all
save_reflns.number_obs
save_reflns.observed_criterion
save_reflns.R_free_details
save_REFLNS_SCALE
save_reflns_scale.group_code
save_reflns_scale.meas_F
save_reflns_scale.meas_F_squared
save_reflns_scale.meas_intensity
save_REFLNS_SHELL
save_reflns_shell.number_measured_all
save_reflns_shell.number_measured_obs
save_reflns_shell.number_possible
save_reflns_shell.number_unique_all
save_reflns_shell.number_unique_obs
save_reflns_shell.d_res_high
save_reflns_shell.d_res_low
save_reflns_shell.meanI/sigI_all
save_reflns_shell.meanI/sigI_obs
save_reflns_shell.percent_possible_all
save_reflns_shell.percent_possible_obs
save_reflns_shell.Rmerge_F_all
save_reflns_shell.Rmerge_F_obs
save_reflns_shell.Rmerge_I_all
save_reflns_shell.Rmerge_I_obs
save_STRUCT
save_struct.block_id
save_struct.keywords
save_struct.title
save_STRUCT_ASYM
save_struct_asym.details
save_struct_asym.entity_id
save_struct_asym.id
save_STRUCT_BIOL
save_struct_biol.details
save_struct_biol.id
save_STRUCT_BIOL_GEN
save_struct_biol_gen.asym_id
save_struct_biol_gen.biol_id
save_struct_biol_gen.details
save_struct_biol_gen.symmetry
save_STRUCT_BIOL_KEYWORDS
save_struct_biol_keywords.biol_id
save_struct_biol_keywords.text
save_STRUCT_BIOL_VIEW
save_struct_biol_view.biol_id
save_struct_biol_view.details
save_struct_biol_view.id
save_struct_biol_view.rot_matrix
save_STRUCT_CONF
save_struct_conf.beg_label_asym_id
save_struct_conf.beg_label_res_id
save_struct_conf.beg_label_seq_id
save_struct_conf.conf_type_id
save_struct_conf.details
save_struct_conf.end_label_asym_id
save_struct_conf.end_label_res_id
save_struct_conf.end_label_seq_id
save_struct_conf.id
save_STRUCT_CONF_TYPE
save_struct_conf_type.criteria
save_struct_conf_type.id
save_struct_conf_type.reference
save_STRUCT_CONN
save_struct_conn.conn_type_id
save_struct_conn.details
save_struct_conn.id
save_struct_conn.ptnr1_label_alt_id
save_struct_conn.ptnr1_label_asym_id
save_struct_conn.ptnr1_label_atom_id
save_struct_conn.ptnr1_label_res_id
save_struct_conn.ptnr1_label_seq_id
save_struct_conn.ptnr1_role
save_struct_conn.ptnr1_symmetry
save_struct_conn.ptnr2_label_alt_id
save_struct_conn.ptnr2_label_asym_id
save_struct_conn.ptnr2_label_atom_id
save_struct_conn.ptnr2_label_res_id
save_struct_conn.ptnr2_label_seq_id
save_struct_conn.ptnr2_role
save_struct_conn.ptnr2_symmetry
save_STRUCT_CONN_TYPE
save_struct_conn_type.criteria
save_struct_conn_type.id
save_struct_conn_type.reference
save_STRUCT_MON_DETAILS
save_struct_mon_details.block_id
save_struct_mon_details.prot_cis
save_struct_mon_details.RSCC
save_struct_mon_details.RSR
save_STRUCT_MON_NUCL
save_struct_mon_nucl.alpha
save_struct_mon_nucl.beta
save_struct_mon_nucl.chi1
save_struct_mon_nucl.chi2
save_struct_mon_nucl.delta
save_struct_mon_nucl.details
save_struct_mon_nucl.epsilon
save_struct_mon_nucl.gamma
save_struct_mon_nucl.label_alt_id
save_struct_mon_nucl.label_asym_id
save_struct_mon_nucl.label_res_id
save_struct_mon_nucl.label_seq_id
save_struct_mon_nucl.mean_B_all
save_struct_mon_nucl.mean_B_base
save_struct_mon_nucl.mean_B_phos
save_struct_mon_nucl.mean_B_sugar
save_struct_mon_nucl.nu0
save_struct_mon_nucl.nu1
save_struct_mon_nucl.nu2
save_struct_mon_nucl.nu3
save_struct_mon_nucl.nu4
save_struct_mon_nucl.RSCC_all
save_struct_mon_nucl.RSCC_base
save_struct_mon_nucl.RSCC_phos
save_struct_mon_nucl.RSCC_sugar
save_struct_mon_nucl.RSR_all
save_struct_mon_nucl.RSR_base
save_struct_mon_nucl.RSR_phos
save_struct_mon_nucl.RSR_sugar
save_struct_mon_nucl.zeta
save_STRUCT_MON_PROT
save_struct_mon_prot.chi1
save_struct_mon_prot.chi2
save_struct_mon_prot.chi3
save_struct_mon_prot.chi4
save_struct_mon_prot.chi5
save_struct_mon_prot.details
save_struct_mon_prot.label_alt_id
save_struct_mon_prot.label_asym_id
save_struct_mon_prot.label_res_id
save_struct_mon_prot.label_seq_id
save_struct_mon_prot.RSCC_all
save_struct_mon_prot.RSCC_main
save_struct_mon_prot.RSCC_side
save_struct_mon_prot.RSR_all
save_struct_mon_prot.RSR_main
save_struct_mon_prot.RSR_side
save_struct_mon_prot.mean_B_all
save_struct_mon_prot.mean_B_main
save_struct_mon_prot.mean_B_side
save_struct_mon_prot.omega
save_struct_mon_prot.phi
save_struct_mon_prot.psi
save_STRUCT_MON_CIS
save_struct_mon_prot_cis.label_alt_id
save_struct_mon_prot_cis.label_asym_id
save_struct_mon_prot_cis.label_res_id
save_struct_mon_prot_cis.label_seq_id
save_STRUCT_NCS_DOM
save_struct_ncs_dom.details
save_struct_ncs_dom.id
save_STRUCT_NCS_DOM_GEN
save_struct_ncs_dom_gen.beg_label_alt_id
save_struct_ncs_dom_gen.beg_label_asym_id
save_struct_ncs_dom_gen.beg_label_res_id
save_struct_ncs_dom_gen.beg_label_seq_id
save_struct_ncs_dom_gen.dom_id
save_struct_ncs_dom_gen.end_label_alt_id
save_struct_ncs_dom_gen.end_label_asym_id
save_struct_ncs_dom_gen.end_label_res_id
save_struct_ncs_dom_gen.end_label_seq_id
save_STRUCT_NCS_ENS
save_struct_ncs_ens.details
save_struct_ncs_ens.id
save_struct_ncs_ens.point_group
save_STRUCT_NCS_ENS_OPER
save_struct_ncs_ens_oper.details
save_struct_ncs_ens_oper.dom_id_1
save_struct_ncs_ens_oper.dom_id_2
save_struct_ncs_ens_oper.ens_id
save_struct_ncs_ens_oper.kappa
save_struct_ncs_ens_oper.phi
save_struct_ncs_ens_oper.psi
save_STRUCT_SITE
save_struct_site.details
save_struct_site.id
save_STRUCT_SITE_GEN
save_struct_site_gen.details
save_struct_site_gen.id
save_struct_site_gen.label_alt_id
save_struct_site_gen.label_asym_id
save_struct_site_gen.label_atom_id
save_struct_site_gen.label_res_id
save_struct_site_gen.label_seq_id
save_struct_site_gen.site_id
save_struct_site_gen.symmetry
save_STRUCT_SITE_KEYWORDS
save_struct_site_keywords.site_id
save_struct_site_keywords.text
save_STRUCT_SITE_VIEW
save_struct_site_view.details
save_struct_site_view.id
save_struct_site_view.rot_matrix
save_struct_site_view.site_id
save_SYMMETRY
save_symmetry.block_id
save_symmetry.cell_setting
save_symmetry.Int_Tables_number
save_symmetry.space_group_name_Hall
save_symmetry.space_group_name_H-M
save_SYMMETRY_EQUIV
save_symmetry_equiv.id
save_symmetry_equiv.pos_as_xyz
_category.description
;
Data items in the ATOM_SITE category record details about
the atom sites in a macromolecular crystal structure, such as
the positional coordinates, atomic displacement parameters,
magnetic moments and directions, and so on.
The data items for describing anisotropic temperature or thermal
displacement factors are only used if the corresponding items are
not given in the ATOM_SITE_ANISOTROP category.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_site.id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_res_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.cartn_x
_atom_site.cartn_y
_atom_site.cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.footnote_id
_atom_site.entity_id
_atom_site.entity_seq_num
ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 1 11
ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 1 11
ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 1 11
ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 1 11
ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 1 11
ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 1 11
ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 1 11
ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 1 12
ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 1 12
ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 1 12
ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 1 12
ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 1 12
ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 1 12
ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 1 12
ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 1 12
ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 1 12
ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 1 13
ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 1 13
ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 1 13
ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 1 13
ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 1 13
ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 1 13
ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 1 13
# - - - - data truncated for brevity - - - -
ATOM C C1 APS C 300 1 4.171 29.012 7.116 0.58 17.27 1 2 .
ATOM C C2 APS C 300 1 4.949 27.758 6.793 0.58 16.95 1 2 .
ATOM O O3 APS C 300 1 4.800 26.678 7.393 0.58 16.85 1 2 .
ATOM N N4 APS C 300 1 5.930 27.841 5.869 0.58 16.43 1 2 .
# - - - - data truncated for brevity - - - -
;
_item_description.description
;
These are the standard anisotropic atomic displacement
components which appear in the structure factor term:
exp(-1/4 sum~i~ sum~j~ B~ij~ h~i~ h~j~ a*~i~ a*~j~).
The unique components of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_B'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.aniso_U'
'constant'
'_atom_site_anisotrop.U'
'constant'
'_atom_site.aniso_U'
'alternative_exclusive'
'_atom_site_anisotrop.B'
'alternative_exclusive'
'_atom_site_anisotrop.U'
'alternative_exclusive'
_item_structure.code 'matrix3x3'
_item_structure.organization 'rs_rowwise'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description ; The estimated standard deviation of _atom_site.aniso_B. ; _item.name '_atom_site.aniso_B_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U_esd' 'constant' '_atom_site_anisotrop.U_esd' 'constant' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
_item_description.description
;
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
_item.name '_atom_site.aniso_ratio'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_atom_site_anisotrop.ratio'
'alternative_exclusive'
_item_range.maximum ?
_item_range.minimum 1.0
_item_type.code float
_item_description.description
;
These are the standard anisotropic atomic displacement
components which appear in the structure factor term:
exp(-2pi^2^ sum~i~ sum~j~ U~ij~ h~i~ h~j~ a*~i~ a*~j~).
The unique components of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.aniso_B'
'constant'
'_atom_site_anisotrop.B'
'constant'
'_atom_site.aniso_B'
'alternative_exclusive'
'_atom_site_anisotrop.B'
'alternative_exclusive'
'_atom_site_anisotrop.U'
'alternative_exclusive'
_item_structure.code 'matrix3x3'
_item_structure.organization 'rs_rowwise'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[1][1] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[1][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_11'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[1][2] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[1][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_12'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[1][3] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[1][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_13'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[2][2] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[2][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_22'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[2][3] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[2][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_23'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description
;
The U[3][3] standard anisotropic atomic displacement
component. This data item is only present in this dictionary
for compliance (via the alias) with previous dictionaries.
;
_item.name '_atom_site.aniso_U[3][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_33'
_item_default.value 0.0
_item_related.related_name '_atom_site.aniso_U'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
_item_description.description ; The estimated standard deviation of _atom_site.aniso_U. ; _item.name '_atom_site.aniso_U_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B_esd' 'constant' '_atom_site_anisotrop.B_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.attached_hydrogens.
_item_description.description
;
The number of hydrogen atoms attached to the atom at this site
excluding any H atoms for which coordinates (measured or
calculated) are given.
;
_item.name '_atom_site.attached_hydrogens'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_attached_hydrogens'
_item_default.value 0
_item_range.maximum 4
_item_range.minimum 0
_item_type.code int
loop_
_item_examples.case
_item_examples.detail
2
'water oxygen'
1
'hydroxyl oxygen'
4
'ammonium nitrogen'
save_atom_site.B_iso_or_equiv.
_item_description.description
;
Isotropic temperature factor parameter, or equivalent isotropic
temperature factor calculated from anisotropic temperature
factor parameters. The latter must be calculated as
B(equiv) = (1/3) sumi{sumj(Bij a*i a*j Ai.Aj)} where A are the
real cell, a* the reciprocal cell lengths, and Bij = 8pi**2Uij
(see Fischer R X and Tillmanns E, Acta Cryst. C44 (1988)
775-776).
;
_item.name '_atom_site.B_iso_or_equiv'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_related.related_name '_atom_site.U_iso_or_equiv'
_item_related.function_code constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
save_atom_site.B_iso_or_equiv_esd.
_item_description.description ; The estimated standard deviation of _atom_site.B_iso_or_equiv. ; _item.name '_atom_site.B_iso_or_equiv_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_atom_site.U_iso_or_equiv_esd' _item_related.function_code constant _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.calc_attached_atom.
_item_description.description
;
The _atom_site.label of the atom site to which the 'geometry-
calculated' atom site is attached.
;
_item.name '_atom_site.calc_attached_atom'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_calc_attached_atom'
_item_type.code char
_item_description.description
;
A standard code to signal if the site data has been determined
by diffraction data or calculated from the geometry of
surrounding sites, or has been assigned dummy coordinates. The
abbreviation 'c' may be used in place of 'calc'.
;
_item.name '_atom_site.calc_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_calc_flag'
_item_default.value d
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
d
'determined from diffraction measurements'
calc
'calculated from molecular geometry'
c
'abbreviation for "calc"'
dum
'dummy site with meaningless coordinates'
_item_description.description
;
The x coordinate of the atom site position specified as
orthogonal Angstroms. The orthogonal Cartesian axes are related
to the cell axes as specified by the description given in
_atom_sites.cartn_transform_axes.
;
_item.name '_atom_site.cartn_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
_item_aliases.alias_name '_atom_site_cartn_x'
loop_
_item_dependent.dependent_name
'_atom_site.cartn_y'
'_atom_site.cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_x. ; _item.name '_atom_site.cartn_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_y_esd' '_atom_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
The y coordinate of the atom site position specified as
orthogonal Angstroms. The orthogonal Cartesian axes are related
to the cell axes as specified by the description given in
_atom_sites.cartn_transform_axes.
;
_item.name '_atom_site.cartn_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
_item_aliases.alias_name '_atom_site_cartn_y'
loop_
_item_dependent.dependent_name
'_atom_site.cartn_x'
'_atom_site.cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_y. ; _item.name '_atom_site.cartn_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_x_esd' '_atom_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
The z coordinate of the atom site position specified as
orthogonal Angstroms. The orthogonal Cartesian axes are related
to the cell axes as specified by the description given in
_atom_sites.cartn_transform_axes.
;
_item.name '_atom_site.cartn_z'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
_item_aliases.alias_name '_atom_site_cartn_z'
loop_
_item_dependent.dependent_name
'_atom_site.cartn_x'
'_atom_site.cartn_y'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _atom_site.cartn_z. ; _item.name '_atom_site.cartn_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.cartn_x_esd' '_atom_site.cartn_y_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
A description of the constraints applied to parameters at this
site during refinement. See also _atom_site.refinement_flags
and _refine_ls_number_constraints.
;
_item.name '_atom_site.constraints'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_constraints'
_item_default.value '.'
_item_type.code char
_item_examples.case 'pop=1.0-pop(Zn3)'
_item_description.description
;
A description of special aspects of this site. See also
_atom_site.refinement_flags.
;
_item.name '_atom_site.description'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_description'
_item_type.code char
_item_examples.case 'Ag/Si disordered'
save_atom_site.disorder_group.
_item_description.description
;
A code to link disordered atom sites of a group that exist
simultaneously in the crystal structure.
;
_item.name '_atom_site.disorder_group'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value '.'
_item_type.code char
_item_examples.case 'A'
_item_description.description
;
The x coordinate of the atom site position specified as a
fraction of _cell.length_a.
;
_item.name '_atom_site.fract_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
_item_aliases.alias_name '_atom_site_fract_x'
loop_
_item_dependent.dependent_name
'_atom_site.fract_y'
'_atom_site.fract_z'
_item_type.code float
_item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_x. ; _item.name '_atom_site.fract_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y_esd' '_atom_site.fract_z_esd' _item_type.code float
_item_description.description
;
The y coordinate of the atom site position specified as a
fraction of _cell.length_b.
;
_item.name '_atom_site.fract_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
_item_aliases.alias_name '_atom_site_fract_y'
loop_
_item_dependent.dependent_name
'_atom_site.fract_x'
'_atom_site.fract_z'
_item_type.code float
_item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_y. ; _item.name '_atom_site.fract_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_z_esd' _item_type.code float
_item_description.description
;
The z coordinate of the atom site position specified as a
fraction of _cell.length_c.
;
_item.name '_atom_site.fract_z'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
_item_aliases.alias_name '_atom_site_fract_z'
loop_
_item_dependent.dependent_name
'_atom_site.fract_x'
'_atom_site.fract_y'
_item_type.code float
_item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.fract_z. ; _item.name '_atom_site.fract_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item.sub_category_id 'fractional_coordinate_esd' loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_y_esd' _item_type.code float
_item_description.description
;
The group of atoms to which the _atom_site. belongs. This
data item is provided for compatibility with the original Protein
Data Bank format, and only for that purpose.
;
_item.name '_atom_site.group_PDB'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
ATOM
HETATM
_item_description.description
;
The value of _atom_site.id must uniquely identify a record in the
ATOM_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
For compatibility with older files, _atom_site.label is aliases
to _atom_site.id.
;
_item.name '_atom_site.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
_item_description.description
;
The _atom_site.label is a unique identifier for a particular site
in the crystal. This code is made up of a sequence of up to seven
components, _atom_site.label_component_0 to *_6, which may be
specified as separate data items. Component 0 usually matches one
of the specified _atom_type.symbol codes. This is not mandatory
if an _atom_site.type_symbol item is included in the atom site
list. The _atom_site.type_symbol always takes precedence over
an _atom_site.label in the identification of the atom type. The
label components 1 to 6 are optional, and normally only
components 0 and 1 are used. Note that components 0 and 1 are
concatenated, while all other components, if specified, are
separated by an underline character. Underline separators are
only used if higher-order components exist. If an intermediate
component is not used it may be omitted provided the underline
separators are inserted. For example the label 'C233__ggg' is
acceptable and represents the components C, 233, '', and ggg.
Each label may have a different number of components.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.label'
atom_site
yes
'_atom_site_anisotrop.label'
atom_site_anisotrop
yes
'_geom_angle.atom_site_label_1'
geom_angle
yes
'_geom_angle.atom_site_label_2'
geom_angle
yes
'_geom_angle.atom_site_label_3'
geom_angle
yes
'_geom_bond.atom_site_label_1'
geom_bond
yes
'_geom_bond.atom_site_label_2'
geom_bond
yes
'_geom_contact.atom_site_label_1'
geom_contact
yes
'_geom_contact.atom_site_label_2'
geom_contact
yes
'_geom_torsion.atom_site_label_1'
geom_torsion
yes
'_geom_torsion.atom_site_label_2'
geom_torsion
yes
'_geom_torsion.atom_site_label_3'
geom_torsion
yes
'_geom_torsion.atom_site_label_4'
geom_torsion
yes
loop_
_item_aliases.alias_name
'_atom_site_label'
'_atom_site.id'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site_anisotrop.label'
'_atom_site.label'
'_geom_angle.atom_site_label_1'
'_atom_site.label'
'_geom_angle.atom_site_label_2'
'_atom_site.label'
'_geom_angle.atom_site_label_3'
'_atom_site.label'
'_geom_bond.atom_site_label_1'
'_atom_site.label'
'_geom_bond.atom_site_label_2'
'_atom_site.label'
'_geom_contact.atom_site_label_1'
'_atom_site.label'
'_geom_contact.atom_site_label_2'
'_atom_site.label'
'_geom_torsion.atom_site_label_1'
'_atom_site.label'
'_geom_torsion.atom_site_label_2'
'_atom_site.label'
'_geom_torsion.atom_site_label_3'
'_atom_site.label'
'_geom_torsion.atom_site_label_4'
'_atom_site.label'
_item_type.code char
loop_
_item_examples.case
C12
Ca3g28
Fe3+17
H*251
boron2a
C_a_phe_83_a_0
Zn_Zn_301_A_0
_item_description.description
;
A component of the macromolecular identifier for this atom site.
Note that this is not necessarily a number and does not have to
correspond to the value of _atom_site.entity_seq_num.
_atom_site.label_seq_id may be used for homology numbering,
sequence numbering, and so on.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.label_seq_id'
atom_site
yes
'_struct_conf.beg_label_seq_id'
struct_conf
yes
'_struct_conf.end_label_seq_id'
struct_conf
yes
'_struct_conn.ptnr1_label_seq_id'
struct_conn
yes
'_struct_conn.ptnr2_label_seq_id'
struct_conn
yes
'_struct_mon_nucl.label_seq_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_seq_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_seq_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_seq_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_seq_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_seq_id'
struct_site_gen
yes
_item.sub_category_id 'mm_atom_site_label'
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conf.beg_label_seq_id'
'_atom_site.label_seq_id'
'_struct_conf.end_label_seq_id'
'_atom_site.label_seq_id'
'_struct_conn.ptnr1_label_seq_id'
'_atom_site.label_seq_id'
'_struct_conn.ptnr2_label_seq_id'
'_atom_site.label_seq_id'
'_struct_mon_nucl.label_seq_id'
'_atom_site.label_seq_id'
'_struct_mon_prot.label_seq_id'
'_atom_site.label_seq_id'
'_struct_mon_prot_cis.label_seq_id'
'_atom_site.label_seq_id'
'_struct_ncs_dom_gen.beg_label_seq_id'
'_atom_site.label_seq_id'
'_struct_ncs_dom_gen.end_label_seq_id'
'_atom_site.label_seq_id'
'_struct_site_gen.label_seq_id'
'_atom_site.label_seq_id'
_item_type.code char
_item_description.description
;
The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site.
;
_item.name '_atom_site.occupancy'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_occupancy'
_item_default.value 1.0
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_description.description ; The estimated standard deviation of _atom_site.occupancy. ; _item.name '_atom_site.occupancy_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_atom_site.refinement_flags.
_item_description.description
;
A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site.
;
_item.name '_atom_site.refinement_flags'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_refinement_flags'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
.
'no refinement constraints'
S
'special position constraint on site'
G
'rigid group refinement of site'
R
;
riding atom site attached to non-riding
atom
;
D
'distance or angle restraint on site'
T
'thermal displacement constraints'
U
'Uiso or Uij restraint (rigid bond)'
P
'partial occupancy constraint'
_item_description.description
;
A description of restraints applied to specific parameters at
this site during refinement. See also
_atom_site.refinement_flags and _refine_ls_number_restraints.
;
_item.name '_atom_site.restraints'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_restraints'
_item_type.code char
_item_examples.case 'restrained to planar ring'
save_atom_site.symmetry_multiplicity.
_item_description.description
;
The multiplicity of a site due to the space-group symmetry as is
given in International Tables for Crystallography, Vol. A (1987).
;
_item.name '_atom_site.symmetry_multiplicity'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_symmetry_multiplicity'
_item_range.maximum 192
_item_range.minimum 1
_item_type.code int
save_atom_site.thermal_displace_type.
_item_description.description
;
A standard code used to describe the type of atomic displacement
parameters used for the site.
;
_item.name '_atom_site.thermal_displace_type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_thermal_displace_item_type'
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
Uani
'anisotropic Uij'
Uiso
'isotropic U'
Uovl
'overall U'
Umpe
'multipole expansion U'
Bani
'anisotropic Bij'
Biso
'isotropic B'
Bovl
'overall B'
save_atom_site.U_iso_or_equiv.
_item_description.description
;
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter calculated from anisotropic
atomic displacement parameters. The latter must be calculated as
U(equiv) = (1/3) sumi{sumj(Uij a*i a*j Ai.Aj)} where A are the
real-cell and a* the reciprocal-cell lengths [see Fischer, R. X.
and Tillmanns, E. (1988). Acta Cryst. C44, 775-776].
;
_item.name '_atom_site.U_iso_or_equiv'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_U_iso_or_equiv'
_item_range.maximum 10.0
_item_range.minimum 0.0
_item_related.related_name '_atom_site.B_iso_or_equiv'
_item_related.function_code constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
save_atom_site.U_iso_or_equiv_esd.
_item_description.description ; The estimated standard deviation of _atom_site.U_iso_or_equiv. ; _item.name '_atom_site.U_iso_or_equiv_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_atom_site.B_iso_or_equiv_esd' _item_related.function_code constant _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site.Wyckoff_symbol.
_item_description.description
;
The Wyckoff symbol (letter) as listed in the space-group section
of International Tables for Crystallography, Vol. A (1987).
;
_item.name '_atom_site.Wyckoff_symbol'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_Wychkoff_symbol'
_item_type.code char
_category.description
;
Data items in the ATOM_SITE_ANISTROP category record details
about temperature or thermal displacement factors, if those data
items are contained in a separate list from the ATOM_SITE list.
If the ATOM_SITE_ANISOTROP category is used for storing these
data, the corresponding ATOM_SITE data items are not used.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_site_anisotrop.label'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - need example
;
;
End of Example 1
;
_item_description.description
;
These are the standard anisotropic atomic displacement
components which appear in the structure factor term:
exp(-1/4 sum~i~ sum~j~ B~ij~ h~i~ h~j~ a*~i~ a*~j~).
The unique components of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.B'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.aniso_U'
'constant'
'_atom_site_anisotrop.U'
'constant'
'_atom_site.aniso_B'
'alternative_exclusive'
'_atom_site.aniso_U'
'alternative_exclusive'
'_atom_site_anisotrop.U'
'alternative_exclusive'
_item_structure.code 'matrix3x3'
_item_structure.organization 'rs_rowwise'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
save_atom_site_anisotrop.B_esd.
_item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B. ; _item.name '_atom_site_anisotrop.B_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U_esd' 'constant' '_atom_site_anisotrop.U_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.U_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
save_atom_site_anisotrop.label.
_item_description.description
;
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
save_atom_site_anisotrop.ratio.
_item_description.description
;
Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
_item.name '_atom_site_anisotrop.ratio'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 1.0
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.aniso_ratio'
'alternative_exclusive'
_item_type.code float
_item_description.description
;
These are the standard anisotropic atomic displacement
components which appear in the structure factor term:
exp(-2pi^2^ sum~i~ sum~j~ U~ij~ h~i~ h~j~ a*~i~ a*~j~).
The unique components of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.aniso_B'
'constant'
'_atom_site_anisotrop.B'
'constant'
'_atom_site.aniso_B'
'alternative_exclusive'
'_atom_site.aniso_U'
'alternative_exclusive'
'_atom_site_anisotrop.B'
'alternative_exclusive'
_item_structure.code 'matrix3x3'
_item_structure.organization 'rs_rowwise'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_squared'
save_atom_site_anisotrop.U_esd.
_item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U. ; _item.name '_atom_site_anisotrop.U_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B_esd' 'constant' '_atom_site_anisotrop.B_esd' 'constant' '_atom_site.aniso_B_esd' 'alternative_exclusive' '_atom_site.aniso_U_esd' 'alternative_exclusive' '_atom_site_anisotrop.B_esd' 'alternative_exclusive' _item_structure.code 'matrix3x3' _item_structure.organization 'rs_rowwise' _item_type.code float _item_units.code 'angstroms_squared'
_category.description
;
Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_sites.block_id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and/or laboratory records for the
structure corresponding to PDB entry 5HVP
(Using simple matrix input)
;
;
_atom_sites.cartn_transform_axes 'c along z, astar along x, b along y'
_atom_sites.cartn_tran_matrix 58.39
0.00
0.00
0.00
86.70
0.00
0.00
0.00
46.27
;
;
Example 2 - based on PDB entry 5HVP and/or laboratory records for the
structure corresponding to PDB entry 5HVP
(Using matrix element enumeration)
;
;
_atom_sites.cartn_transform_axes 'c along z, astar along x, b along y'
_atom_sites.cartn_tran_matrix[1][1] 58.39
_atom_sites.cartn_tran_matrix[1][2] 0.00
_atom_sites.cartn_tran_matrix[1][3] 0.00
_atom_sites.cartn_tran_matrix[2][1] 0.00
_atom_sites.cartn_tran_matrix[2][2] 86.70
_atom_sites.cartn_tran_matrix[2][3] 0.00
_atom_sites.cartn_tran_matrix[3][1] 0.00
_atom_sites.cartn_tran_matrix[3][2] 0.00
_atom_sites.cartn_tran_matrix[3][3] 46.27
;
save_atom_sites.cartn_tran_matrix.
_item_description.description
;
The matrix used to transform fractional coordinates in the
ATOM_SITE category to Cartesian coordinates in the same category.
The axial alignments of this transformation are described in
_atom_sites.cartn_transform_axes.
|11 12 13| x x'
|21 22 23| ( y ) fractional = ( y' ) Cartesian
|31 32 33| z z'
;
_item.name '_atom_sites.cartn_tran_matrix'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
save_atom_sites.cartn_tran_matrix[1][1].
_item_description.description
;
The [1][1] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[1][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_11'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[1][2].
_item_description.description
;
The [1][2] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[1][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_12'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[1][3].
_item_description.description
;
The [1][3] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[1][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_13'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[2][1].
_item_description.description
;
The [2][1] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[2][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_21'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[2][2].
_item_description.description
;
The [2][2] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[2][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_22'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[2][3].
_item_description.description
;
The [2][3] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[2][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_21'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[3][1].
_item_description.description
;
The [3][1] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[3][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_31'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[3][2].
_item_description.description
;
The [3][2] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[3][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_32'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_tran_matrix[3][3].
_item_description.description
;
The [3][3] element of the 3x3 matrix
atom_sites.cartn_tran_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_atom_sites.cartn_tran_matrix[3][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_tran_matrix_33'
_item_related.related_name '_atom_sites.cartn_tran_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_atom_sites.cartn_transform_axes.
_item_description.description
;
A description of the relative alignment of the crystal cell axes
to the Cartesian orthogonal axes as applied in the transform-
ation matrix _atom_sites.cartn_tran_matrix
;
_item.name '_atom_sites.cartn_transform_axes'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_cartn_transform_axes'
_item_type.code char
_item_examples.case 'a parallel to x; b in the plane of y & z'
save_atom_sites.frac_tran_matrix.
_item_description.description
;
The matrix used to transform Cartesian coordinates in the
ATOM_SITE category fractional coordinates in the same category.
The axial alignments of this transformation are described in
_atom_sites.cartn_transform_axes.
|11 12 13| x x'
|21 22 23| ( y ) Cartesian = ( y' ) fractional
|31 32 33| z z'
;
_item.name '_atom_sites.frac_tran_matrix'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
save_atom_sites.solution_hydrogens.
_item_description.description
;
A codes which identifies the methods used to locate the initial
atomic sites. The solution_hydrogens code identifies how the
hydrogens were located.
;
_item.name '_atom_sites.solution_hydrogens'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
difmap
'difference Fourier map'
vecmap
'real-space vector search'
heavy
'heavy-atom method'
direct
'structure-invariant direct methods'
geom
'inferred from neighbouring sites'
disper
'anomalous-dispersion techniques'
isomor
'isomorphous structure methods'
save_atom_sites.solution_primary.
_item_description.description
;
A code which identifies the methods used to locate the initial
atomic sites. The solution_primary code identifies how the first
atom sites were determined.
;
_item.name '_atom_sites.solution_primary'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
difmap
'difference Fourier map'
vecmap
'real-space vector search'
heavy
'heavy-atom method'
direct
'structure-invariant direct methods'
geom
'inferred from neighbouring sites'
disper
'anomalous-dispersion techniques'
isomor
'isomorphous structure methods'
save_atom_sites.solution_secondary.
_item_description.description
;
A code which identifies the methods used to locate the initial
atomic sites. The solution_secondary code identifies
how the non-hydrogen sites not include in solution_primary
were located.
;
_item.name '_atom_sites.solution_secondary'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
difmap
'difference Fourier map'
vecmap
'real-space vector search'
heavy
'heavy-atom method'
direct
'structure-invariant direct methods'
geom
'inferred from neighbouring sites'
disper
'anomalous-dispersion techniques'
isomor
'isomorphous structure methods'
_category.description
;
Data items in the ATOM_SITES_ALT category record details
about the structural ensembles that should be generated from
atom sites or groups of atom sites that are modelled in
alternative conformations in this CIF.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_sites_alt.id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_sites_alt.id
_atom_sites_alt.details
'.'
; Atom sites with the alternative id set to null are not modelled in
alternative conformations
;
'1'
; Atom sites with the alternative id set to 1 have been modelled in
alternative conformations with respect to atom sites marked with
alternative id 2. The conformations of amino acid side chains
and solvent atoms with alternative id set to 1 correlate with the
conformation of the inhibitor marked with alternative id 1. They
have been given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.
;
'2'
; Atom sites with the alternative id set to 2 have been modelled in
alternative conformations with respect to atom sites marked with
alternative id 1. The conformations of amino acid side chains
and solvent atoms with alternative id set to 2 correlate with the
conformation of the inhibitor marked with alternative id 2. They
have been given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.
;
'3'
; Atom sites with the alternative id set to 3 have been modelled in
alternative conformations with respect to atoms marked with alternative
id 4. The conformations of amino acid side chains and solvent atoms with
alternative id set to 3 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given an occupancy of
0.50.
;
'4'
; Atom sites with the alternative id set to 4 have been modelled in
alternative conformations with respect to atoms marked with alternative
id 3. The conformations of amino acid side chains and solvent atoms with
alternative id set to 4 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given an occupancy of
0.50.
;
;
_item_description.description
;
A description of special aspects of the modeling of atoms in
alternative conformations.
;
_item.name '_atom_sites_alt.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code text
_item_description.description
;
The value of _atom_sites_alt.id must uniquely identify
a record in the _atom_sites_alt. list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_alt.id'
atom_sites_alt
yes
'_atom_site.label_alt_id'
atom_site
yes
'_atom_sites_alt_gen.alt_id'
atom_sites_alt_gen
yes
'_struct_conn.ptnr1_label_alt_id'
struct_conn
yes
'_struct_conn.ptnr2_label_alt_id'
struct_conn
yes
'_struct_mon_nucl.label_alt_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_alt_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_alt_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_alt_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_alt_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_alt_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_alt_id'
'_atom_sites_alt.id'
'_atom_sites_alt_gen.alt_id'
'_atom_sites_alt.id'
'_struct_conn.ptnr1_label_alt_id'
'_atom_site.label_alt_id'
'_struct_conn.ptnr2_label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_nucl.label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_prot.label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_prot_cis.label_alt_id'
'_atom_site.label_alt_id'
'_struct_ncs_dom_gen.beg_label_alt_id'
'_atom_site.label_alt_id'
'_struct_ncs_dom_gen.end_label_alt_id'
'_atom_site.label_alt_id'
'_struct_site_gen.label_alt_id'
'_atom_site.label_alt_id'
_item_type.code char
loop_
_item_examples.case
'Orientation 1'
'Molecule abc'
_item_description.description
;
The value of _atom_sites_alt.id must uniquely identify
a record in the _atom_sites_alt. list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_alt.id'
atom_sites_alt
yes
'_atom_site.label_alt_id'
atom_site
yes
'_atom_sites_alt_gen.alt_id'
atom_sites_alt_gen
yes
'_struct_conn.ptnr1_label_alt_id'
struct_conn
yes
'_struct_conn.ptnr2_label_alt_id'
struct_conn
yes
'_struct_mon_nucl.label_alt_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_alt_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_alt_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_alt_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_alt_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_alt_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_alt_id'
'_atom_sites_alt.id'
'_atom_sites_alt_gen.alt_id'
'_atom_sites_alt.id'
'_struct_conn.ptnr1_label_alt_id'
'_atom_site.label_alt_id'
'_struct_conn.ptnr2_label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_nucl.label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_prot.label_alt_id'
'_atom_site.label_alt_id'
'_struct_mon_prot_cis.label_alt_id'
'_atom_site.label_alt_id'
'_struct_ncs_dom_gen.beg_label_alt_id'
'_atom_site.label_alt_id'
'_struct_ncs_dom_gen.end_label_alt_id'
'_atom_site.label_alt_id'
'_struct_site_gen.label_alt_id'
'_atom_site.label_alt_id'
_item_type.code char
loop_
_item_examples.case
'Orientation 1'
'Molecule abc'
_category.description
;
Data items in the ATOM_SITES_ALT_ENS category record details
about the ensemble structure generated from atoms with various
alternative conformation ids.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_sites_alt_ens.id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_sites_alt_ens.id
_atom_sites_alt_ens.details
'Ensemble 1-A'
; The inhibitor binds to the enzyme in two, roughly twofold symmetric,
alternative conformations.
This conformational ensemble includes the more populated conformation of
the inhibitor (id=1) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=3) of side chains with alternative
conformations when the conformations are not correlated with the
inhibitor conformation.
;
'Ensemble 1-B'
; The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternative conformations.
This conformational ensemble includes the more populated conformation of
the inhibitor (id=1) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=4) of side chains with alternative
conformations when the conformations are not correlated with the
inhibitor conformation.
;
'Ensemble 2-A'
; The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternative conformations.
This conformational ensemble includes the less populated conformation of
the inhibitor (id=2) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=3) of side chains with alternative
conformations when the conformations are not correlated with the
inhibitor conformation.
;
'Ensemble 2-B'
; The inhibitor binds to the enzyme in two, roughly twofold symmetric
alternative conformations.
This conformational ensemble includes the less populated conformation of
the inhibitor (id=2) and the amino acid side chains and solvent structure
that correlate with this inhibitor conformation.
Also included are one set (id=4) of side chains with alternative
conformations when the conformations are not correlated with the
inhibitor conformation.
;
;
save_atom_sites_alt_ens.details.
_item_description.description
;
A description of special aspects of the ensemble structure
generated from atoms with various alternative ids.
;
_item.name '_atom_sites_alt_ens.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code text
_item_description.description
;
The value of _atom_sites_alt_ens.id must uniquely identify a
record in the _atom_sites_alt_ens. list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_alt_ens.id'
atom_sites_alt_ens
yes
'_atom_sites_alt_gen.ens_id'
atom_sites_alt_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_sites_alt_gen.ens_id'
'_atom_sites_alt_ens.id'
_item_type.code char
_category.description
;
Data items in the ATOM_SITES_ALT_GEN category record details
about the interpretation of multiple conformations in the
structure.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_atom_sites_alt_gen.ens_id'
'_atom_sites_alt_gen.alt_id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_sites_alt_gen.ens_id
_atom_sites_alt_gen.alt_id
'Ensemble 1-A' '.'
'Ensemble 1-A' '1'
'Ensemble 1-A' '3'
'Ensemble 1-B' '.'
'Ensemble 1-B' '1'
'Ensemble 1-B' '4'
'Ensemble 2-A' '.'
'Ensemble 2-A' '2'
'Ensemble 2-A' '3'
'Ensemble 2-B' '.'
'Ensemble 2-B' '2'
'Ensemble 2-B' '4'
;
save_atom_sites_alt_gen.alt_id.
_item_description.description
;
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_atom_sites_alt_gen.ens_id.
_item_description.description
;
This data item is a pointer to _atom_sites_alt_ens.id in the
ATOM_SITES_ALT_ENS category.
;
_category.description
;
Data items in the ATOM_SITES_FOOTNOTE category record detailed
comments about an atom site or group of atom sites.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_sites_footnote.id'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_sites_footnote.id
_atom_sites_footnote.text
1
; The inhibitor binds to the enzyme in two alternative orientations. The
two orientations have been assigned alternative ids *1* and *2*.
;
2
; Side chains of these residues adopt alternative orientations that
correlate with the alternative orientations of the inhibitor.
Side chains with alternative id *1* and occupancy 0.58 correlate with
inhibitor orientation *1*.
Side chains with alternative id *2* and occupancy 0.42 correlate with
inhibitor orientation *2*.
;
3
; The positions of these water molecules correlate with the alternative
orientations of the inhibitor.
Water molecules with alternative id *1* and occupancy 0.58 correlate with
inhibitor orientation *1*.
Water molecules with alternative id *2* and occupancy 0.42 correlate with
inhibitor orientation *2*.
;
4
; Side chains of these residues adopt alternative orientations that do not
correlate with the alternative orientation of the inhibitor. ;
5
; The positions of these water molecules correlate with alternative
orientations of amino acid side chains that do not correlate with
alternative orientations of the inhibitor.
;
;
_item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case a b 1 2
_item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case a b 1 2
save_atom_sites_footnote.text.
_item_description.description
;
The text of the footnote. Footnotes are used to describe
an atom site or group of atom sites in the ATOM_SITE list.
For example, footnotes may be used to indicate atoms for which
the electron density is very weak, or atoms for which static
disorder has been modelled, among many other possibilities.
;
_item.name '_atom_sites_footnote.text'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the ATOM_TYPE category record details about
properties of the atoms that occupy the atom sites, such as the
atomic scattering factors.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_atom_type.symbol'
loop_
_category_group.id
'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
C 0 2.31000 20.8439 1.02000 10.2075
1.58860 0.568700 0.865000 51.6512 0.21560
N 0 12.2126 0.005700 3.13220 9.89330
2.01250 28.9975 1.16630 0.582600 -11.529
O 0 3.04850 13.2771 2.28680 5.70110
1.54630 0.323900 0.867000 32.9089 0.250800
S 0 6.90530 1.46790 5.20340 22.2151
1.43790 0.253600 1.58630 56.1720 0.866900
CL -1 18.2915 0.006600 7.20840 1.17170
6.53370 19.5424 2.33860 60.4486 -16.378
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.number_in_cell
_atom_type.scat_dispersion_real
_atom_type.scat_dispersion_imag
_atom_type.scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
;
save_atom_type.analytical_mass_%.
_item_description.description ; Mass percentage of this atom type derived from chemical analysis. ; _item.name '_atom_type.analytical_mass_%' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_analytical_mass_%' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description
;
A description of the atom(s) designated by this atom type. In
most cases this will be the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
;
_item.name '_atom_type.description'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_description'
_item_type.code char
loop_
_item_examples.case
deuterium
0.34Fe+0.66Ni
save_atom_type.number_in_cell.
_item_description.description ; Total number of atoms of this atom type in the unit cell. ; _item.name '_atom_type.number_in_cell' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_number_in_cell' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_atom_type.oxidation_number.
_item_description.description ; Formal oxidation state of this atom type in the structure. ; _item.name '_atom_type.oxidation_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_oxidation_number' _item_default.value 0 _item_range.maximum 6 _item_range.minimum -6 _item_type.code int
_item_description.description
;
The effective intrarmolecular bonding radii of this
atom type.
;
_item.name '_atom_type.radius_bond'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_radius_bond'
_item_range.maximum 4.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_atom_type.radius_contact.
_item_description.description
;
The effective intermolecular bonding radii of this
atom type.
;
_item.name '_atom_type.radius_contact'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_radius_contact'
_item_range.maximum 4.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_atom_type.scat_Cromer_Mann_a1.
_item_description.description
;
The a1 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_a1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_a2.
_item_description.description
;
The a2 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_a2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_a3.
_item_description.description
;
The a3 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_a3'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_a4.
_item_description.description
;
The a4 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_a4'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_b1.
_item_description.description
;
The b1 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_b1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_b2.
_item_description.description
;
The b2 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_b2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_b3.
_item_description.description
;
The b3 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_b3'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_b4.
_item_description.description
;
The b4 Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_b4'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_atom_type.scat_Cromer_Mann_c.
_item_description.description
;
The c Cromer-Mann scattering-factor coefficient used to
calculate the scattering factors for this atom type. See
International Tables for X-ray Crystallography, Vol. IV, Table
2.2B (1974); or International Tables for Crystallography, Vol. C,
Tables 6.1.1.4 and 6.1.1.5 (1991).
;
_item.name '_atom_type.scat_Cromer_Mann_c'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c'
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
_item_type.code float
save_atom_type.scat_dispersion_imag.
_item_description.description
;
The imaginary component of the anomalous dispersion
scattering factors, f'' and f' (in electrons) for this atom type
and the radiation given in _diffrn_radiation.wavelength.
;
_item.name '_atom_type.scat_dispersion_imag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_dispersion_imag'
_item_default.value 0.0
_item_dependent.dependent_name '_atom_type.scat_dispersion_real'
_item_type.code float
save_atom_type.scat_dispersion_real.
_item_description.description
;
The real component of the anomalous dispersion
scattering factors, f'' and f' (in electrons) for this atom type
and the radiation given in _diffrn_radiation.wavelength.
;
_item.name '_atom_type.scat_dispersion_real'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_dispersion_real'
_item_default.value 0.0
_item_dependent.dependent_name '_atom_type.scat_dispersion_imag'
_item_type.code float
_item_description.description ; Reference to source of scattering factors used for this atom type ; _item.name '_atom_type.scat_source' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_source' _item_type.code float _item_examples.case 'International Tables Vol IV Table 2.4.6B'
save_atom_type.scat_versus_stol_list.
_item_description.description
;
A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly recommended
;
_item.name '_atom_type.scat_versus_stol_list'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_versus_stol_list'
_item_type.code char
_item_description.description
;
The code used to identify the atom specie(s) representing this
atom type. Normally this code is the element symbol. The code
may be composed of any character except an underline with the
additional proviso that digits designate an oxidation state and
must be followed by a + or - character.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_type.symbol'
atom_type
yes
'_atom_site.type_symbol'
atom_site
yes
'_atom_site_anisotrop.type_symbol'
atom_site_anisotrop
yes
'_chemical_conn_atom.type_symbol'
chemical_conn_atom
yes
'_entity_mon_atom.type_symbol'
entity_mon_atom
yes
'_phasing_MIR_site.atom_type_symbol'
phasing_MIR_der
yes
_item_aliases.alias_name '_atom_type_symbol'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.type_symbol'
'_atom_type.symbol'
'_atom_site_anisotrop.type_symbol'
'_atom_type.symbol'
'_chemical_conn_atom.type_symbol'
'_atom_type.symbol'
'_entity_mon_atom.type_symbol'
'_atom_type.symbol'
'_phasing_MIR_site.atom_type_symbol'
'_atom_type.symbol'
_item_type.code code
loop_
_item_examples.case
C
Cu2+
H(SDS)
dummy
FeNi
_item_description.description
;
The code used to identify the atom specie(s) representing this
atom type. Normally this code is the element symbol. The code
may be composed of any character except an underline with the
additional proviso that digits designate an oxidation state and
must be followed by a + or - character.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_type.symbol'
atom_type
yes
'_atom_site.type_symbol'
atom_site
yes
'_atom_site_anisotrop.type_symbol'
atom_site_anisotrop
yes
'_chemical_conn_atom.type_symbol'
chemical_conn_atom
yes
'_entity_mon_atom.type_symbol'
entity_mon_atom
yes
'_phasing_MIR_site.atom_type_symbol'
phasing_MIR_der
yes
_item_aliases.alias_name '_atom_type_symbol'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.type_symbol'
'_atom_type.symbol'
'_atom_site_anisotrop.type_symbol'
'_atom_type.symbol'
'_chemical_conn_atom.type_symbol'
'_atom_type.symbol'
'_entity_mon_atom.type_symbol'
'_atom_type.symbol'
'_phasing_MIR_site.atom_type_symbol'
'_atom_type.symbol'
_item_type.code code
loop_
_item_examples.case
C
Cu2+
H(SDS)
dummy
FeNi
_item_description.description
;
The code used to identify the atom specie(s) representing this
atom type. Normally this code is the element symbol. The code
may be composed of any character except an underline with the
additional proviso that digits designate an oxidation state and
must be followed by a + or - character.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_type.symbol'
atom_type
yes
'_atom_site.type_symbol'
atom_site
yes
'_atom_site_anisotrop.type_symbol'
atom_site_anisotrop
yes
'_chemical_conn_atom.type_symbol'
chemical_conn_atom
yes
'_entity_mon_atom.type_symbol'
entity_mon_atom
yes
'_phasing_MIR_site.atom_type_symbol'
phasing_MIR_der
yes
_item_aliases.alias_name '_atom_type_symbol'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.type_symbol'
'_atom_type.symbol'
'_atom_site_anisotrop.type_symbol'
'_atom_type.symbol'
'_chemical_conn_atom.type_symbol'
'_atom_type.symbol'
'_entity_mon_atom.type_symbol'
'_atom_type.symbol'
'_phasing_MIR_site.atom_type_symbol'
'_atom_type.symbol'
_item_type.code code
loop_
_item_examples.case
C
Cu2+
H(SDS)
dummy
FeNi
_category.description
;
Data items in the AUDIT category record details about the
creation and subsequent updating of the CIF.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_audit.revision_id'
loop_
_category_group.id
'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_audit.creation_date '1992-12-08'
_audit.creation_method
; Created by hand from PDB entry 5HVP, from the JBC paper describing this
structure and from laboratory records
;
_audit.update_record
; 1992-12-09 adjusted to reflect comments from Brian McKeever
1992-12-10 adjusted to reflect comments from Helen Berman
1992-12-12 adjusted to reflect comments from Keith Watenpaugh
;
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_audit.creation_date 1991-03-20
_audit.creation_method from_xtal_archive_file_using_CIFIO
_audit.update_record
; 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor with diagram as manuscript HL7.
1991-04-17 adjustments based on first referees report.
1991-04-18 adjustments based on second referees report.
;
;
_item_description.description ; A date that the CIF was created. The date format is yyyy-mm-dd. ; _item.name '_audit.creation_date' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_audit_creation_date' _item_type.code char _item_examples.case 1990-07-12
_item_description.description ; A description of how data was entered into the CIF. ; _item.name '_audit.creation_method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_audit_creation_method' _item_type.code char _item_examples.case 'spawned by the program QBEE'
_item_description.description
;
The value of _audit.revision_id must uniquely identify a record
in the AUDIT list.
;
_item.name '_audit.revision_id'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'rev1'
_item_description.description
;
A record of any changes to the CIF. The update format is a date
(yyyy-mm-dd) followed by a description of the changes. The
latest update entry is added to the bottom of this record.
;
_item.name '_audit.update_record'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_audit_update_record'
_item_type.code char
_item_examples.case '1990-07-15 Updated by the Co-editor'
_category.description
;
Data items in the AUDIT_AUTHOR category record details about
the author(s) of the CIF.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_audit_author.name'
loop_
_category_group.id
'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_audit_author.name
_audit_author.address
'Fitzgerald, Paula M.D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'McKeever, Brian M.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Van Middlesworth, J.F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Springer, James P.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
;
_item_description.description
;
The address of an author of this CIF. If there are multiple
authors, _audit_author.address will be looped with
_audit_author.name.
;
_item.name '_audit_author.address'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Department
Institute
Street
City and postcode
COUNTRY
;
_item_description.description
;
The name of an author of this CIF. If there are multiple authors,
_audit_author.name will be looped with _audit_author.address.
The family name(s) followed by a comma, precedes the first
name(s) or initial(s).
;
_item.name '_audit_author.name'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
_category.description
;
Data items in the AUDIT_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the contents of this CIF.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_audit_contact_author.name'
loop_
_category_group.id
'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_audit_contact_author.name 'Fitzgerald, Paula M.D.'
_audit_contact_author.address
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
_audit_contact_author.phone '908 594 5510'
_audit_contact_author.fax '908 594 6645'
_audit_contact_author.email '[email protected]'
;
save_audit_contact_author.address.
_item_description.description
;
The mailing address of the author of the CIF to whom correspon-
dence should be addressed.
;
_item.name '_audit_contact_author.address'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Department
Institute
Street
City and postcode
COUNTRY
;
save_audit_contact_author.email.
_item_description.description
;
The electronic mail address of the author of the CIF to whom
correspondence should be addressed, in a form recognisable to
international networks.
;
_item.name '_audit_contact_author.email'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
[email protected]
[email protected]
save_audit_contact_author.fax.
_item_description.description
;
The facsimile telephone number of the author of the CIF to whom
correspondence should be addressed.
The international code is given in brackets and any extension
number is preceded by 'ext'.
;
_item.name '_audit_contact_author.fax'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '(12) 34 947 7334'
save_audit_contact_author.name.
_item_description.description
;
The name of the author of the CIF to whom correspondence should
be addressed.
The family name(s) followed by a comma, precedes the first
name(s) or initial(s).
;
_item.name '_audit_contact_author.name'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_audit_contact_author.phone.
_item_description.description
;
The telephone number of the author of the CIF to whom
correspondence should be addressed.
The international code is given in brackets and any extension
number is preceded by 'ext'.
;
_item.name '_audit_contact_author.phone'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '(12) 34 947 7330 ext 5543'
_category.description
;
There is only one item in the BLOCK category, _block.id. This
data item gives a name to the data block, an indirectly a key to
the categories (such as CELL, GEOM, EXPTL) that desribe
information pertinent to the entire data block.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_block.id'
loop_
_category_group.id
'inclusive_group'
'block_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_block.id 5HVP
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_block.id TOZ
;
_item_description.description
;
The value of _block.id identies the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_block.id'
block
yes
'_atom_sites.block_id'
atom_sites
yes
'_cell.block_id'
cell
yes
'_cell_measurement.block_id'
cell_measurement
yes
'_chemical.block_id'
chemical
yes
'_chemical_formula.block_id'
chemical_formula
yes
'_computing.block_id'
computing
yes
'_database.block_id'
database
yes
'_diffrn.block_id'
diffrn
yes
'_diffrn_measurement.block_id'
diffrn_measurement
yes
'_diffrn_orient_matrix.block_id'
diffrn_orient_matrix
yes
'_diffrn_radiation.block_id'
diffrn_radiation
yes
'_diffrn_reflns.block_id'
diffrn_reflns
yes
'_diffrn_standards.block_id'
diffrn_standards
yes
'_exptl.block_id'
exptl
yes
'_geom.block_id'
geom
yes
'_journal.block_id'
journal
yes
'_phasing_averaging.block_id'
phasing_averaging
yes
'_phasing_isomorphous.block_id'
phasing_isomorphous
yes
'_phasing_MAD.block_id'
phasing_MAD
yes
'_phasing_MIR.block_id'
phasing_MIR
yes
'_phasing_MR.block_id'
phasing_MR
yes
'_publ.block_id'
publ
yes
'_publ_manuscript_incl.block_id'
publ_manuscript_incl
yes
'_refine.block_id'
refine
yes
'_reflns.block_id'
reflns
yes
'_struct.block_id'
struct
yes
'_struct_mon_details.block_id'
struct_mon_details
yes
'_symmetry.block_id'
symmetry
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_sites.block_id'
'_block.id'
'_cell.block_id'
'_block.id'
'_cell_measurement.block_id'
'_block.id'
'_chemical.block_id'
'_block.id'
'_chemical_formula.block_id'
'_block.id'
'_computing.block_id'
'_block.id'
'_database.block_id'
'_block.id'
'_diffrn.block_id'
'_block.id'
'_diffrn_measurement.block_id'
'_block.id'
'_diffrn_orient_matrix.block_id'
'_block.id'
'_diffrn_radiation.block_id'
'_block.id'
'_diffrn_reflns.block_id'
'_block.id'
'_diffrn_standards.block_id'
'_block.id'
'_exptl.block_id'
'_block.id'
'_geom.block_id'
'_block.id'
'_journal.block_id'
'_block.id'
'_phasing_averaging.block_id'
'_block.id'
'_phasing_isomorphous.block_id'
'_block.id'
'_phasing_MAD.block_id'
'_block.id'
'_phasing_MIR.block_id'
'_block.id'
'_phasing_MR.block_id'
'_block.id'
'_publ.block_id'
'_block.id'
'_publ_manuscript_incl.block_id'
'_block.id'
'_refine.block_id'
'_block.id'
'_reflns.block_id'
'_block.id'
'_struct.block_id'
'_block.id'
'_struct_mon_details.block_id'
'_block.id'
'_symmetry.block_id'
'_block.id'
_item_type.code char
_item_description.description
;
The value of _block.id identies the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_block.id'
block
yes
'_atom_sites.block_id'
atom_sites
yes
'_cell.block_id'
cell
yes
'_cell_measurement.block_id'
cell_measurement
yes
'_chemical.block_id'
chemical
yes
'_chemical_formula.block_id'
chemical_formula
yes
'_computing.block_id'
computing
yes
'_database.block_id'
database
yes
'_diffrn.block_id'
diffrn
yes
'_diffrn_measurement.block_id'
diffrn_measurement
yes
'_diffrn_orient_matrix.block_id'
diffrn_orient_matrix
yes
'_diffrn_radiation.block_id'
diffrn_radiation
yes
'_diffrn_reflns.block_id'
diffrn_reflns
yes
'_diffrn_standards.block_id'
diffrn_standards
yes
'_exptl.block_id'
exptl
yes
'_geom.block_id'
geom
yes
'_journal.block_id'
journal
yes
'_phasing_averaging.block_id'
phasing_averaging
yes
'_phasing_isomorphous.block_id'
phasing_isomorphous
yes
'_phasing_MAD.block_id'
phasing_MAD
yes
'_phasing_MIR.block_id'
phasing_MIR
yes
'_phasing_MR.block_id'
phasing_MR
yes
'_publ.block_id'
publ
yes
'_publ_manuscript_incl.block_id'
publ_manuscript_incl
yes
'_refine.block_id'
refine
yes
'_reflns.block_id'
reflns
yes
'_struct.block_id'
struct
yes
'_struct_mon_details.block_id'
struct_mon_details
yes
'_symmetry.block_id'
symmetry
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_sites.block_id'
'_block.id'
'_cell.block_id'
'_block.id'
'_cell_measurement.block_id'
'_block.id'
'_chemical.block_id'
'_block.id'
'_chemical_formula.block_id'
'_block.id'
'_computing.block_id'
'_block.id'
'_database.block_id'
'_block.id'
'_diffrn.block_id'
'_block.id'
'_diffrn_measurement.block_id'
'_block.id'
'_diffrn_orient_matrix.block_id'
'_block.id'
'_diffrn_radiation.block_id'
'_block.id'
'_diffrn_reflns.block_id'
'_block.id'
'_diffrn_standards.block_id'
'_block.id'
'_exptl.block_id'
'_block.id'
'_geom.block_id'
'_block.id'
'_journal.block_id'
'_block.id'
'_phasing_averaging.block_id'
'_block.id'
'_phasing_isomorphous.block_id'
'_block.id'
'_phasing_MAD.block_id'
'_block.id'
'_phasing_MIR.block_id'
'_block.id'
'_phasing_MR.block_id'
'_block.id'
'_publ.block_id'
'_block.id'
'_publ_manuscript_incl.block_id'
'_block.id'
'_refine.block_id'
'_block.id'
'_reflns.block_id'
'_block.id'
'_struct.block_id'
'_block.id'
'_struct_mon_details.block_id'
'_block.id'
'_symmetry.block_id'
'_block.id'
_item_type.code char
_category.description
;
Data items in the CELL category record details about the
crystallographic cell parameters.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_cell.block_id'
loop_
_category_group.id
'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_cell.length_a 58.39(5)
_cell.length_b 86.70(12)
_cell.length_c 46.27(6)
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.volume 234237
_cell.details
; The cell parameters were refined every twenty frames during data
integration. The cell lengths given are the mean of 55 such refinements;
the esds given are the root mean square deviations of these 55
observations from that mean.
;
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_cell.length_a 5.959(1)
_cell.length_b 14.956(1)
_cell.length_c 19.737(3)
_cell.angle_alpha 90
_cell.angle_beta 90
_cell.angle_gamma 90
_cell.volume 1759.0(3)
;
_item_description.description ; Unit-cell angle alpha in degrees of the reported structure. ; _item.name '_cell.angle_alpha' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_alpha' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_beta' '_cell.angle_gamma' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_alpha. ; _item.name '_cell.angle_alpha_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_beta_esd' '_cell.angle_gamma_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Unit-cell angle beta in degrees of the reported structure. ; _item.name '_cell.angle_beta' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_beta' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_gamma' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_beta. ; _item.name '_cell.angle_beta_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_gamma_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Unit-cell angle gamma in degrees of the reported structure. ; _item.name '_cell.angle_gamma' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle' _item_aliases.alias_name '_cell_angle_gamma' _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_beta' _item_range.maximum 180.0 _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _cell.angle_gamma. ; _item.name '_cell.angle_gamma_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_angle_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_beta_esd' _item_type.code float _item_units.code 'degrees'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
A description of special aspects of the cell choice, noting
possible alternative settings.
;
_item.name '_cell.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_special_details'
_item_type.code char
loop_
_item_examples.case
'pseudo-orthorhombic'
;
standard setting from 45 deg rotation
around c
;
_item_description.description
;
The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
_chemical_formula.sum.
;
_item.name '_cell.formula_units_Z'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_formula_units_Z'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
_item_description.description ; Unit-cell length a corresponding to the structure reported. ; _item.name '_cell.length_a' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_a' loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_a. ; _item.name '_cell.length_a_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_b_esd' '_cell.length_c_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Unit-cell length b corresponding to the structure reported. ; _item.name '_cell.length_b' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_b' loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_b. ; _item.name '_cell.length_b_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_c_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description ; Unit-cell length c corresponding to the structure reported. ; _item.name '_cell.length_c' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length' _item_aliases.alias_name '_cell_length_c' loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_b' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _cell.length_c. ; _item.name '_cell.length_c_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cell_length_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_b_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
Volume calculated from the values of _cell.length_a,
_cell.length_b, _cell.length_c, _cell.angle_alpha,
_cell.angle_beta, and _cell.angle_gamma.
%% Need real formula here.
;
_item.name '_cell.volume'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_volume'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_cubed'
_item_description.description ; The estimated standard deviation of _cell.volume. ; _item.name '_cell.volume_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms_cubed'
_category.description
;
Data items in the CELL_MEASUREMENT category record details
about the measurement of the crystallographic cell parameters.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_cell_measurement.block_id'
loop_
_category_group.id
'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_cell_measurement.temperature 293(3)
_cell_measurement.theta_min 11
_cell_measurement.theta_max 31
_cell_measurement.wavelength 1.54
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_cell_measurement.temperature 293
_cell_measurement.reflns_used 25
_cell_measurement.theta_min 25
_cell_measurement.theta_max 31
;
save_cell_measurement.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_cell_measurement.pressure.
_item_description.description
;
The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure used to synthesize the sample).
;
_item.name '_cell_measurement.pressure'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_pressure'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kilopascals'
save_cell_measurement.pressure_esd.
_item_description.description ; The estimated standard deviation of _cell_measurement.pressure. ; _item.name '_cell_measurement.pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_cell_measurement.radiation.
_item_description.description
;
Description of the radiation used to measure the unit-cell data.
See also _cell_measurement.wavelength.
;
_item.name '_cell_measurement.radiation'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_radiation'
_item_type.code char
loop_
_item_examples.case
'neutron'
'Cu K\a'
'synchrotron'
save_cell_measurement.reflns_used.
_item_description.description
;
The total number of reflections used to determine the unit cell.
These reflections may be specified as CELL_MEASUREMENT_REFLN
data items.
;
_item.name '_cell_measurement.reflns_used'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_reflns_used'
_item_type.code int
save_cell_measurement.temperature.
_item_description.description
;
The temperature in degrees Kelvin at which the unit-cell
parameters were measured (not the temperature of synthesis).
;
_item.name '_cell_measurement.temperature'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_temperature'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kelvin'
save_cell_measurement.temperature_esd.
_item_description.description
;
The estimated standard deviation of
_cell_measurement.temperature.
;
_item.name '_cell_measurement.temperature_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'kelvin'
save_cell_measurement.theta_max.
_item_description.description
;
The maximum theta angle in degrees of reflections used to measure
the unit cell.
;
_item.name '_cell_measurement.theta_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_theta_max'
_item_range.maximum 90.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'degrees'
save_cell_measurement.theta_min.
_item_description.description
;
The minimum theta angle in degrees of reflections used to measure
the unit cell.
;
_item.name '_cell_measurement.theta_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_theta_min'
_item_range.maximum 90.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'degrees'
save_cell_measurement.wavelength.
_item_description.description
;
The wavelength of the radiation used to measure the unit cell.
If this is not specified, the wavelength is assumed to be the
same as that given in _diffrn_radiation.wavelength.
;
_item.name '_cell_measurement.wavelength'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_wavelength'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_category.description
;
Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used in determination of the
crystallographic cell parameters.
The CELL_MEASUREMENT_REFLN data items would in general be used
only for diffractometer data.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l'
loop_
_category_group.id
'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
save_cell_measurement_refln.index_h.
_item_description.description
;
Miller index h of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_cell_measurement_refln_index_h'
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l'
_item_type.code int
save_cell_measurement_refln.index_k.
_item_description.description
;
Miller index k of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_cell_measurement_refln_index_k'
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_l'
_item_type.code int
save_cell_measurement_refln.index_l.
_item_description.description
;
Miller index l of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_cell_measurement_refln_index_l'
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
_item_type.code int
save_cell_measurement_refln.theta.
_item_description.description
;
Theta angle in degrees of a reflection used for measurement of
the unit cell.
;
_item.name '_cell_measurement_refln.theta'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_refln_theta'
_item_range.maximum 90.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'degrees'
_category.description
;
Data items in the CHEMICAL category record details about the
composition and chemical properties of the compounds. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
Data items in the CHEMICAL category would not, in general, be
used in a macromolecular CIF. See instead the ENTITY data
items.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_chemical.block_id'
loop_
_category_group.id
'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
_chemical.name_systematic
trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_chemical.compound_source.
_item_description.description
;
Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
;
_item.name '_chemical.compound_source'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_compound_source'
_item_type.code char
loop_
_item_examples.case
'From Norilsk (USSR)'
'Extracted from the bark of Cinchona Naturalis'
_item_description.description ; The melting point in degees Kelvin of the crystal. ; _item.name '_chemical.melting_point' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_melting_point' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description ; Trivial name by which compound is commonly known. ; _item.name '_chemical.name_common' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_common' _item_type.code char _item_examples.case '1-bromoestradiol'
_item_description.description
;
Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
_chemical.compound_source.
;
_item.name '_chemical.name_mineral'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_mineral'
_item_type.code char
_item_examples.case chalcopyrite
save_chemical.name_structure_type.
_item_description.description
;
Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
;
_item.name '_chemical.name_structure_type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_structure_type'
_item_type.code char
loop_
_item_examples.case
perovskite
sphalerite
A15
save_chemical.name_systematic.
_item_description.description ; IUPAC or Chemical Abstracts full name of compound. ; _item.name '_chemical.name_systematic' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_name_systematic' _item_type.code char _item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol'
_category.description
;
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the 2D chemical structure of the
molecular species. They allowa 2D chemical diagram to be
reconstructed for use in a publication or in a database search
for structural and substructural relationships.
The CHEMICAL_CONN_ATOM data items provide information about the
chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide
they must also contain symmetry-generated atoms, so that the
CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always
describe a complete chemical entity.
Data items in the CHEMICAL_CONN_ATOM category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_chemical_conn_atom.number'
loop_
_category_group.id
'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 2
;
save_chemical_conn_atom.charge.
_item_description.description
;
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
_item.name '_chemical_conn_atom.charge'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_charge'
_item_default.value 0
_item_range.maximum 6
_item_range.minimum -6
_item_type.code int
loop_
_item_examples.case
_item_examples.detail
1
'for an ammonium nitrogen'
-1
'for a chloride ion'
save_chemical_conn_atom.display_x.
_item_description.description
;
The 2D Cartesian x coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure. If absent, values
will be assigned by the journals' or database staff.
;
_item.name '_chemical_conn_atom.display_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_display_x'
_item_dependent.dependent_name '_chemical_conn_atom.display_y'
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
save_chemical_conn_atom.display_y.
_item_description.description
;
The 2D Cartesian y coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure. If absent, values
will be assigned by the journals' or database staff.
;
_item.name '_chemical_conn_atom.display_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_display_y'
_item_dependent.dependent_name '_chemical_conn_atom.display_x'
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
_item_description.description ; The Number of Connected Atoms excluding terminal hydrogen atoms. ; _item.name '_chemical_conn_atom.NCA' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NCA' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_item_description.description
;
The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the ATOM_SITE list. This number will be the same as
_atom_site.attached_hydrogens only if none of the hydrogen
atoms appear in the ATOM_SITE list.
;
_item.name '_chemical_conn_atom.NH'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_NH'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_chemical_conn_atom.number.
_item_description.description
;
The chemical sequence number to be associated with this atom.
Within an ATOM_SITE list this number must match with one of
the _atom_site.chemical_conn_number values.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chemical_conn_atom.number'
chemical_conn_atom
yes
'_atom_site.chemical_conn_number'
atom_site
yes
'_chemical_conn_bond.atom_1'
chemical_conn_bond
yes
'_chemical_conn_bond.atom_2'
chemical_conn_bond
yes
_item_aliases.alias_name '_chemical_conn_atom_number'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.chemical_conn_number'
'_chemical_conn_atom.number'
'_chemical_conn_bond.atom_1'
'_chemical_conn_atom.number'
'_chemical_conn_bond.atom_2'
'_chemical_conn_atom.number'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
save_chemical_conn_atom.number.
_item_description.description
;
The chemical sequence number to be associated with this atom.
Within an ATOM_SITE list this number must match with one of
the _atom_site.chemical_conn_number values.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chemical_conn_atom.number'
chemical_conn_atom
yes
'_atom_site.chemical_conn_number'
atom_site
yes
'_chemical_conn_bond.atom_1'
chemical_conn_bond
yes
'_chemical_conn_bond.atom_2'
chemical_conn_bond
yes
_item_aliases.alias_name '_chemical_conn_atom_number'
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.chemical_conn_number'
'_chemical_conn_atom.number'
'_chemical_conn_bond.atom_1'
'_chemical_conn_atom.number'
'_chemical_conn_bond.atom_2'
'_chemical_conn_atom.number'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
save_chemical_conn_atom.type_symbol.
_item_description.description
;
This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_item_aliases.alias_name '_chemical_conn_atom_type_symbol'
_category.description
;
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the 2D chemical structure of the
molecular species. They allowa 2D chemical diagram to be
reconstructed for use in a publication or in a database search
for structural and substructural relationships.
The CHEMICAL_CONN_BOND data items specify the connections
between the atoms in the _chemical_conn_atom. list and the nature
of the chemical bond between these atoms.
Data items in the CHEMICAL_CONN_BOND category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_chemical_conn_bond.atom_1'
'_chemical_conn_bond.atom_2'
loop_
_category_group.id
'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on
;
;
Need Example 2
;
save_chemical_conn_bond.atom_1.
_item_description.description
;
This data item is a pointer to _chemical_conn_atom.number in the
CHEMICAL_CONN_ATOM category.
;
_item_aliases.alias_name '_chemical_conn_bond_atom_1'
_item_dependent.dependent_name '_chemical_conn_bond.atom_2'
save_chemical_conn_bond.atom_2.
_item_description.description
;
This data item is a pointer to _chemical_conn_atom.number in the
CHEMICAL_CONN_ATOM category.
;
_item_aliases.alias_name '_chemical_conn_bond_atom_2'
_item_dependent.dependent_name '_chemical_conn_bond.atom_1'
_item_description.description
;
The chemical bond type associated with the connection between
the two sites _chemical_conn_bond.atom_1 and *_2.
;
_item.name '_chemical_conn_bond.type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_bond_type'
_item_default.value sing
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
sing
'single bond'
doub
'double bond'
trip
'triple bond'
quad
'quadruple bond'
arom
'aromatic bond'
poly
'polymeric bond'
delo
'delocalized double bond'
pi
'pi bond'
_category.description
;
Data items in the CHEMICAL_FORMULA category specify the
composition and chemical properties of the compound. The formula
data items must agree with those that specify the density, unit
cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula.analytical, _chemical_formula.structural and
_chemical_formula.sum. For the data item
_chemical_formula.moiety the formula construction is broken up
into residues or moieties, i.e. groups of atoms that form a
molecular unit or molecular ion. The rules given below apply
within each moiety but different requirements apply to the way
that moieties are connected (see _chemical_formula.moiety).
1. Only recognized element symbols may be used.
2. Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
3. A space or parenthesis must separate each element symbol and
its count.
4. Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parentheses.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. [An exception to this rule
exists for _chemical_formula.moiety formulae where pre- and
post-multipliers are permitted for molecular units].
5. Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
_chemical_formula.structural, the order of the elements within
any group or moiety should be: C, H followed by the other
elements in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula.moiety and _chemical_formula.sum.
Data items in the CHEMICAL_FORMULA category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_chemical_formula.block_id'
loop_
_category_group.id
'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_chemical_formula.moiety 'C18 H25 N O3'
_chemical_formula.sum 'C18 H25 N O3'
_chemical_formula.weight 303.40
;
save_chemical_formula.analytical.
_item_description.description
;
Formula determined by standard chemical analysis including trace
elements. See _chemical_formula.appendix for rules for writing
chemical formulae. Parentheses are used only for e.s.d.'s.
;
_item.name '_chemical_formula.analytical'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_analytical'
_item_type.code char
_item_examples.case 'Fe2.45(2) Ni1.60(3) S4'
save_chemical_formula.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
Formula with each discrete bonded residue or ion shown as a
separate moiety. See above _chemical_formula.appendix for rules
for writing chemical formulae. In addition to the general
formulae requirements, the following rules apply:
1. Moieties are separated by commas ','.
2. The order of elements within a moiety follows general rule
5 in _chemical_formula.appendix.
3. Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
4. Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
;
_item.name '_chemical_formula.moiety'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_moiety'
_item_type.code char
loop_
_item_examples.case
'C7 H4 Cl Hg N O3 S'
'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5(H2 O1)'
"(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)"
save_chemical_formula.structural.
_item_description.description
;
See _chemical_formula.appendix for the rules for writing chemical
formulae for inorganics, organometallics, metal complexes etc.,
in which bonded groups are preserved as discrete entities within
parentheses, with post-multipliers as required. The order of the
elements should give as much information as possible about the
chemical structure. Parentheses may be used and nested as
required. This formula should correspond to the structure as
actually reported, i.e. trace elements not included in atom type
and atom site data should not be included in this formula (see
also _chemical_formula.analytical).
;
_item.name '_chemical_formula.structural'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_structural'
_item_type.code char
loop_
_item_examples.case
'Ca ((Cl O3)2 O)2 (H2 O)6'
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
_item_description.description
;
See _chemical_formula.appendix for the rules for writing chemical
formulae in which all discrete bonded residues and ions are
summed over the constituent elements, following the ordering
given in general rule 5 in _chemical_formula.appendix.
Parentheses are not normally used.
;
_item.name '_chemical_formula.sum'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_sum'
_item_type.code char
loop_
_item_examples.case
'C18 H19 N7 O8 S'
_item_description.description
;
Formula mass in daltons. This mass should correspond to the
formulae given under _chemical_formula.structural, *_moiety or
*_sum and, together with the Z value and cell parameters, should
yield the density given as _exptl_crystal_density_diffrn.
;
_item.name '_chemical_formula.weight'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_weight'
_item_range.maximum ?
_item_range.minimum 1.0
_item_type.code float
save_chemical_formula.weight_meas.
_item_description.description ; Formula mass in daltons measured by a non-diffraction experiment. ; _item.name '_chemical_formula.weight_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight_meas' _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_category.description
;
Data items in the CITATION category record details about the
literature cited relevant to the contents of the data block.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_citation.id'
loop_
_category_group.id
'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_citation.id
_citation.coordinate_linkage
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.journal_issue
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_coden_ASTM
_citation.journal_coden_ISSN
_citation.journal_coden_PDB
_citation.book_title
_citation.book_publisher
_citation.book_coden_ISBN
_citation.details
primary yes
; Crystallographic analysis of a complex between human immunodeficiency
virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.
;
US 'J. Biol. Chem.' 265 . 14209 14219 1990
HBCHA3 0021-9258 071 . . .
; The publication that directly relates to this coordinate set.
;
2 no
; Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.
;
UK 'Nature' 337 . 615 619 1989
NATUAS 0028-0836 006 . . .
; Determination of the structure of the unliganded enzyme.
;
3 no
; Crystallization of the aspartylprotease from human immunodeficiency
virus, HIV-1.
;
US 'J. Biol. Chem.' 264 . 1919 1921 1989
HBCHA3 0021-9258 071 . . .
; Crystallization of the unliganded enzyme.
;
4 no
; Human immunodeficiency virus protease. Bacterial expression and
characterization of the purified aspartic protease.
;
US 'J. Biol. Chem.' 264 . 2307 2312 1989
HBCHA3 0021-9258 071 . . .
; Expression and purification of the enzyme.
;
;
_item_description.description
;
Abstract for the citation. This will be used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
;
_item.name '_citation.abstract'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_citation.book_coden_ISBN.
_item_description.description
;
The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for book chapters.
;
_item.name '_citation.book_coden_ISBN'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The name and location of the publisher of the citation; relevant
for book chapters.
;
_item.name '_citation.book_publisher'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'John Wiley and Sons, New York'
_item_description.description
;
The title of the book in which the citation appeared; relevant
for book chapters.
;
_item.name '_citation.book_title'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_citation.coordinate_linkage.
_item_description.description
;
_citation.coordinate_linkage states whether or not this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to creation of the data block, the value of this data item
would be no.
;
_item.name '_citation.coordinate_linkage'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
yes
no
_item_description.description
;
The country of publication; relevant for both journal articles
and book chapters.
;
_item.name '_citation.country'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
A description of special aspects that describe the relationship
of the contents of the data block to the literature item cited.
;
_item.name '_citation.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
;
citation relates to this precise
coordinate set
;
;
citation relates to earlier low-resolution
structure
;
;
citation relates to further refinement of
structure reported in citation 2
;
_item_description.description
;
The value of _citation.id must uniquely identify a record in the
CITATION list.
The _citation.id 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_citation.id'
citation
yes
'_citation_author.citation_id'
citation_author
yes
'_citation_editor.citation_id'
citation_editor
yes
'_comp_prog.citation_id'
comp_prog
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_citation_author.citation_id'
'_citation.id'
'_citation_editor.citation_id'
'_citation.id'
'_comp_prog.citation_id'
'_citation.id'
_item_type.code char
loop_
_item_examples.case
primary
1
2
_item_description.description
;
Abbreviated name of the journal cited; abbreviations are
according to the rules of ??
;
_item.name '_citation.journal_abbrev'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'J. Mol. Biol.'
save_citation.journal_coden_ASTM.
_item_description.description
;
The American Society for Testing of Materials (ASTM) code
assigned to the journal cited; relevant for journal articles.
;
_item.name '_citation.journal_coden_ASTM'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_citation.journal_coden_ISSN.
_item_description.description
;
The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
;
_item.name '_citation.journal_coden_ISSN'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_citation.journal_coden_PDB.
_item_description.description
;
The Protein Data Bank (PDB) code assigned to the journal cited;
relevant for journal articles.
;
_item.name '_citation.journal_coden_PDB'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '070'
_item_description.description ; Full name of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case 'Journal of Molecular Biology'
_item_description.description
;
Issue number of the journal cited; relevant for journal
articles.
;
_item.name '_citation.journal_issue'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 2
_item_description.description
;
Volume number of the journal cited; relevant for journal
articles.
;
_item.name '_citation.journal_volume'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 174
_item_description.description ; Language in which the citation appears. ; _item.name '_citation.language' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case german
_item_description.description
;
Ascession number used by Medline to categorize a specific
bibliographic entry.
;
_item.name '_citation.Medline_AN'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
_item_examples.case 89064067
_item_description.description
;
The first page of the citation; relevant for journal
articles and book chapters.
;
_item.name '_citation.page_first'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The last page of the citation; relevant for journal
articles and book chapters.
;
_item.name '_citation.page_last'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The title of the citation; relevant for both journal articles
and book chapters.
;
_item.name '_citation.title'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Structure of Blah-Blah at 2.1 \%Angstr\"om
Resolution.
;
_item_description.description
;
The year of the citation; relevant for both journal articles
and book chapters.
;
_item.name '_citation.year'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
_item_examples.case 1984
_category.description
;
Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
CITATION list.
;
_category.id _category.id
_category.mandatory no
loop_
_category_key.name
'_citation_author.citation_id'
'_citation_author.name'
loop_
_category_group.id
'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and/or laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_citation_author.citation_id
_citation_author.name
primary 'Fitzgerald, P.M.D.'
primary 'McKeever, B.M.'
primary 'Van Middlesworth, J.F.'
primary 'Springer, J.P.'
primary 'Heimbach, J.C.'
primary 'Leu, C.-T.'
primary 'Herber, W.K.'
primary 'Dixon, R.A.F.'
primary 'Darke, P.L.'
2 'Navia, M.A.'
2 'Fitzgerald, P.M.D.'
2 'McKeever, B.M.'
2 'Leu, C.-T.'
2 'Heimbach, J.C.'
2 'Herber, W.K.'
2 'Sigal, I.S.'
2 'Darke, P.L.'
2 'Springer, J.P.'
3 'McKeever, B.M.'
3 'Navia, M.A.'
3 'Fitzgerald, P.M.D.'
3 'Springer, J.P.'
3 'Leu, C.-T.'
3 'Heimbach, J.C.'
3 'Herber, W.K.'
3 'Sigal, I.S.'
3 'Darke, P.L.'
4 'Darke, P.L.'
4 'Leu, C.-T.'
4 'Davis, L.J.'
4 'Heimbach, J.C.'
4 'Diehl, R.E.'
4 'Hill, W.S.'
4 'Dixon, R.A.F.'
4 'Sigal, I.S.'
;
save_citation_author.citation_id.
_item_description.description
;
This data item is a pointer to _citation.id in the CITATION
category.
;
_item_description.description
;
Name of an author of the citation; relevant for both journal
articles and book chapters.
The family name(s) followed by a comma, precedes the first
name(s) or initial(s).
;
_item.name '_citation_author.name'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
_category.description
;
Data items in the CITATION_EDITOR category record details
about the editor associated with book chapter citations in
the CITATION list.
;
_category.id _category.id
_category.mandatory no
loop_
_category_key.name
'_citation_editor.citation_id'
'_citation_editor.name'
loop_
_category_group.id
'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - example is completely hypothetical
;
;
loop_
_citation_editor.citation_id
_citation_editor.name
5 'McKeever, B.M.'
5 'Navia, M.A.'
5 'Fitzgerald, P.M.D.'
5 'Springer, J.P.'
;
save_citation_editor.citation_id.
_item_description.description
;
This data item is a pointer to _citation.id in the CITATION
category.
;
_item_description.description
;
Names of an editor of the citation; relevant for book chapters.
The family name(s) followed by a comma, precedes the first
name(s) or initial(s).
;
_item.name '_citation_editor.name'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
_category.description
;
Data items in the COMP_PROG category record details about the
computer programs used in the structure analysis. These data
items provide an alternative, and more thorough, method for
referencing computer programs than do data items in the
COMPUTING category.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_comp_prog.task'
'_comp_prog.name'
'_comp_prog.version'
loop_
_category_group.id
'inclusive_group'
'computing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_comp_prog.task
_comp_prog.name
_comp.prog.version
_comp.prog.citation_id
'data collection' Collect x.x ?
'data reduction' Xengen 1.3 ?
'phasing_MR Merlot 2.2 ?
'molecular graphics' Protein x.x ?
'moleuclar graphics' Frodo x.x ?
'structure refinement' Protin/Prolsq x.x ?
;
_item_description.description
;
This data item is a pointer to _citation.id in the CITATION
category.
;
_item_description.description ; The task for which the computer program was employed. ; _item.name '_comp_prog.task' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'cell refinement' 'data collection' 'data reduction' 'molecular graphics' 'phasing averaging' 'phasing MAD' 'phasing MIR' 'phasing MR' 'publication material' 'structure refinement'
_item_description.description ; The version of the computer program. ; _item.name '_comp_prog.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_category.description
;
Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_computing.block_id'
loop_
_category_group.id
'inclusive_group'
'computing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_computing.data_collection 'Collect (Siemens)'
_computing.data_reduction 'Xengen (Howard)'
_computing.phasing_MR 'Merlot (Fitzgerald)'
_computing.molecular_graphics 'Protein (Steigemann), Frodo (Jones)'
_computing.structure_refinement 'Protin/Prolsq (Konnert, Hendrickson)'
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_computing.data_collection 'Philips PW1100/20 software 1976'
_computing.cell_refinement 'LATCON (Xtal: Schwarzenbach & King)'
_computing.data_reduction
'pwredu (McLaughlin) ADDREF SORTRF (Xtal)'
_computing.structure_solution 'SHELXS86 (Sheldrick)'
_computing.structure_refinement
'SHELX76 (Sheldrick) CRYLSQ (Xtal: Olthof)'
_computing.publication_material 'BONDLA CIFIO (Xtal: Hall)'
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_computing.cell_refinement.
_item_description.description
;
Software used in refining the cell.
Give the program or package name and a brief reference.
;
_item.name '_computing.cell_refinement'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_cell_refinement'
_item_type.code char
_item_examples.case 'CAD4 (Enraf Nonius)'
save_computing.data_collection.
_item_description.description
;
Software used for data collection.
Give the program or package name and a brief reference.
;
_item.name '_computing.data_collection'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_data_collection'
_item_type.code char
_item_examples.case 'CAD4 (Enraf Nonius)'
save_computing.data_reduction.
_item_description.description
;
Software used for data reduction.
Give the program or package name and a brief reference.
;
_item.name '_computing.data_reduction'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_data_reduction'
_item_type.code char
_item_examples.case 'DIFDAT, SORTRF, ADDREF (XTAL3.0, 1990)'
save_computing.molecular_graphics.
_item_description.description
;
Software used for molecular graphics.
Give the program or package name and a brief reference.
;
_item.name '_computing.molecular_graphics'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_molecular_graphics'
_item_type.code char
_item_examples.case 'FRODO (Jones, 1986) & ORTEP (Johnson, 1965)'
save_computing.publication_material.
_item_description.description
;
Software used for generating material for publication.
Give the program or package name and a brief reference.
;
_item.name '_computing.publication_material'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_publication_material'
_item_type.code char
save_computing.structure_refinement.
_item_description.description
;
Software used for refinement of the structure.
Give the program or package name and a brief reference.
;
_item.name '_computing.structure_refinement'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_structure_refinement'
_item_type.code char
loop_
_item_examples.case
'SHELX85 (Sheldrick, 1985)'
'X-PLOR (Brunger, 198?)'
save_computing.structure_solution.
_item_description.description
;
Software used for solution of the structure.
Give the program or package name and a brief reference.
;
_item.name '_computing.structure_solution'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_computing_structure_solution'
_item_type.code char
_item_examples.case 'SHELX85 (Sheldrick, 1985)'
_category.description
;
Data items in the DATABASE category have been supercedes by
data items in the DATEBASE_NEW category. They are included
here only for compliance with older files.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_database.block_id'
loop_
_category_group.id
'inclusive_group'
'compliance_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_database.code_PDB 5HVP
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The code assigned by Chemical Abstracts. ; _item.name '_database.code_CAS' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_CAS' _item_type.code char
_item_description.description
;
The code assigned by Cambridge Structural Data Base (organic and
metal-organic compounds).
;
_item.name '_database.code_CSD'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_database_code_CSD'
_item_type.code char
_item_description.description ; The code assigned by the Inorganic Crystal Structure Data Base. ; _item.name '_database.code_ICSD' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_ICSD' _item_type.code char
_item_description.description ; The code assigned by the Metals Data File (metal structures). ; _item.name '_database.code_MDF' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_MDF' _item_type.code char
_item_description.description
;
The code assigned by the NBS (NIST) Crystal Data Database
(lattice parameters).
;
_item.name '_database.code_NBS'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_database_code_NBS'
_item_type.code char
_item_description.description ; The code assigned by the Powder Diffraction File (JCPDS/ICDD). ; _item.name '_database.code_PDF' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_code_PDF' _item_type.code char
_item_description.description
;
The ASTM coden for a journal as given in the Chemical Source
List.
;
_item.name '_database.journal_ASTM'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_database_journal_ASTM'
_item_type.code char
_item_description.description ; The journal code used in the Cambridge Structural Database. ; _item.name '_database.journal_CSD' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_database_journal_CSD' _item_type.code char
_category.description
;
Data items in the DATABASE_NEW category record details about the
database identifiers of the CIF.
These data items are assigned by database managers and should
only appear in a CIF if they originate from that source.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_database_new.database_id'
'_database_new.database_code'
loop_
_category_group.id
'inclusive_group'
'database_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_database_new.database_id PDB
_database_new.database_code 5HVP
;
save_database_new.database_code.
_item_description.description
;
The code assigned by the database identified in
_database_new.database_id.
;
_item.name '_database_new.database_code'
_item.category_id _item.category_id
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code
'_database.code_CAS'
'replace'
'_database.code_CSD'
'replace'
'_database.code_ICSD'
'replace'
'_database.code_MDF'
'replace'
'_database.code_NBS'
'replace'
'_database.code_PDF'
'replace'
_item_type.code char
loop_
_item_enumeration.value
1ABC
ABCDEF
save_database_new.database_id.
_item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_new.database_id' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' 'replace' '_database.code_CSD' 'replace' '_database.code_ICSD' 'replace' '_database.code_MDF' 'replace' '_database.code_NBS' 'replace' '_database.code_PDF' 'replace' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail 'CAS' ; Chemical Abstracts ; 'CSD' ; Cambridge Structural Data Base (organic and metal-organic compounds) ; 'ICSD' ; Inorganic Crystal Structure Data Base ; 'MDF' ; Metals Data File (metal structures) ; 'NDB' ; Nucleic Acids Database ; 'NBS' ; NBS (NIST) Crystal Data Database (lattice parameters) ; 'PDB' ; Protein Data Bank ; 'PDF' ; Powder Diffraction File (JCPDS/ICDD) ;
_category.description
;
Data items in the DATABASE_PDB_REMARK category record details
about the CIF as archived by the Protein Data Bank (PDB).
Some data appearing in PDB REMARK records can be
algorithmically extracted into the appropriate data items
in the CIF.
These data items are included only for consistency with older
PDB format files. They should appear in a CIF only if that
CIF was created by reformatting a PDB format file.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_database_PDB_remark.num'
loop_
_category_group.id
'inclusive_group'
'database_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_database_PDB_remark.num
_database_PDB_remark.text
2
;
RESOLUTION. 2.0 ANGSTROMS.
;
3
;
REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J.
KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R
VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION
RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I).
# - - - - data truncated for brevity - - - -
;
;
_item_description.description
;
The value of _database_PDB_remark.num corresponds to the number
assigned to the remark in the PDB file.
In PDB files, each line of a remark is preceded with REMARK n,
where n is the remark number. A given remark may cover any
number of lines.
In the CIF representation, the remark number is translated into
_database_PDB_remark.num and the text of the remark become a
single text block, _database_PDB_remark.text.
;
_item.name '_database_PDB_remark.num'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code int
save_database_PDB_remark.text.
_item_description.description
;
The text of the PDB remark, with the last eight characters (PDB
code and PDB record number) excised. Multilined remarks are
converted to a single text block (with 'REMARK n ' removed).
;
_item.name '_database_PDB_remark.text'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the DATABASE_PDB_REV category record details
about the history of the CIF as archived by the Protein Data
Bank (PDB).
These data items are assigned by the PDB database managers and
should only appear in a CIF if they originate from that source.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_database_PDB_rev.num'
loop_
_category_group.id
'inclusive_group'
'database_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_database_PDB_rev.num
_database_PDB_rev.author_name
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.status
_database_PDB_rev.mod_type
1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30 'full release' 0
;
save_database_PDB_rev.author_name.
_item_description.description
;
The name of the person responsible for submitting this revision
to the PDB.
The family name(s) followed by a comma, precedes the first
name(s) or initial(s).
;
_item.name '_database_PDB_rev.author_name'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
_item_description.description ; Date the PDB revision took place. Taken from the REVDAT record. ; _item.name '_database_PDB_rev.date' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_database_PDB_rev.date_original.
_item_description.description
;
Date the entry first entered the PDB database in the form:
yyyy-mm-dd. Taken from the PDB HEADER record.
;
_item.name '_database_PDB_rev.date_original'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '1980-08-21'
save_database_PDB_rev.mod_type.
_item_description.description
;
Taken from the REVDAT record. Refer to the Protein Data Bank
format description for details.
;
_item.name '_database_PDB_rev.mod_type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
0
'initial entry'
1
'all other types of modification'
2
'modifications to CONECT records'
3
;
modifications affecting the coordinates
or their transforms (CRYST1, ORIGX, SCALE,
MTRIX, TVECT, ATOM, HETATM, SIGATM records)
;
_item_description.description
;
The value of _database_PDB_rev.num must uniquely and
sequentially identify a record in the _database_PDB_rev. list.
Note that this item must be a number, and that modification
numbers will be assigned in increasing numerical order.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_database_PDB_rev.num'
database_PDB_rev
yes
'_database_PDB_rev_record.rev_num'
database_PDB_rev_record
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_database_PDB_rev_record.rev_num'
'_database_PDB_rev.num'
_item_type.code int
save_database_PDB_rev.replaced_by.
_item_description.description
;
The PDB code for a subsequent PDB entry that replaced the
PDB file corresponding to this CIF.
;
_item.name '_database_PDB_rev.replaced_by'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_database_PDB_rev.replaces.
_item_description.description
;
The PDB code for a previous PDB entry that was replaced by
the PDB file corresponding to this CIF.
;
_item.name '_database_PDB_rev.replaces'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
This definition is preliminary - need to consult with PDB about
what they need here.
;
_item.name '_database_PDB_rev.status'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
'in preparation'
'prerelease'
'full release'
'obsolete'
_category.description
;
Data items in the DATABASE_PDB_REV_RECORD category record
details about specific record types that were changed in a
given revision of a PDB entry.
These data items are assigned by the PDB database managers and
should only appear in a CIF if they originate from that source.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_database_PDB_rev_record.rev_num'
loop_
_category_group.id
'inclusive_group'
'database_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - example is completely hypothetical
;
;
loop_
_database_PDB_rev_record.rev_num
_database_PDB_rev_record.type
_database_PDB_rev_record.details
1 CONECT 'Error fix - incorrect connection between atoms 2312 and 2317'
2 MATRIX 'For consistency with 1995-08-04 style-guide'
3 ORIGX 'Based on new data from author'
;
save_database_PDB_rev_record.details.
_item_description.description
;
A description of special aspects of the revision of records in
this PDB entry.
;
_item.name '_database_PDB_rev_record.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Based on new data from author'
'For consistency with 1995-08-04 style-guide'
'For consistency with structural class'
save_database_PDB_rev_record.rev_num.
_item_description.description
;
This data item is a pointer to _database_PDB_rev.num in the
DATABASE_PDB_REV category.
;
save_database_PDB_rev_record.type.
_item_description.description
;
The types of records that were changed in this revision to a
PDB entry.
;
_item.name '_database_PDB_rev_record.type'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'CRYST1'
'SCALE'
'MTRIX'
'ATOM'
'HETATM'
_category.description
;
Data items in the DIFFRN category record details about the
diffraction data and its measurement.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn.ambient_temperature 293(3)
_diffrn.ambient_environment
; Mother liquor from the reservoir of the vapor diffusion experiment,
mounted in room air
;
_diffrn.crystal_support
; 0.7 mm glass capillary, sealed with dental wax
;
_diffrn.crystal_treatment
; Equilibrated in rotating anode radiation enclosure for 18 hours prior
to beginning of data collection.
;
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn.details
;
\q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per min.
Background counts for 5 sec on each side every scan.
;
_diffrn.ambient_temperature 293
;
save_diffrn.ambient_environment.
_item_description.description ; The gas or liquid surrounding the sample, if not air or vacuum. ; _item.name '_diffrn.ambient_environment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description
;
The pressure in kilopascals at which the diffraction data were
measured.
;
_item.name '_diffrn.ambient_pressure'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_ambient_pressure'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kilopascals'
save_diffrn.ambient_pressure_esd.
_item_description.description ; The estimated standard deviation of _diffrn.ambient_pressure. ; _item.name '_diffrn.ambient_pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_diffrn.ambient_temperature.
_item_description.description
;
The mean temperature in degrees Kelvin at which the diffraction
data were measured.
;
_item.name '_diffrn.ambient_temperature'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_ambient_temperature'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kelvin'
save_diffrn.ambient_temperature_esd.
_item_description.description ; The estimated standard deviation of _diffrn.ambient_temperature. ; _item.name '_diffrn.ambient_temperature_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn.crystal_support'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_diffrn.crystal_treatment.
_item_description.description
;
Remarks about how the crystal was treated prior to data
collection. Particularly relevant when data were measured at
low temperature.
;
_item.name '_diffrn.crystal_treatment'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
_item_description.description
;
Special details of the diffraction measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
;
_item.name '_diffrn.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_special_details'
_item_type.code char
_category.description
;
Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_attenuator.code'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_diffrn_attenuator.code
_diffrn_attenuator.scale 1 16.976
;
_item_description.description
;
A code associated with a particular attenuator setting. This code
is referenced by the _diffrn_refln.attenuator_code which is
stored with the diffraction data. See _diffrn_attenuator.scale.
;
_item.name '_diffrn_attenuator.code'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_attenuator_code'
_item_type.code char
_item_description.description
;
The intensity scale associated with a particular attenuator
setting identified by _diffrn_attenuator.code.
;
_item.name '_diffrn_attenuator.scale'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_attenuator_scale'
_item_range.maximum ?
_item_range.minimum 1.0
_item_type.code float
_category.description
;
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_measurement.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.device_type '3-circle camera'
_diffrn_measurement.device_specific 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle
22.5 degrees
;
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.device 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method \q/2\q
;
save_diffrn_measurement.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_measurement.details.
_item_description.description
;
A description of special aspects of the data measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees
;
save_diffrn_measurement.device.
_item_description.description
;
Description of the diffractometer or camera used to measure the
diffraction intensities.
;
_item.name '_diffrn_measurement.device'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device'
_item_type.code char
_item_examples.case 'Gandolfi 114mm powder camera'
save_diffrn_measurement.device_details.
_item_description.description
;
A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Need new example here.
;
save_diffrn_measurement.device_specific.
_item_description.description
;
The particular device used to measure the diffraction
intensities. In general this will be a manufacturer,
description, model number of some combination of these.r
;
_item.name '_diffrn_measurement.device_specific'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_diffrn_measurement.device_type.
_item_description.description
;
The general class of the device used to measure the
diffraction intensities.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_diffrn_measurement.method.
_item_description.description ; Method used to measure diffraction data. ; _item.name '_diffrn_measurement.method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_method' _item_type.code char _item_examples.case 'profile data from theta/2theta scans'
_category.description
;
Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in data measurement.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_orient_matrix.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on
;
;
Need Example 2
;
save_diffrn_orient_matrix.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_orient_matrix.type.
_item_description.description
;
A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
;
_item.name '_diffrn_orient_matrix.type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_type'
_item_type.code char
_item_description.description
;
The elements of the diffractometer orientation matrix. These
define the dimensions of the reciprocal cell and its orientation
to the local diffractometer axes. See _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
save_diffrn_orient_matrix.UB[1][1].
_item_description.description
;
The [1][1] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[1][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_11'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[1][2].
_item_description.description
;
The [1][2] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[1][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_12'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[1][3].
_item_description.description
;
The [1][3] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[1][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_13'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[2][1].
_item_description.description
;
The [2][1] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[2][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_21'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[2][2].
_item_description.description
;
The [2][2] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[2][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_22'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[2][3].
_item_description.description
;
The [2][3] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[2][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_23'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[3][1].
_item_description.description
;
The [3][1] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[3][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_31'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[3][2].
_item_description.description
;
The [3][2] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[3][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_32'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_orient_matrix.UB[3][3].
_item_description.description
;
The [3][3] element of the 3x3 matrix _diffrn_orient_matrix.UB.
This data item is only present in this dictionary for compliance
(via the alias) with previous dictionaries.
;
_item.name '_diffrn_orient_matrix.UB[3][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_33'
_item_related.related_name '_diffrn_orient_matrix.UB'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_category.description
;
Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
measurement of diffraction intensities.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln.index_l'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on
;
;
Need Example 2
;
save_diffrn_orient_refln.angle_chi.
_item_description.description
;
Diffractometer angle chi in degrees of a reflection used to
define the orientation matrix. See _diffrn_orient_matrix.UB and
the Miller indices in the DIFFRN_ORIENT_RELFN category.
;
_item.name '_diffrn_orient_refln.angle_chi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_chi'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_orient_refln.angle_kappa.
_item_description.description
;
Diffractometer angle kappa in degrees of a reflection used to
define the orientation matrix. See _diffrn_orient_matrix.UB and
the Miller indices in the DIFFRN_ORIENT_RELFN category.
;
_item.name '_diffrn_orient_refln.angle_kappa'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_kappa'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_orient_refln.angle_phi.
_item_description.description
;
Diffractometer angle phi in degrees of a reflection used to
define the orientation matrix. See _diffrn_orient_matrix.UB and
the Miller indices in the DIFFRN_ORIENT_RELFN category.
;
_item.name '_diffrn_orient_refln.angle_phi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_phi'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_psi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_orient_refln.angle_psi.
_item_description.description
;
Diffractometer angle psi in degrees of a reflection used to
define the orientation matrix. See _diffrn_orient_matrix.UB and
the Miller indices in the DIFFRN_ORIENT_RELFN category.
;
_item.name '_diffrn_orient_refln.angle_psi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_psi'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_phi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_orient_refln.index_h.
_item_description.description
;
Miller index h of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_orient_refln_index_h'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln.index_l'
_item_type.code int
save_diffrn_orient_refln.index_k.
_item_description.description
;
Miller index k of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_orient_refln_index_k'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_l'
_item_type.code int
save_diffrn_orient_refln.index_l.
_item_description.description
;
Miller index l of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_orient_refln_index_l'
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_l'
_item_type.code int
_category.description
;
Data items in the DIFFRN_RADIATION category record details
about the radiation and detector used in measuring diffraction
intensities.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_radiation.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.detector_type 'multiwire'
_diffrn_radiation.detector_specific 'Siemens'
_diffrn_radiation.source_type 'rotating anode'
_diffrn_radiation.source_specific 'Rigaku RU-200'
_diffrn_radiation.source_power '50 kw, 180 mA'
_diffrn_radiation.source_target '8mm x 0.4 mm broad-focus'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength 1.54
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength 1.5418
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.source 'X-ray tube'
;
save_diffrn_radiation.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_radiation.collimation.
_item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_diffrn_radiation.collimation' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors'
save_diffrn_radiation.detector.
_item_description.description ; The detector used to measure the diffraction intensities. ; _item.name '_diffrn_radiation.detector' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_detector' _item_type.code char loop_ _item_examples.case 'scintillation' 'LiI' 'video tube' 'Kodak II film'
save_diffrn_radiation.detector_dtime.
_item_description.description ; The deadtime in microseconds of _diffrn_radiation.detector. ; _item.name '_diffrn_radiation.detector_dtime' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_detector_dtime' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'microseconds'
save_diffrn_radiation.detector_specific.
_item_description.description
;
The particular radiation detector. In general this will be a
manufacturer, description, model number or some combination of
these.
;
_item.name '_diffrn_radiation.detector_specific'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Siemens model x'
'Kodak XG'
'MAR Research model y'
save_diffrn_radiation.detector_type.
_item_description.description ; The general class of the radiation detector. ; _item.name '_diffrn_radiation.detector_type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'multiwire' 'imaging plate' 'CCD' 'film'
save_diffrn_radiation.filter_edge.
_item_description.description ; Absorption edge of the radiation filter used. ; _item.name '_diffrn_radiation.filter_edge' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_filter_edge' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_diffrn_radiation.inhomogeneity.
_item_description.description
;
Half-width in millimetres of the incident beam in the perpendic-
ular direction with respect to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
save_diffrn_radiation.monochromator.
_item_description.description
;
The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_type.code char
loop_
_item_examples.case
'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_diffrn_radiation.polarisn_norm.
_item_description.description
;
The angle in degrees of the perpendicular polarisation component
to the diffraction plane. See _diffrn_radiation.polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'degrees'
save_diffrn_radiation.polarisn_ratio.
_item_description.description
;
Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the plane
containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_description.description ; The source of radiation. ; _item.name '_diffrn_radiation.source' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_source' _item_type.code char loop_ _item_examples.case 'RU2 Rigaku Denki rotating Cu anode' 'fine focus Philips Mo tube' '5MeV synchrotron' 'HIFAR reactor'
save_diffrn_radiation.source_details.
_item_description.description ; A description of special aspects of the source of radiation. ; _item.name '_diffrn_radiation.source_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Need new example here. ;
save_diffrn_radiation.source_power.
_item_description.description ; The power of the radiation source. ; _item.name '_diffrn_radiation.source_power' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '50 kV, 35 mA' '8 kW' '12 GeV'
save_diffrn_radiation.source_specific.
_item_description.description
;
The particular source of radiation. In general this will be a
manufacturer, description, or model number (or some combination
of these) for laboratory sources and an institution name and
beamline name for synchrotron sources.
;
_item.name '_diffrn_radiation.source_specific'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'Rigaku RU200'
'Philips fine focus Mo'
'NSLS beamline X8C'
save_diffrn_radiation.source_target.
_item_description.description ; The nature of the cathode target of the radiation source. ; _item.name '_diffrn_radiation.source_target' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '8mm x 0.4 mm fine-focus' 'broad focus'
save_diffrn_radiation.source_type.
_item_description.description ; The general class of the source of radiation. ; _item.name '_diffrn_radiation.source_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_source_type' _item_type.code char loop_ _item_examples.case 'sealed tube' 'rotating anode' 'synchrotron'
_item_description.description ; The nature of the radiation. ; _item.name '_diffrn_radiation.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case CuK\a neutron electron
save_diffrn_radiation.wavelength.
_item_description.description ; The radiation wavelength. ; _item.name '_diffrn_radiation.wavelength' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_wavelength' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_diffrn_radiation.wavelength_id.
_item_description.description
;
The code identifying each value of _diffrn_radiation.wavelength.
Items in the the DIFFRN_RADIATION category are looped when
multiple wavelengths are used. This code is used to link with the
DIFFRN_REFLN list. It must match with one of the
_diffrn_refln.wavelength_id codes.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_radiation.wavelength_id'
diffrn_radiation
yes
'_diffrn_refln.wavelength_id'
diffrn_refln
yes
'_refln.wavelength_id'
refln
yes
_item_aliases.alias_name '_diffrn_radiation_wavelength_id'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.wavelength_id'
'_diffrn_radiation.wavelength_id'
'_refln.wavelength_id'
'_diffrn_radiation.wavelength_id'
loop_
_item_type.code
char
loop_
_item_examples.case
x1
x2
neut
save_diffrn_radiation.wavelength_wt.
_item_description.description
;
The relative weight of a wavelength identified by the code
_diffrn_radiation.wavelength_id in the list of wavelengths.
;
_item.name '_diffrn_radiation.wavelength_wt'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_wavelength_wt'
_item_default.value 1.0
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
save_diffrn_radiation_detector_details.
_item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_diffrn_radiation.detector_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; Need new example here. ;
_category.description
;
Data items in the DIFFRN_REFLN category record details about
the intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements, and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLN data items
are not looped.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_refln.id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on
;
;
Need Example 2
;
_item_description.description
;
The diffractometer angle chi in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_chi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_chi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_refln.angle_kappa.
_item_description.description
;
The diffractometer angle kappa in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_kappa'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_kappa'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_refln.angle_omega.
_item_description.description
;
The diffractometer angle omega in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_omega'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_omega'
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The diffractometer angle phi in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_phi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_phi'
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The diffractometer angle psi in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_psi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_psi'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_refln.angle_theta.
_item_description.description
;
The diffractometer angle theta in degrees of a reflection. This
angle corresponds correspond to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_theta'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_theta'
_item_type.code float
_item_units.code 'degrees'
save_diffrn_refln.attenuator_code.
_item_description.description
;
The code identifying the attenuator setting for this reflection.
This code must match one of the _diffrn.attenuator_code values.
;
_item.name '_diffrn_refln.attenuator_code'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_attenuator_code'
_item_type.code char
save_diffrn_refln.counts_bg_1.
_item_description.description
;
The diffractometer counts for the measurement of the background
before the peak.
;
_item.name '_diffrn_refln.counts_bg_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_bg_1'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_refln.counts_bg_2.
_item_description.description
;
The diffractometer counts for the measurement of the background
background after the peak.
;
_item.name '_diffrn_refln.counts_bg_2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_bg_2'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_item_description.description
;
The diffractometer counts for the measurement of net counts after
background removal.
;
_item.name '_diffrn_refln.counts_net'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_net'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_refln.counts_peak.
_item_description.description
;
The diffractometer counts for the measurement of counts for the
peak scan or position.
;
_item.name '_diffrn_refln.counts_peak'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_peak'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_refln.counts_total.
_item_description.description
;
The diffractometer counts for the measurement of total counts
(background plus peak).
;
_item.name '_diffrn_refln.counts_total'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_total'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_refln.detect_slit_horiz.
_item_description.description ; Total horizontal slit apertures in degrees. ; _item.name '_diffrn_refln.detect_slit_horiz' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_horiz' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.detect_slit_vert.
_item_description.description ; Total vertical slit apertures in degrees. ; _item.name '_diffrn_refln.detect_slit_vert' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_vert' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_refln.elapsed_time.
_item_description.description
;
Elapsed time in minutes from the start of diffraction measurement
to the measurement of this intensity.
;
_item.name '_diffrn_refln.elapsed_time'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_elapsed_time'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'minutes'
_item_description.description
;
The value of diffrn_refln.id must uniquely identify a record in
the DIFFRN_REFLN category.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_diffrn_refln.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
_item_description.description
;
Miller index h of a diffraction reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Millder indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are described in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix.
;
_item.name '_diffrn_refln.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_refln_index_h'
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_k'
_item_type.code int
_item_description.description
;
Miller index k of a diffraction reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Millder indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are described in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix.
;
_item.name '_diffrn_refln.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_refln_index_k'
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_l'
_item_type.code int
_item_description.description
;
Miller index l of a diffraction reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Millder indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are described in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix.
;
_item.name '_diffrn_refln.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_refln_index_l'
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_k'
_item_type.code int
save_diffrn_refln.intensity_net.
_item_description.description
;
Net intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
;
_item.name '_diffrn_refln.intensity_net'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_intensity_net'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code float
save_diffrn_refln.intensity_sigma.
_item_description.description
;
E.s.d. of the intensity calculated from the diffraction counts
after the attenuator and standard scales have been applied.
;
_item.name '_diffrn_refln.intensity_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_intensity_sigma'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code float
_item_description.description
;
The code identifying the mode of scanning with a diffractometer.
See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
;
_item.name '_diffrn_refln.scan_mode'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_mode'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
om
'omega scan'
ot
'omega/2theta scan'
save_diffrn_refln.scan_mode_backgd.
_item_description.description
;
The code identifying the mode of scanning a reflection to measure
the background intensity.
;
_item.name '_diffrn_refln.scan_mode_backgd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_mode_backgd'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
st
'stationary counter background'
mo
'moving counter background'
_item_description.description
;
The scan width in degrees of the scan mode defined by the code
_diffrn_refln.scan_mode.
;
_item.name '_diffrn_refln.scan_width'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_width'
_item_range.maximum 90.0
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'degrees'
save_diffrn_refln.sint/lambda.
_item_description.description ; The sine theta over wavelength value for this reflection. ; _item.name '_diffrn_refln.sint/lambda' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_sint/lambda' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'reciprocal_angstroms'
_item_description.description
;
The mean wavelength of radiation used to measure diffraction for
this reflection. This is an important parameter for data
collected using energy dispersive detectors or the Laue method.
;
_item.name '_diffrn_refln.wavelength'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_wavelength'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_diffrn_refln.wavelength_id.
_item_description.description
;
This data item is a pointer to _diffrn_radiation.wavelength_id in
the DIFFRN_RADIATION category.
;
_item_aliases.alias_name '_diffrn_refln_wavelength_id'
_category.description
;
Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements, and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLN data items
are not looped.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_reflns.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_reflns.number 1592
_diffrn_reflns.av_R_equivalents 0
_diffrn_reflns.av_sigmaI/netI .027
_diffrn_reflns.limit_h_min 0
_diffrn_reflns.limit_h_max 6
_diffrn_reflns.limit_k_min -17
_diffrn_reflns.limit_k_max 0
_diffrn_reflns.limit_l_min 0
_diffrn_reflns.limit_l_max 22
_diffrn_reflns.theta_min 3.71
_diffrn_reflns.theta_max 61.97
;
save_diffrn_reflns.av_R_equivalents.
_item_description.description
;
The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I). The
avdel(I) term is the average difference between av(I) and the
individual intensities.
;
_item.name '_diffrn_reflns.av_R_equivalents'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_av_R_equivalents'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_diffrn_reflns.av_sigmaI/netI.
_item_description.description ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. ; _item.name '_diffrn_reflns.av_sigmaI/netI' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_sigmaI/netI' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_reflns.limit_h_max.
_item_description.description
;
The maximum value of the diffraction reflection data specified
by _diffrn_refln.index_h.
;
_item.name '_diffrn_reflns.limit_h_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_h_max'
_item_type.code int
save_diffrn_reflns.limit_h_min.
_item_description.description
;
The minimum value of the diffraction reflection data specified
by _diffrn_refln.index_h.
;
_item.name '_diffrn_reflns.limit_h_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_h_min'
_item_type.code int
save_diffrn_reflns.limit_k_max.
_item_description.description
;
The maximum value of the diffraction reflection data specified
by _diffrn_refln.index_k.
;
_item.name '_diffrn_reflns.limit_k_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_k_max'
_item_type.code int
save_diffrn_reflns.limit_k_min.
_item_description.description
;
The minimum value of the diffraction reflection data specified
by _diffrn_refln.index_k.
;
_item.name '_diffrn_reflns.limit_k_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_k_min'
_item_type.code int
save_diffrn_reflns.limit_l_max.
_item_description.description
;
The maximum value of the diffraction reflection data specified
by _diffrn_refln.index_l.
;
_item.name '_diffrn_reflns.limit_l_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_l_max'
_item_type.code int
save_diffrn_reflns.limit_l_min.
_item_description.description
;
The minimum value of the diffraction reflection data specified
by _diffrn_refln.index_l.
;
_item.name '_diffrn_reflns.limit_l_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_l_min'
_item_type.code int
_item_description.description ; The total number of measured diffraction data. ; _item.name '_diffrn_reflns.number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_number' _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_diffrn_reflns.reduction_process.
_item_description.description
;
A description of the process used to reduce the intensity data
into structure-factor magnitudes.
;
_item.name '_diffrn_reflns.reduction_process'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_reduction_process'
_item_type.code char
_item_examples.case 'data averaged using Fisher test'
_item_description.description ; Maximum theta angle in degrees for the measured diffraction data. ; _item.name '_diffrn_reflns.theta_max' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_max' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
_item_description.description ; Minimum theta angle in degrees for the measured diffraction data. ; _item.name '_diffrn_reflns.theta_min' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_min' _item_range.maximum 90.0 _item_range.minimum 0.0 _item_type.code float _item_units.code 'degrees'
save_diffrn_reflns.transf_matrix.
_item_description.description
;
The matrix used to transform Miller indices in the DIFFRN_REFLN
category into the Miller indices in the REFLN category.
|11 12 13|
(h k l) diffraction |21 22 23| = (h' k' l')
|31 32 33|
;
_item.name '_diffrn_reflns.transf_matrix'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
save_diffrn_reflns.transf_matrix[1][1].
_item_description.description
;
The [1][1] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[1][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_11'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[1][2].
_item_description.description
;
The [1][2] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[1][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_12'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[1][3].
_item_description.description
;
The [1][3] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[1][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_13'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[2][1].
_item_description.description
;
The [2][1] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[2][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_21'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[2][2].
_item_description.description
;
The [2][2] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[2][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_22'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[2][3].
_item_description.description
;
The [2][3] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[2][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_23'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[3][1].
_item_description.description
;
The [3][1] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[3][1]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_31'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[3][2].
_item_description.description
;
The [3][2] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[3][2]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_32'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
save_diffrn_reflns.transf_matrix[3][3].
_item_description.description
;
The [3][3] element of the 3x3 matrix
_diffrn_reflns.transf_matrix. This data item is only present in
this dictionary for compliance (via the alias) with previous
dictionaries.
;
_item.name '_diffrn_reflns.transf_matrix[3][3]'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_33'
_item_related.related_name '_diffrn_reflns.transf_matrix'
_item_related.function_code 'alternative_exclusive'
_item_type.code float
_category.description
;
Data items in the DIFFRN_SCALE_GROUP category record details
about the reflections used to scale the diffraction intensities.
Scaling groups might, for instance, correspond to each film in a
multi-film data set, or each crystal in a mutli-crystal data set.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_scale_group.code'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on
;
;
Need Example 2
;
_item_description.description
;
The value of diffrn_scale_group.code must uniquely identify a
record in the DIFFRN_SCALE_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scale_group.code'
diffrn_scale_group
yes
'_diffrn_refln.scale_group_code'
diffrn_refln
yes
_item_aliases.alias_name '_diffrn_scale_group_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.scale_group_code'
'_diffrn_scale_group.code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
c1
c2
c3
_item_description.description
;
The value of diffrn_scale_group.code must uniquely identify a
record in the DIFFRN_SCALE_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scale_group.code'
diffrn_scale_group
yes
'_diffrn_refln.scale_group_code'
diffrn_refln
yes
_item_aliases.alias_name '_diffrn_scale_group_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.scale_group_code'
'_diffrn_scale_group.code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
c1
c2
c3
save_diffrn_scale_group.I_net.
_item_description.description
;
The scale for a specific measurement group which is to
multiplied with the net intensity to place all intensities
in the _diffrn_refln. or REFLN list on a common scale.
;
_item.name '_diffrn_scale_group.I_net'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_scale_group_I_net'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_category.description
;
Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_standard_refln.code'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_diffrn_standard_refln.index_h
_diffrn_standard_refln.index_k
_diffrn_standard_refln.index_l
3 2 4 1 9 1 3 0 10
;
save_diffrn_standard_refln.code.
_item_description.description
;
The code identifying a reflection measured as a standard
reflection with the indices _diffrn_standard_refln.index_.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_standard_refln.code'
diffrn_standard_refln
yes
'_diffrn_refln.standard_code'
diffrn_refln
yes
_item_aliases.alias_name '_diffrn_standard_refln_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.standard_code'
'_diffrn_standard_refln.code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
save_diffrn_standard_refln.code.
_item_description.description
;
The code identifying a reflection measured as a standard
reflection with the indices _diffrn_standard_refln.index_.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_standard_refln.code'
diffrn_standard_refln
yes
'_diffrn_refln.standard_code'
diffrn_refln
yes
_item_aliases.alias_name '_diffrn_standard_refln_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.standard_code'
'_diffrn_standard_refln.code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
save_diffrn_standard_refln.index_h.
_item_description.description
;
Miller index h of a standard reflection used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_standard_refln_index_h'
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_k'
'_diffrn_standard_refln.index_l'
_item_type.code int
save_diffrn_standard_refln.index_k.
_item_description.description
;
Miller index k of a standard reflections used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_standard_refln_index_k'
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_h'
'_diffrn_standard_refln.index_l'
_item_type.code int
save_diffrn_standard_refln.index_l.
_item_description.description
;
Miller index l of a standard reflections used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_diffrn_standard_refln_index_l'
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_h'
'_diffrn_standard_refln.index_k'
_item_type.code int
_category.description
;
Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_diffrn_standards.block_id'
loop_
_category_group.id
'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_standards.number 3
_diffrn_standards.interval_time 120
_diffrn_standards.decay_% 0
;
save_diffrn_standards.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_diffrn_standards.decay_%.
_item_description.description
;
The percentage variation of the mean intensity for all standard
reflections.
;
_item.name '_diffrn_standards.decay_%'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_decay_%'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_diffrn_standards.interval_count.
_item_description.description
;
The number of reflection intensities between the measurement of
standard reflection intensities.
;
_item.name '_diffrn_standards.interval_count'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_interval_count'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_standards.interval_time.
_item_description.description
;
The time in minutes between the measurement of standard
reflection intensities.
;
_item.name '_diffrn_standards.interval_time'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_interval_time'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code float
_item_units.code 'minutes'
_item_description.description
;
The number of unique standard reflections used in the diffraction
measurements.
;
_item.name '_diffrn_standards.number'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_number'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_diffrn_standards.scale_sigma.
_item_description.description
;
The e.s.d. of the individual mean standard scales applied to the
intensity data.
;
_item.name '_diffrn_standards.scale_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_scale_sigma'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_category.description
;
Data items in the ENTITY category record details (such as
chemical composition, name, and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY sub-categories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications, and replaces the function of the _chemical. data
items in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented in the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation,
and can most usefully be though of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity.id
_entity.type
_entity.formula_weight
_entity.details
1 polymer 10916
; The enzymatically competent form of HIV protease is a
dimer. This entity corresponds to one monomer of an
active dimer.
;
2 non-polymer 'need number here' '.'
3 water 18 '.'
;
_item_description.description ; A description of special aspects of the entity. ; _item.name '_entity.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description ; Formula mass in daltons of the entity. ; _item.name '_entity.formula_weight' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 1.0 _item_type.code float
_item_description.description
;
The value of _entity.id must uniquely identify a record in the
ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity.id'
entity
yes
'_atom_site.entity_id'
atom_site
yes
'_entity_keywords.entity_id'
entity_keywords
yes
'_entity_name_com.entity_id'
entity_name_com
yes
'_entity_name_sys.entity_id'
entity_name_sys
yes
'_entity_poly.entity_id'
entity_poly
yes
'_entity_poly_seq.entity_id'
entity_poly_seq
yes
'_entity_poly_seq_dif.entity_id'
entity_poly_seq_dif
yes
'_entity_reference.entity_id'
entity_reference
yes
'_entity_src_gen.entity_id'
entity_src_gen
yes
'_entity_src_nat.entity_id'
entity_src_nat
yes
'_struct_asym.entity_id'
struct_asym
yes
_item_type.code char
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.entity_id'
'_entity.id'
'_entity_keywords.entity_id'
'_entity.id'
'_entity_name_com.entity_id'
'_entity.id'
'_entity_name_sys.entity_id'
'_entity.id'
'_entity_poly.entity_id'
'_entity.id'
'_entity_poly_seq.entity_id'
'_entity_poly.entity_id'
'_entity_poly_seq_dif.entity_id'
'_entity_poly_seq.entity_id'
'_entity_reference.entity_id'
'_entity.id'
'_entity_src_gen.entity_id'
'_entity.id'
'_entity_src_nat.entity_id'
'_entity.id'
'_struct_asym.entity_id'
'_entity.id'
_item_description.description
;
The value of _entity.id must uniquely identify a record in the
ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity.id'
entity
yes
'_atom_site.entity_id'
atom_site
yes
'_entity_keywords.entity_id'
entity_keywords
yes
'_entity_name_com.entity_id'
entity_name_com
yes
'_entity_name_sys.entity_id'
entity_name_sys
yes
'_entity_poly.entity_id'
entity_poly
yes
'_entity_poly_seq.entity_id'
entity_poly_seq
yes
'_entity_poly_seq_dif.entity_id'
entity_poly_seq_dif
yes
'_entity_reference.entity_id'
entity_reference
yes
'_entity_src_gen.entity_id'
entity_src_gen
yes
'_entity_src_nat.entity_id'
entity_src_nat
yes
'_struct_asym.entity_id'
struct_asym
yes
_item_type.code char
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.entity_id'
'_entity.id'
'_entity_keywords.entity_id'
'_entity.id'
'_entity_name_com.entity_id'
'_entity.id'
'_entity_name_sys.entity_id'
'_entity.id'
'_entity_poly.entity_id'
'_entity.id'
'_entity_poly_seq.entity_id'
'_entity_poly.entity_id'
'_entity_poly_seq_dif.entity_id'
'_entity_poly_seq.entity_id'
'_entity_reference.entity_id'
'_entity.id'
'_entity_src_gen.entity_id'
'_entity.id'
'_entity_src_nat.entity_id'
'_entity.id'
'_struct_asym.entity_id'
'_entity.id'
_item_description.description
;
The method by which the sample for the entity was produced.
Entities isolated directly from natural sources (tissues, soil
samples, etc.) are expected to have further information in the
ENTITY_SRC_NAT category. Entities isolated from genetically
manipulated sources are expected to have further information in
the ENTITY_SRC_GEN category.
;
_item.name '_entity.src_method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
nat
'entity was isolated from a natural source'
man
;
entity was isolated from a genetically
manipulated source
;
_item_description.description
;
Defines the type of the entity.
Polymer entities will be expected to have corresponding
ENTITY_POLY and associated entries.
Non-polymer entities will be expected to have corresponding
ENTITY_NPOL and associated entries.
Water entities are not expected to have corresponding
entries in the ENTITY category.
;
_item.name '_entity.type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
polymer
'entity is a polymer'
non-polymer
'entity is not a polymer'
water
'water in the solvent model'
_category.description
;
Data items in the ENTITY_KEYWORDS category specify keywords
relevant to the molecular entities. Note that this list of
keywords is separate from the list that is used to keyword the
STRUCT_BIOL data items, and is intended to provide only the
information that one would know about the molecular entity *if
one did not know its structure*. Hence polypeptides are simply
polypeptides, and not cytokines or beta-alpha-barrels, and
polyribonucleic acids are simply poly-RNA, and not transfer-
RNA.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_keywords.entity_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 'polypeptide'
2 'natural product'
2 'inhibitor'
2 'reduced peptide'
;
save_entity_keywords.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; Keywords describing this entity. ; _item.name '_entity_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'polypeptide' 'natural product' 'polysaccharide'
_category.description
;
Data items in the ENTITY_LINK category give details about the
linkages between monomers in a polymer.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_link.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 -
;
;
Need Example 1
;
_item_description.description
;
A description of special aspects of a linkage between monomers
in a polymer.
;
_item.name '_entity_link.model_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The value of _entity_link.id must uniquely identify each item in
the ENTITY_LINK list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_link.id'
entity_link
yes
'_entity_link_angle.link_id'
entity_link_angle
yes
'_entity_link_bond.link_id'
entity_link_bond
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_link_angle.link_id'
'_entity_link.id'
'_entity_link_bond.link_id'
'_entity_link.id'
_item_type.code char
loop_
_item_examples.case
'peptide'
'oligosaccharide 1,4'
'DNA'
_item_description.description
;
The value of _entity_link.id must uniquely identify each item in
the ENTITY_LINK list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_link.id'
entity_link
yes
'_entity_link_angle.link_id'
entity_link_angle
yes
'_entity_link_bond.link_id'
entity_link_bond
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_link_angle.link_id'
'_entity_link.id'
'_entity_link_bond.link_id'
'_entity_link.id'
_item_type.code char
loop_
_item_examples.case
'peptide'
'oligosaccharide 1,4'
'DNA'
_item_description.description
;
The value of _entity_link.id must uniquely identify each item in
the ENTITY_LINK list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_link.id'
entity_link
yes
'_entity_link_angle.link_id'
entity_link_angle
yes
'_entity_link_bond.link_id'
entity_link_bond
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_link_angle.link_id'
'_entity_link.id'
'_entity_link_bond.link_id'
'_entity_link.id'
_item_type.code char
loop_
_item_examples.case
'peptide'
'oligosaccharide 1,4'
'DNA'
_item_description.description
;
The type of the second of the two monomers joined by the linkage.
This data item is a pointer to _entity_mon.type in the
ENTITY_MON category.
;
_item.name '_entity_link.type_mon_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the ENTITY_LINK_ANGLE category record details about
angles in a linkage between monomers in a polymer.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_link_angle.link_id'
'_entity_link_angle.atom_id_1'
'_entity_link_angle.atom_id_2'
'_entity_link_angle.atom_id_3'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 -
;
;
Need Example 1
;
save_entity_link_angle.atom_1_atom_id.
_item_description.description
;
The id of the first of the three atoms that define the angle.
As this data item does not point to a specific atom in a
specific monomer, it is not a child in the linkage sense.
;
_item.name '_entity_link_angle.atom_1_atom_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_2_atom_id'
'_entity_link_angle.atom_3_atom_id'
_item.mandatory_code no
_item_type.code char
save_entity_link_angle.atom_1_mon_id.
_item_description.description
;
This data item indiates whether atom 1 is found in the first
or the second of the two monomers connected by the linkage.
;
_item.name '_entity_link_angle.atom_1_mon_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_2_mon_id'
'_entity_link_angle.atom_3_mon_id'
_item.mandatory_code no
loop_
_item_enumeration.code
_item_enumeration.detail
1
'the atom is in monomer 1'
2
'the atom is in monomer 2'
save_entity_link_angle.atom_2_atom_id.
_item_description.description
;
The id of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
As this data item does not point to a specific atom in a
specific monomer, it is not a child in the linkage sense.
;
_item.name '_entity_link_angle.atom_2_atom_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_1_atom_id'
'_entity_link_angle.atom_3_atom_id'
_item.mandatory_code no
_item_type.code char
save_entity_link_angle.atom_2_mon_id.
_item_description.description
;
This data item indiates whether atom 2 is found in the first
or the second of the two monomers connected by the linkage.
;
_item.name '_entity_link_angle.atom_2_mon_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_1_mon_id'
'_entity_link_angle.atom_3_mon_id'
_item.mandatory_code no
loop_
_item_enumeration.code
_item_enumeration.detail
1
'the atom is in monomer 1'
2
'the atom is in monomer 2'
save_entity_link_angle.atom_3_atom_id.
_item_description.description
;
The id of the third of the three atoms that define the angle.
As this data item does not point to a specific atom in a
specific monomer, it is not a child in the linkage sense.
;
_item.name '_entity_link_angle.atom_3_atom_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_1_atom_id'
'_entity_link_angle.atom_2_atom_id'
_item.mandatory_code no
_item_type.code char
save_entity_link_angle.atom_3_mon_id.
_item_description.description
;
This data item indiates whether atom 3 is found in the first
or the second of the two monomers connected by the linkage.
;
_item.name '_entity_link_angle.atom_3_mon_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_angle.atom_1_mon_id'
'_entity_link_angle.atom_2_mon_id'
_item.mandatory_code no
loop_
_item_enumeration.code
_item_enumeration.detail
1
'the atom is in monomer 1'
2
'the atom is in monomer 2'
save_entity_link_angle.value_angle.
_item_description.description
;
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
;
_item.name '_entity_link_angle.value_angle'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum 180.0
_item_range.minimum 0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'degrees'
save_entity_link_angle.value_angle_esd.
_item_description.description
;
The estimated standard deviation of
_entity_link_angle.value_angle.
;
_item.name '_entity_link_angle.value_angle_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum 180.0
_item_range.minimum 0
_item_type.code float
_item_units.code 'degrees'
save_entity_link_angle.value_dist.
_item_description.description
;
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by _entity_mon_angle.atom_id_1 and
_entity_mon_angle.atom_id_3.
;
_item.name '_entity_link_angle.value_dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_link_angle.value_dist_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_angle.value_dist_esd.
;
_item.name '_entity_link_angle.value_dist_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_category.description
;
Data items in the ENTITY_LINK_BOND category record details about
bonds in a linkage between monomers in a polymer.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_link_bond.link_id'
'_entity_link_bond.atom_id_1'
'_entity_link_bond.atom_id_2'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 -
;
;
Need Example 1
;
save_entity_link_bond.atom_1_atom_id.
_item_description.description
;
The id of the first of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific monomer, it is not a child in the linkage sense.
;
_item.name '_entity_link_bond.atom_1_atom_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_bond.atom_2_atom_id'
_item.mandatory_code no
_item_type.code char
save_entity_link_bond.atom_1_mon_id.
_item_description.description
;
This data item indiates whether atom 1 is found in the first
or the second of the two monomers connected by the linkage.
;
_item.name '_entity_link_bond.atom_1_mon_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_bond.atom_2_mon_id'
_item.mandatory_code no
loop_
_item_enumeration.code
_item_enumeration.detail
1
'the atom is in monomer 1'
2
'the atom is in monomer 2'
save_entity_link_bond.atom_2_atom_id.
_item_description.description
;
The id of the second of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific monomer, it is not a child in the linkage sense.
;
_item.name '_entity_link_bond.atom_2_atom_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_bond.atom_1_atom_id'
_item.mandatory_code no
_item_type.code char
save_entity_link_bond.atom_2_mon_id.
_item_description.description
;
This data item indiates whether atom 2 is found in the first
or the second of the two monomers connected by the linkage.
;
_item.name '_entity_link_bond.atom_2_mon_id'
_item.category_id _item.category_id
loop_
_item_dependent.dependent_name
'_entity_link_bond.atom_1_mon_id'
_item.mandatory_code no
loop_
_item_enumeration.code
_item_enumeration.detail
1
'the atom is in monomer 1'
2
'the atom is in monomer 2'
save_entity_link_bond.value_dist.
_item_description.description
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_item.name '_entity_link_bond.value_dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_link_bond.value_dist_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_bond.value_dist_esd.
;
_item.name '_entity_link_bond.value_dist_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_entity_link_bond.value_order.
_item_description.description
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
;
_item.name '_entity_link_bond.value_order'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value sing
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
sing
'single bond'
doub
'double bond'
trip
'triple bond'
quad
'quadruple bond'
arom
'aromatic bond'
poly
'polymeric bond'
delo
'delocalised double bond'
pi
'pi bond'
_category.description
;
Data items in the ENTITY_MON category give details (such as
name, mass, charge, etc.) about each of the monomers from which
the relevant polymers can be constructed.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_mon.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon.id
_entity_mon.model_source
_entity_mon.name
phe '1987 Protin/Prolsq Ideals file' phenylalanine
val '1987 Protin/Prolsq Ideals file' alanine
# - - - - data truncated for brevity - - - -
;
_item_description.description
;
The value of _entity_mon.id must uniquely identify each item in
the ENTITY_MON list.
For protein polymer entities, this is the three-letter code for
amino acids.
For nucleic acid polymer entities, this is the one-letter code
for the bases.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon.id'
entity_mon
yes
'_atom_site.label_res_id'
atom_site
yes
'_entity_mon_atom.mon_id'
entity_mon_atom
yes
'_entity_mon_angle.mon_id'
entity_mon_angle
yes
'_entity_mon_bond.mon_id'
entity_mon_bond
yes
'_entity_mon_chir.mon_id'
entity_mon_chir
yes
'_entity_mon_plane.mon_id'
entity_mon_plane
yes
'_entity_mon_tor.mon_id'
entity_mon_tor
yes
'_entity_poly_seq.mon_id'
entity_poly_seq
yes
'_entity_poly_seq_dif.mon_id'
entity_poly_seq_dif
yes
'_entity_poly_seq_dif.db_mon_id'
entity_poly_seq_dif
yes
'_struct_conf.beg_label_res_id'
struct_conf
yes
'_struct_conf.end_label_res_id'
struct_conf
yes
'_struct_conn.ptnr1_label_res_id'
struct_conn
yes
'_struct_conn.ptnr2_label_res_id'
struct_conn
yes
'_struct_mon_nucl.label_res_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_res_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_res_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_res_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_res_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_res_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_res_id'
'_entity_mon.id'
'_entity_mon_atom.mon_id'
'_entity_mon.id'
'_entity_mon_chir.mon_id'
'_entity_mon.id'
'_entity_mon_plane.mon_id'
'_entity_mon.id'
'_entity_poly_seq.mon_id'
'_entity_mon.id'
'_entity_poly_seq_dif.db_mon_id'
'_entity_mon.id'
'_entity_mon_angle.mon_id'
'_entity_mon_atom.mon_id'
'_entity_mon_bond.mon_id'
'_entity_mon_atom.mon_id'
'_entity_mon_tor.mon_id'
'_entity_mon_atom.mon_id'
'_entity_poly_seq_dif.mon_id'
'_entity_poly_seq.mon_id'
'_struct_conf.beg_label_res_id'
'_atom_site.label_res_id'
'_struct_conf.end_label_res_id'
'_atom_site.label_res_id'
'_struct_conn.ptnr1_label_res_id'
'_atom_site.label_res_id'
'_struct_conn.ptnr2_label_res_id'
'_atom_site.label_res_id'
'_struct_mon_nucl.label_res_id'
'_atom_site.label_res_id'
'_struct_mon_prot.label_res_id'
'_atom_site.label_res_id'
'_struct_mon_prot_cis.label_res_id'
'_atom_site.label_res_id'
'_struct_ncs_dom_gen.beg_label_res_id'
'_atom_site.label_res_id'
'_struct_ncs_dom_gen.end_label_res_id'
'_atom_site.label_res_id'
'_struct_site_gen.label_res_id'
'_atom_site.label_res_id'
_item_type.code char
loop_
_item_examples.case
'ala'
'val'
'A'
'C'
_item_description.description
;
The value of _entity_mon.id must uniquely identify each item in
the ENTITY_MON list.
For protein polymer entities, this is the three-letter code for
amino acids.
For nucleic acid polymer entities, this is the one-letter code
for the bases.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon.id'
entity_mon
yes
'_atom_site.label_res_id'
atom_site
yes
'_entity_mon_atom.mon_id'
entity_mon_atom
yes
'_entity_mon_angle.mon_id'
entity_mon_angle
yes
'_entity_mon_bond.mon_id'
entity_mon_bond
yes
'_entity_mon_chir.mon_id'
entity_mon_chir
yes
'_entity_mon_plane.mon_id'
entity_mon_plane
yes
'_entity_mon_tor.mon_id'
entity_mon_tor
yes
'_entity_poly_seq.mon_id'
entity_poly_seq
yes
'_entity_poly_seq_dif.mon_id'
entity_poly_seq_dif
yes
'_entity_poly_seq_dif.db_mon_id'
entity_poly_seq_dif
yes
'_struct_conf.beg_label_res_id'
struct_conf
yes
'_struct_conf.end_label_res_id'
struct_conf
yes
'_struct_conn.ptnr1_label_res_id'
struct_conn
yes
'_struct_conn.ptnr2_label_res_id'
struct_conn
yes
'_struct_mon_nucl.label_res_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_res_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_res_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_res_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_res_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_res_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_res_id'
'_entity_mon.id'
'_entity_mon_atom.mon_id'
'_entity_mon.id'
'_entity_mon_chir.mon_id'
'_entity_mon.id'
'_entity_mon_plane.mon_id'
'_entity_mon.id'
'_entity_poly_seq.mon_id'
'_entity_mon.id'
'_entity_poly_seq_dif.db_mon_id'
'_entity_mon.id'
'_entity_mon_angle.mon_id'
'_entity_mon_atom.mon_id'
'_entity_mon_bond.mon_id'
'_entity_mon_atom.mon_id'
'_entity_mon_tor.mon_id'
'_entity_mon_atom.mon_id'
'_entity_poly_seq_dif.mon_id'
'_entity_poly_seq.mon_id'
'_struct_conf.beg_label_res_id'
'_atom_site.label_res_id'
'_struct_conf.end_label_res_id'
'_atom_site.label_res_id'
'_struct_conn.ptnr1_label_res_id'
'_atom_site.label_res_id'
'_struct_conn.ptnr2_label_res_id'
'_atom_site.label_res_id'
'_struct_mon_nucl.label_res_id'
'_atom_site.label_res_id'
'_struct_mon_prot.label_res_id'
'_atom_site.label_res_id'
'_struct_mon_prot_cis.label_res_id'
'_atom_site.label_res_id'
'_struct_ncs_dom_gen.beg_label_res_id'
'_atom_site.label_res_id'
'_struct_ncs_dom_gen.end_label_res_id'
'_atom_site.label_res_id'
'_struct_site_gen.label_res_id'
'_atom_site.label_res_id'
_item_type.code char
loop_
_item_examples.case
'ala'
'val'
'A'
'C'
save_entity_mon.model_details.
_item_description.description
;
A description of special aspects of the generation of the
coordinates for the model of the monomer.
;
_item.name '_entity_mon.model_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'geometry idealized but not minimized'
_item_description.description
;
A pointer to an 'external reference file', if the atomic
description of the monomer is taken from such a file.
;
_item.name '_entity_mon.model_erf'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The source of the coordinates for the model of the non-polymer
entity.
;
_item.name '_entity_mon.model_source'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'CSD entry ABCDEF'
'built using Quanta/Charmm'
_item_description.description ; The full name of the monomer. ; _item.name '_entity_mon.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine'
_item_description.description
;
A description of the class of the non-standard monomer, if the
group represents a modification of a standard monomer.
;
_item.name '_entity_mon.nstd_class'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'iodinated base'
'phosporylated amino acid'
'bromined base'
'modified amino acid'
'glycosylated amino acid'
_item_description.description ; A description of special details of the non-standard monomer. ; _item.name '_entity_mon.nstd_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description
;
'yes' indicates that this is a "standard" monomer, 'no' that it
is "non-standard." Non-standard monomers should be further
described using the _entity_mon.nstd_parent,
_entity_mon.nstd_class, and _entity_mon.nstd_details data items.
;
_item.name '_entity_mon.nstd_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
yes
no
_item_description.description
;
A name of the parent monomer of the non-standard monomer, if the
group represents a modification of a standard monomer.
;
_item.name '_entity_mon.nstd_parent'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'tyrosine'
'cytosine'
save_entity_mon.number_atoms_all.
_item_description.description ; The total number of atoms in the monomer. ; _item.name '_entity_mon.number_atoms_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon.number_atoms_nh.
_item_description.description ; The number of non-hydrogen atoms in the monomer. ; _item.name '_entity_mon.number_atoms_nh' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon.one_letter_code.
_item_description.description
;
The one-letter code for the monomer. If there is not a standard
one letter code for this monomer, or if this is a non-polymer
monomer, the one-letter code should be given as 'X'.
;
_item.name '_entity_mon.one_letter_code'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
A
'alanine'
R
'arginine'
N
'asparagine'
D
'aspartic-acid'
C
'cysteine'
C
'cystine'
Q
'glutamine'
E
'glutamic-acid'
G
'glycine'
H
'histidine'
I
'isoleucine'
L
'leucine'
K
'lysine'
M
'methionine'
F
'phenylalanine'
P
'proline'
S
'serine'
T
'threonine'
W
'tryptophan'
Y
'tyrosine'
V
'valine'
A
'adenine'
C
'cytosine'
G
'guanine'
T
'thymine'
U
'uracil'
O
'water'
X
'other'
_item_description.description
;
The type of the monomer. Note that monomers that will form
polymers are of three types: linking monomers, monomers with
some type of N-terminal (or 5') cap, and monomers with some type
of C-terminal (or 3') cap.
;
_item.name '_entity_mon.type'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
'D-peptide linking'
'L-peptide linking'
'D-peptide NH3 amino terminus'
'L-peptide NH3 amino terminus'
'D-peptide COOH carboxy terminus'
'L-peptide COOH carboxy terminus'
'DNA linking'
'RNA linking'
'DNA OH 5'
terminus
'RNA OH 5'
terminus
'DNA OH 3'
terminus
'RNA OH 3'
terminus
'D-saccharide 1,4 and 1,4 linking'
'L-saccharide 1,4 and 1,4 linking'
'D-saccharide 1,4 and 1,6 linking'
'L-saccharide 1,4 and 1,6 linking'
'non-polymer'
'other'
_category.description
;
Data items in the ENTITY_MON_ANGLE category record details about
angles in a monomer entity. Angles are designated by three
atoms, with the second atom forming the vertex of the angle.
Target values may be specified as angles in degrees, as a
distance between the first and third atoms, or both.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_angle.mon_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_angle.atom_id_2'
'_entity_mon_angle.atom_id_3'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_angle.mon_id
_entity_mon_angle.atom_id_1
_entity_mon_angle.atom_id_2
_entity_mon_angle.atom_id_3
_entity_mon_angle.value_angle
_entity_mon_angle.value_dist
phe N CA C xxx.xx x.xx
phe CA C O xxx.xx x.xx
phe CB CA C xxx.xx x.xx
phe CB CA N xxx.xx x.xx
phe CA CB CG xxx.xx x.xx
phe CB CG CD1 xxx.xx x.xx
phe CB CG CD2 xxx.xx x.xx
phe CD1 CG CD2 xxx.xx x.xx
phe CG CD1 CE1 xxx.xx x.xx
phe CD1 CE1 CZ xxx.xx x.xx
phe CE1 CZ CE2 xxx.xx x.xx
phe CZ CE2 CD2 xxx.xx x.xx
phe CG CD2 CE2 xxx.xx x.xx
val N CA C xxx.xx x.xx
val CA C O xxx.xx x.xx
val CB CA C xxx.xx x.xx
val CB CA N xxx.xx x.xx
val CA CB CG1 xxx.xx x.xx
val CA CB CG2 xxx.xx x.xx
val CG1 CB CG2 xxx.xx x.xx
;
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_mon_angle.value_angle.
_item_description.description
;
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
;
_item.name '_entity_mon_angle.value_angle'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum 180.0
_item_range.minimum 0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'degrees'
save_entity_mon_angle.value_angle_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_angle.value_angle.
;
_item.name '_entity_mon_angle.value_angle_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum 180.0
_item_range.minimum 0
_item_type.code float
_item_units.code 'degrees'
save_entity_mon_angle.value_dist.
_item_description.description
;
The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by _entity_mon_angle.atom_id_1 and
_entity_mon_angle.atom_id_3.
;
_item.name '_entity_mon_angle.value_dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_mon_angle.value_dist_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_angle.value_dist_esd.
;
_item.name '_entity_mon_angle.value_dist_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_category.description
;
Data items in the ENTITY_MON_ATOM category record details about
the atoms in a monomer entity. Atomic coordinates can be given
for the monomer; specifying coordinates is an alternative to
specifying the structure of the monomer via bonds, angles,
planes, etc., in the appropriate ENTITY_MON subcategories.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_atom.mon_id'
'_entity_mon_atom.atom_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_atom.mon_id
_entity_mon_atom.atom_id
_entity_mon_atom.type_symbol
_entity_mon_atom.substruct_code
_entity_mon_atom.model_cartn_x
_entity_mon_atom.model_cartn_y
_entity_mon_atom.model_cartn_z
phe N N main 1.20134 0.84658 0.00000
phe CA C main 0.00000 0.00000 0.00000
phe C C main -1.25029 0.88107 0.00000
phe O O main -2.18525 0.66029 -0.78409
phe CB C side 0.00662 -1.03603 1.11081
phe CG C side 0.03254 -0.49711 2.50951
phe CD1 C side -1.15813 -0.12084 3.13467
phe CE1 C side -1.15720 0.38038 4.42732
phe CZ C side 0.05385 0.51332 5.11032
phe CE2 C side 1.26137 0.11613 4.50975
phe CD2 C side 1.23668 -0.38351 3.20288
val N N main 1.20134 0.84658 0.00000
val CA C main 0.00000 0.00000 0.00000
val C C main -1.25029 0.88107 0.00000
val O O main -2.18525 0.66029 -0.78409
val CB C side 0.05260 -0.99339 1.17429
val CG1 C side -0.13288 -0.31545 2.52668
val CG2 C side -0.94265 -2.12930 0.99811
;
save_entity_mon_atom.alt_atom_id.
_item_description.description
;
An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a monomer.
;
_item.name '_entity_mon_atom.alt_atom_id'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The value of _entity_mon_atom.atom_id must uniquely identify
each atom in each monomer in the ENTITY_MON_ATOM list.
The atom identifiers need not be unique over all atoms in the
CIF; they need only be unique for each atom in a monomer.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_atom.atom_id'
entity_mon_atom
yes
'_atom_site.label_atom_id'
atom_site
yes
'_entity_mon_angle.atom_id_1'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_2'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_3'
entity_mon_angle
yes
'_entity_mon_bond.atom_id_1'
entity_mon_bond
yes
'_entity_mon_bond.atom_id_2'
entity_mon_bond
yes
'_entity_mon_chir.atom_id'
entity_mon_chir
yes
'_entity_mon_chir_atom.atom_id'
entity_mon_chir_atom
yes
'_entity_mon_plane_atom.atom_id'
entity_mon_plane_atom
yes
'_entity_mon_tor.atom_id_1'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_2'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_3'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_4'
entity_mon_tor
yes
'_struct_conn.ptnr1_label_atom_id'
struct_conn
yes
'_struct_conn.ptnr2_label_atom_id'
struct_conn
yes
'_struct_site_gen.label_atom_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_chir.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_chir_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_plane_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_4'
'_entity_mon_atom.atom_id'
'_struct_conn.ptnr1_label_atom_id'
'_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id'
'_atom_site.label_atom_id'
_item_type.code char
_item_description.description
;
The value of _entity_mon_atom.atom_id must uniquely identify
each atom in each monomer in the ENTITY_MON_ATOM list.
The atom identifiers need not be unique over all atoms in the
CIF; they need only be unique for each atom in a monomer.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_atom.atom_id'
entity_mon_atom
yes
'_atom_site.label_atom_id'
atom_site
yes
'_entity_mon_angle.atom_id_1'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_2'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_3'
entity_mon_angle
yes
'_entity_mon_bond.atom_id_1'
entity_mon_bond
yes
'_entity_mon_bond.atom_id_2'
entity_mon_bond
yes
'_entity_mon_chir.atom_id'
entity_mon_chir
yes
'_entity_mon_chir_atom.atom_id'
entity_mon_chir_atom
yes
'_entity_mon_plane_atom.atom_id'
entity_mon_plane_atom
yes
'_entity_mon_tor.atom_id_1'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_2'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_3'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_4'
entity_mon_tor
yes
'_struct_conn.ptnr1_label_atom_id'
struct_conn
yes
'_struct_conn.ptnr2_label_atom_id'
struct_conn
yes
'_struct_site_gen.label_atom_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_chir.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_chir_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_plane_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_4'
'_entity_mon_atom.atom_id'
'_struct_conn.ptnr1_label_atom_id'
'_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id'
'_atom_site.label_atom_id'
_item_type.code char
_item_description.description
;
The value of _entity_mon_atom.atom_id must uniquely identify
each atom in each monomer in the ENTITY_MON_ATOM list.
The atom identifiers need not be unique over all atoms in the
CIF; they need only be unique for each atom in a monomer.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_atom.atom_id'
entity_mon_atom
yes
'_atom_site.label_atom_id'
atom_site
yes
'_entity_mon_angle.atom_id_1'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_2'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_3'
entity_mon_angle
yes
'_entity_mon_bond.atom_id_1'
entity_mon_bond
yes
'_entity_mon_bond.atom_id_2'
entity_mon_bond
yes
'_entity_mon_chir.atom_id'
entity_mon_chir
yes
'_entity_mon_chir_atom.atom_id'
entity_mon_chir_atom
yes
'_entity_mon_plane_atom.atom_id'
entity_mon_plane_atom
yes
'_entity_mon_tor.atom_id_1'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_2'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_3'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_4'
entity_mon_tor
yes
'_struct_conn.ptnr1_label_atom_id'
struct_conn
yes
'_struct_conn.ptnr2_label_atom_id'
struct_conn
yes
'_struct_site_gen.label_atom_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_chir.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_chir_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_plane_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_4'
'_entity_mon_atom.atom_id'
'_struct_conn.ptnr1_label_atom_id'
'_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id'
'_atom_site.label_atom_id'
_item_type.code char
_item_description.description
;
The value of _entity_mon_atom.atom_id must uniquely identify
each atom in each monomer in the ENTITY_MON_ATOM list.
The atom identifiers need not be unique over all atoms in the
CIF; they need only be unique for each atom in a monomer.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_atom.atom_id'
entity_mon_atom
yes
'_atom_site.label_atom_id'
atom_site
yes
'_entity_mon_angle.atom_id_1'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_2'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_3'
entity_mon_angle
yes
'_entity_mon_bond.atom_id_1'
entity_mon_bond
yes
'_entity_mon_bond.atom_id_2'
entity_mon_bond
yes
'_entity_mon_chir.atom_id'
entity_mon_chir
yes
'_entity_mon_chir_atom.atom_id'
entity_mon_chir_atom
yes
'_entity_mon_plane_atom.atom_id'
entity_mon_plane_atom
yes
'_entity_mon_tor.atom_id_1'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_2'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_3'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_4'
entity_mon_tor
yes
'_struct_conn.ptnr1_label_atom_id'
struct_conn
yes
'_struct_conn.ptnr2_label_atom_id'
struct_conn
yes
'_struct_site_gen.label_atom_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_chir.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_chir_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_plane_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_4'
'_entity_mon_atom.atom_id'
'_struct_conn.ptnr1_label_atom_id'
'_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id'
'_atom_site.label_atom_id'
_item_type.code char
_item_description.description
;
The value of _entity_mon_atom.atom_id must uniquely identify
each atom in each monomer in the ENTITY_MON_ATOM list.
The atom identifiers need not be unique over all atoms in the
CIF; they need only be unique for each atom in a monomer.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_atom.atom_id'
entity_mon_atom
yes
'_atom_site.label_atom_id'
atom_site
yes
'_entity_mon_angle.atom_id_1'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_2'
entity_mon_angle
yes
'_entity_mon_angle.atom_id_3'
entity_mon_angle
yes
'_entity_mon_bond.atom_id_1'
entity_mon_bond
yes
'_entity_mon_bond.atom_id_2'
entity_mon_bond
yes
'_entity_mon_chir.atom_id'
entity_mon_chir
yes
'_entity_mon_chir_atom.atom_id'
entity_mon_chir_atom
yes
'_entity_mon_plane_atom.atom_id'
entity_mon_plane_atom
yes
'_entity_mon_tor.atom_id_1'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_2'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_3'
entity_mon_tor
yes
'_entity_mon_tor.atom_id_4'
entity_mon_tor
yes
'_struct_conn.ptnr1_label_atom_id'
struct_conn
yes
'_struct_conn.ptnr2_label_atom_id'
struct_conn
yes
'_struct_site_gen.label_atom_id'
struct_site_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_angle.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_bond.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_chir.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_chir_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_plane_atom.atom_id'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_1'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_2'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_3'
'_entity_mon_atom.atom_id'
'_entity_mon_tor.atom_id_4'
'_entity_mon_atom.atom_id'
'_struct_conn.ptnr1_label_atom_id'
'_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id'
'_atom_site.label_atom_id'
_item_type.code char
_item_description.description
;
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
_item.name '_entity_mon_atom.charge'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0
_item_range.maximum 6
_item_range.minimum -6
_item_type.code int
loop_
_item_examples.case
_item_examples.detail
1
'for an ammonium nitrogen'
-1
'for a chloride ion'
save_entity_mon_atom.model_cartn_x.
_item_description.description
;
The x component of the coordinates for this atom in this monomer
specified as orthogonal Angstroms. The choice of reference axis
frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, and not to atom sites in the _atom_site_
list.
;
_item.name '_entity_mon_atom.model_cartn_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_y'
'_entity_mon_atom.model_cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_x_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_atom.model_cartn_x.
;
_item.name '_entity_mon_atom.model_cartn_x_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate_esd'
_item_default.value 0.0
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_y_esd'
'_entity_mon_atom.model_cartn_z_esd'
_item_type.code float
_item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_y.
_item_description.description
;
The y component of the coordinates for this atom in this monomer
specified as orthogonal Angstroms. The choice of reference axis
frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, and not to atom sites in the _atom_site_
list.
;
_item.name '_entity_mon_atom.model_cartn_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_x'
'_entity_mon_atom.model_cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_y_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_atom.model_cartn_y.
;
_item.name '_entity_mon_atom.model_cartn_y_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate_esd'
_item_default.value 0.0
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_x_esd'
'_entity_mon_atom.model_cartn_z_esd'
_item_type.code float
_item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_z.
_item_description.description
;
The x component of the coordinates for this atom in this monomer
specified as orthogonal Angstroms. The choice of reference axis
frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, and not to atom sites in the _atom_site_
list.
;
_item.name '_entity_mon_atom.model_cartn_z'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_x'
'_entity_mon_atom.model_cartn_y'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_mon_atom.model_cartn_z_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_atom.model_cartn_z.
;
_item.name '_entity_mon_atom.model_cartn_z_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate_esd'
_item_default.value 0.0
loop_
_item_dependent.dependent_name
'_entity_mon_atom.model_cartn_x_esd'
'_entity_mon_atom.model_cartn_y_esd'
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_mon_atom.substruct_code.
_item_description.description
;
This data item assigns the atom to a substructure of the
monomer, if appropriate.
;
_item.name '_entity_mon_atom.substruct_code'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
main
'main chain of an amino acid'
side
'side chain of an amino acid'
base
'base of a nucleic acid'
phos
'phosphate of a nucleic acid'
sugar
'sugar of a nucleic acid'
none
'not appropriate for this monomer'
save_entity_mon_atom.type_symbol.
_item_description.description
;
This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_category.description
;
Data items in the ENTITY_MON_BOND category record details about
the bonds between atoms in the monomer entity. Target values may
be specified as bond orders, as a distance between the two atoms,
or both.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_bond.mon_id'
'_entity_mon_bond.atom_id_1'
'_entity_mon_bond.atom_id_2'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_bond.mon_id
_entity_mon_bond.atom_id_1
_entity_mon_bond.atom_id_2
_entity_mon_bond.value_order
_entity_mon_bond.value_dist
phe N CA sing x.xx
phe CA C sing x.xx
phe C O doub x.xx
phe CB CA sing x.xx
phe CB CG sing x.xx
phe CG CD1 arom x.xx
phe CD1 CE1 arom x.xx
phe CE1 CZ arom x.xx
phe CZ CE2 arom x.xx
phe CE2 CD2 arom x.xx
phe CD2 CG arom x.xx
val N CA sing x.xx
val CA C sing x.xx
val C O doub x.xx
val CB CA sing x.xx
val CB CG1 sing x.xx
val CB CG2 sing x.xx
;
save_entity_mon_bond.atom_id_1.
_item_description.description
;
The id of the first of the two atoms that define the bond.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
_item_dependent.dependent_name '_entity_mon_bond.atom_id_2'
save_entity_mon_bond.atom_id_2.
_item_description.description
;
The id of the second of the two atoms that define the bond.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
_item_dependent.dependent_name '_entity_mon_bond.atom_id_1'
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_mon_bond.value_dist.
_item_description.description
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_item.name '_entity_mon_bond.value_dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_entity_mon_bond.value_dist_esd.
_item_description.description ; The estimated standard deviation of _entity_mon_bond.value_dist. ; _item.name '_entity_mon_bond.value_dist_esd' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'angstroms'
save_entity_mon_bond.value_order.
_item_description.description
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
;
_item.name '_entity_mon_bond.value_order'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value sing
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
sing
'single bond'
doub
'double bond'
trip
'triple bond'
quad
'quadruple bond'
arom
'aromatic bond'
poly
'polymeric bond'
delo
'delocalised double bond'
pi
'pi bond'
_category.description
;
Data items in the ENTITY_MON_CHIR category provide detail about
the chiral centers in a monomer entity. The atoms bonded to
the chiral atom are specified in the ENTITY_MON_CHIR_ATOM
category.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_chir.mon_id'
'_entity_mon_chir.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_chir.mon_id
_entity_mon_chir.id
_entity_mon_chir.atom_id
phe phe1 CA
val val1 CA
# - - - - data truncated for brevity - - - -
;
_item_description.description
;
The id of the atom that is a chiral center.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
_item_description.description
;
The value of _entity_mon_chir.id must uniquely identify a record
in the ENTITY_MON_CHIR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_chir.id'
entity_mon_chir
yes
'_entity_mon_chir_atom.chir_id'
entity_mon_chir_atom
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_mon_chir_atom.chir_id'
'_entity_mon_chir.id'
_item_type.code char
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_mon_chir.number_atoms_all.
_item_description.description
;
The total number of atoms bonded to the atom specified by
_entity_mon_chir.atom_id.
;
_item.name '_entity_mon_chir.number_atoms_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_entity_mon_chir.number_atoms_nh.
_item_description.description
;
The number of non-hydrogen atoms bonded to the atom specified by
_entity_mon_chir.atom_id.
;
_item.name '_entity_mon_chir.number_atoms_nh'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_entity_mon_chir.volume_flag.
_item_description.description
;
A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
;
_item.name '_entity_mon_chir.volume_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
sign
'match magnitude and sign'
nosign
'match magnitude only'
save_entity_mon_chir.volume_three.
_item_description.description
;
The chiral volume Vc, for chiral centers that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
Vc = V1 * [ V2 X V3 ]
V1, V2 and V3 are vector distances from _entity_mon_chir.atom_id
V1 is the distance to the first atom tin the ENTITY_MON_CHIR_ATOM
list, V1 the distance to the second, and V3 the distance to the
third. * indicates the vector dot product, and X indicate the
vector cross product.
;
_item.name '_entity_mon_chir.volume_three'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms_cubed'
save_entity_mon_chir.volume_three_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_chir.volume_three.
;
_item.name '_entity_mon_chir.volume_three_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms_cubed'
_category.description
;
Data items in the ENTITY_MON_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom within a monomer entity.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_chir_atom.chir_id'
'_entity_mon_chir_atom.atom_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_chir_atom.chir_id
_entity_mon_chir_atom.atom_id
phe1 N
phe1 C
phe1 CB
val1 N
val1 C
val1 CB
# - - - - data truncated for brevity - - - -
;
save_entity_mon_chir_atom.atom_id.
_item_description.description
;
The id of an atom bonded to the chiral atom.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
save_entity_mon_chir_atom.chir_id.
_item_description.description
;
This data item is a pointer to _entity_mon_chir.id in the
ENTITY_MON_CHIR category.
;
save_entity_mon_chir_atom.dev.
_item_description.description
;
The estimated standard deviation of the position of this atom
from the plane defined by all of the atoms in the plane.
;
_item.name '_entity_mon_chir_atom.dev'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms'
_category.description
;
Data items in the ENTITY_MON_PLANE category provide identifiers
for the planes in a monomer entity. The atoms in the plane are
specified in the ENTITY_MON_PLANE_ATOM category.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_plane.mon_id'
'_entity_mon_plane.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_plane.mon_id
_entity_mon_plane.id
phe phe1
;
_item_description.description
;
The value of _entity_mon_plane.id must uniquely identify a record
in the ENTITY_MON_PLANE list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_plane.id'
entity_mon_plane
yes
'_entity_mon_plane_atom.plane_id'
entity_mon_plane_atom
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_mon_plane_atom.plane_id'
'_entity_mon_plane.id'
_item_type.code char
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_mon_plane.number_atoms_all.
_item_description.description ; The total number of atoms in the plane. ; _item.name '_entity_mon_plane.number_atoms_all' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_entity_mon_plane.number_atoms_nh.
_item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_entity_mon_plane.number_atoms_all_nh' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
_category.description
;
Data items in the ENTITY_MON_PLANE_ATOM category enumerate the
atoms in a plane within a monomer entity.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_plane_atom.plane_id'
'_entity_mon_plane_atom.atom_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_plane_atom.plane_id
_entity_mon_plane_atom.atom_id
phe1 CB
phe1 CG
phe1 CD1
phe1 CE1
phe1 CZ
phe1 CE2
phe1 CD2
;
save_entity_mon_plane_atom.atom_id.
_item_description.description
;
The id of an atom involved in the plane.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
save_entity_mon_plane_atom.plane_id.
_item_description.description
;
This data item is a pointer to _entity_mon_plane.id in the
ENTITY_MON_PLANE category.
;
_category.description
;
Data items in the ENTITY_MON_TOR category record details about
the torsion angles in a monomer entity. As torsion angles can
have more than one target value, the target values are specified
in the ENTITY_MON_TOR_VALUE category.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_mon_tor.mon_id'
'_entity_mon_tor.id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_tor.mon_id
_entity_mon_tor.id
_entity_mon_tor.atom_id_1
_entity_mon_tor.atom_id_2
_entity_mon_tor.atom_id_3
_entity_mon_tor.atom_id_4
phe phe_chi1 N CA CB CG
phe phe_chi2 CA CB CG CD1
phe phe_ring1 CB CG CD1 CE1
phe phe_ring2 CB CG CD2 CE2
phe phe_ring3 CG CD1 CE1 CZ
phe phe_ring4 CD1 CE1 CZ CE2
phe phe_ring5 CE1 CZ CE2 CD2
;
save_entity_mon_tor.atom_id_1.
_item_description.description
;
The id of the first of the four atoms that define the torsion
angle.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
loop_
_item_dependent.dependent_name
'_entity_mon_tor.atom_id_2'
'_entity_mon_tor.atom_id_3'
'_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_2.
_item_description.description
;
The id of the second of the four atoms that define the torsion
angle.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
loop_
_item_dependent.dependent_name
'_entity_mon_tor.atom_id_1'
'_entity_mon_tor.atom_id_3'
'_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_3.
_item_description.description
;
The id of the third of the four atoms that define the torsion
angle.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
loop_
_item_dependent.dependent_name
'_entity_mon_tor.atom_id_1'
'_entity_mon_tor.atom_id_2'
'_entity_mon_tor.atom_id_4'
save_entity_mon_tor.atom_id_4.
_item_description.description
;
The id of the fourth of the four atoms that define the torsion
angle.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
loop_
_item_dependent.dependent_name
'_entity_mon_tor.atom_id_1'
'_entity_mon_tor.atom_id_2'
'_entity_mon_tor.atom_id_3'
_item_description.description
;
The value of _entity_mon_tor.id must uniquely identify a
record in the ENTITY_MON_TOR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_mon_tor.id'
entity_mon_tor
yes
'_entity_mon_tor_value.tor_id'
entity_mon_tor_value
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_mon_tor_value.tor_id'
'_entity_mon_tor.id'
_item_type.code char
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
_category.description
;
Data items in the ENTITY_MON_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
ENTITY_MON_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_mon_tor_value.tor_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_mon_tor_value.tor_id
_entity_mon_tor_value.angle
_entity_mon_tor_value.dist
phe_chi1 -60.0 2.88
phe_chi1 180.0 3.72
phe_chi1 60.0 2.88
phe_chi2 90.0 3.34
phe_chi2 -90.0 3.34
phe_ring1 180.0 3.75
phe_ring2 180.0 3.75
phe_ring3 0.0 2.80
phe_ring4 0.0 2.80
phe_ring5 0.0 2.80
;
save_entity_mon_tor_value.angle.
_item_description.description
;
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
;
_item.name '_entity_mon_tor_value.angle'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum 180.0
_item_range.minimum -180.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'degrees'
save_entity_mon_tor_value.angle_esd.
_item_description.description ; The estimated statard deviation of _entity_mon_tor_value.angle. ; _item.name '_entity_mon_tor_value.angle_esd' _item.category_id _item.category_id _item.mandatory_code yes _item_range.maximum 180.0 _item_range.minimum -180.0 _item_type.code float _item_units.code 'degrees'
save_entity_mon_tor_value.dist.
_item_description.description
;
A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_entity_mon_tor.atom_id_1 and _entity_mon_tor.atom_id_4 in the
referenced record in the ENTITY_MON_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 will yield the same distance as
a 60 degree angle). However the distance specification can be
useful for refinement in situations in which the angle is already
close to the desired value.
;
_item.name '_entity_mon_tor_value.dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_entity_mon_tor_value.dist_esd.
_item_description.description
;
The estimated standard deviation of
_entity_mon_tor_value.dist_esd.
;
_item.name '_entity_mon_tor_value.dist_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_entity_mon_tor_value.tor_id.
_item_description.description
;
This data item is a pointer to _entity_mon_tor.id in the
ENTITY_MON_TOR category.
;
_category.description
;
Data items in the ENTITY_NAME_COM category record the common name
or names associated with the entity. In some case, the entity
name may not be the same as the name of the biological structure.
For instance, hemoglobin alpha chain would be the entity common
name, not hemoglobin.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_name_com.entity_id'
'_entity_name_com.name'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_name_com.entity_id
_entity.name_com.name
1 'HIV-1 protease monomer'
1 'HIV-1 PR monomer'
2 'acetyl-pepstatin'
2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine'
3 'water'
;
save_entity_name_com.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; A common name for the entity. ; _item.name '_entity_name_com.name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'HIV protease monomer' 'hemoglobin alpha chain' '2-fluoro-1,4-dichloro benzene'
_category.description
;
Data items in the ENTITY_NAME_SYS category record the systematic
name or names associated with the entity, and tell which system
was is the source of the systematic name. In some case, the
entity name may not be the same as the name of the biological
structure. For instance, hemoglobin alpha chain would be the
entity common name, not hemoglobin.
;
_category.id _category.id
_category.mandatory_code
_category_key.name _category_key.name
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_name_sys.entity_id
_entity_name_sys.name
1 ECx.x.x.x
2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta'
3 'H(2)0'
;
save_entity_name_sys.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; The systematic name for the entity. ; _item.name '_entity_name_sys.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'x,x,pyranoside' 'EC 2.1.1.1' '2-fluoro-1,4-dichloro benzene'
_item_description.description ; The system used to generate the systematic name of the entity. ; _item.name '_entity_name_sys.system' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'chemical abstracts conventions' 'enzyme convention' 'Sigma catalog'
_category.description ; Data items in the ENTITY_POLY category... ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_poly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.type_details 1 polypeptide(L) no no no . ;
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_poly.nstd_chirality.
_item_description.description
;
A flag to indicate whether or not the polymer contains at least
one monomer unit with chirality different from that specified in
_entity_poly.type.
;
_item.name '_entity_poly.nstd_chirality'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
yes
no
save_entity_poly.nstd_linkage.
_item_description.description
;
A flag to indicate whether or not the polymer contains at least
one monomer-to-monomer linkage different from that implied by
_entity_poly.type.
;
_item.name '_entity_poly.nstd_linkage'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
yes
no
save_entity_poly.nstd_monomer.
_item_description.description
;
A flag to indicate whether or not the polymer contains at least
one monomer that is not considered standard.
;
_item.name '_entity_poly.nstd_monomer'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
yes
no
save_entity_poly.number_of_monomers.
_item_description.description ; The number of monomers in the polymer. ; _item.name '_entity_poly.number_of_monomers' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
_item_description.description ; The type of the polymer. ; _item.name '_entity_poly.type' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_enumeration.value 'polypeptide(D)' 'polypeptide(L)' 'polydeoxyribonucleotide' 'polyribonucleotide' 'polysaccharide(D)' 'polysaccharide(L)' 'other'
save_entity_poly.type_details.
_item_description.description ; A description of special aspects of the polymer type. ; _item.name '_entity_poly.type_details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'monomer Ala 16 is a D-amino acid' ; the oligomer contains alternating RNA and DNA units ;
_category.description
;
Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer id - the
corresponding ATOM_SITE entries should reflect this
heterogeneity.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_poly_seq.entity_id'
'_entity_poly_seq.num'
'_entity_poly_seq.mon_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU
1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU
1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE
1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS
1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP
# - - - - data truncated for brevity - - - -
;
save_entity_poly_seq.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description
;
A flag to indicate whether or not this monomer in the polymer is
heterogeneous in sequence. This would be a rare phenomenon.
;
_item.name '_entity_poly_seq.hetero'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
no
;
the sequence is not heterogenous at this
monomer
;
n
'abbreviation for "no"'
yes
;
the sequence is heterogenous at this
monomer
;
y
'abbreviation for "yes"'
_item_description.description
;
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
_item_description.description
;
The value of _entity_poly_seq.num must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number, and that the sequence
numbers must progress in increasing numerical order.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_poly_seq.num'
entity_poly_seq
yes
'_atom_site.entity_seq_num'
atom_site
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.entity_seq_num'
'_entity_poly_seq.num'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
_item_description.description
;
The value of _entity_poly_seq.num must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number, and that the sequence
numbers must progress in increasing numerical order.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_poly_seq.num'
entity_poly_seq
yes
'_atom_site.entity_seq_num'
atom_site
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.entity_seq_num'
'_entity_poly_seq.num'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
_category.description
;
Data items in the ENTITY_POLY_SEQ_DIF category provide a
mechanism for indicating and annotating differences between the
sequence of the entity reported in the data block and a sequence
referenced in the ENTITY_REFERENCE data items.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_entity_poly_seq_dif.entity_id'
'_entity_poly_seq_dif.seq_num'
'_entity_poly_seq_dif.mon_id'
'_entity_poly_seq_dif.db_code'
'_entity_poly_seq_dif.db_name'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
save_entity_poly_seq_dif.db_mon_id.
_item_description.description
;
The monomer type found at this position in the database entry
indicated by _entity_mon_seq_dif.db_code and
_entity_mon_sequ_dif.db_name.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_poly_seq_dif.details.
_item_description.description
;
A description of special aspects of the difference between the
sequence reported in the database and the sequence reported in
this data block.
;
_item.name '_entity_poly_seq_dif.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'strain difference'
'potential sequencing error'
save_entity_poly_seq_dif.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_poly_seq_dif.mon_id.
_item_description.description
;
The monomer type found at this position in the entity described
in this data block.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_entity_poly_seq_dif.seq_num.
_item_description.description
;
This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_category.description ; Data items in the ENTITY_REFERENCE category... ; _category.id _category.id _category.mandatory_code no _category_key.name '_entity_reference.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - example is completely hypothetical ; ; loop_ _entity_reference.entity_id _entity_reference.database_name _entity_reference.database_code _entity_reference.details 1 'Genbank' '12345' ; The strain of HIV-1 protease used in this study contains Asn at position 37. The Genbank sequence cited here has Ser at that position. ; 2 'PDB' '1ABC' ; The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rizopuspepsin ; ;
save_entity_reference.database_code.
_item_description.description
;
The code for this entity or a closely related entity in the
named database. If this is a sequence database and there are
difference between the database sequence and the structure
reported in this data block, those difference may be indicated
and annotated using the ENTITY_POLY_SEQ_DIF data items.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_reference.database_code'
entity_reference
yes
'_entity_poly_seq_dif.db_code'
entity_poly_seq_dif
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_poly_seq_dif.db_code'
'_entity_reference.database_code'
_item_type.code char
loop_
_item_examples.case
'1ABC'
'ABCDEF'
save_entity_reference.database_code.
_item_description.description
;
The code for this entity or a closely related entity in the
named database. If this is a sequence database and there are
difference between the database sequence and the structure
reported in this data block, those difference may be indicated
and annotated using the ENTITY_POLY_SEQ_DIF data items.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_reference.database_code'
entity_reference
yes
'_entity_poly_seq_dif.db_code'
entity_poly_seq_dif
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_poly_seq_dif.db_code'
'_entity_reference.database_code'
_item_type.code char
loop_
_item_examples.case
'1ABC'
'ABCDEF'
save_entity_reference.database_name.
_item_description.description
;
The name of the database containing reference information about
this entity.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_reference.database_name'
entity_reference
yes
'_entity_poly_seq_dif.db_name'
entity_poly_seq_dif
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_poly_seq_dif.db_name'
'_entity_reference.database_name'
_item_type.code char
loop_
_item_examples.case
'PDB'
'CSD'
'Genbank'
save_entity_reference.database_name.
_item_description.description
;
The name of the database containing reference information about
this entity.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_reference.database_name'
entity_reference
yes
'_entity_poly_seq_dif.db_name'
entity_poly_seq_dif
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_entity_poly_seq_dif.db_name'
'_entity_reference.database_name'
_item_type.code char
loop_
_item_examples.case
'PDB'
'CSD'
'Genbank'
save_entity_reference.details.
_item_description.description
;
A description of special aspects of the relationship between
the entity as observed in this structure and the entity as it
appears in the named database.
;
_item.name '_entity_reference.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_entity_reference.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_category.description
;
Data items in the ENTITY_SRC_GEN category records details of
the source from which the entity was obtained, in those cases
where the source was a genetically manipulated one. The
following are treated separately: Items pertaining to the tissue
from which the gene was obtained, items pertaining to the host
organism for gene expression and items pertaining to the actual
producting organism (plasmid).
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_src_gen.entity_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_src_gen.entity_id
_entity_src_gen.gene_src_common_name
_entity_src_gen.gene_src_genus
_entity_src_gen.gene_src_species
_entity_src_gen.gene_src_strain
_entity_src_gen.host_org_common_name
_entity_src_gen.host_org_genus
_entity_src_gen.host_org_species
_entity_src_gen.plasmid_name
1 'HIV-1' '?' '?' 'NY-5'
'bacteria' 'Escherichia' 'coli' 'pB322'
;
save_entity_src_gen.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
save_entity_src_gen.gene_src_common_name.
_item_description.description
;
The common name of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_common_name'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'man'
'yeast'
'bacteria'
save_entity_src_gen.gene_src_details.
_item_description.description
;
A description of special aspects of the natural organism from
which the gene was obtained.
;
_item.name '_entity_src_gen.gene_src_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_entity_src_gen.gene_src_genus.
_item_description.description
;
The genus of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_genus'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Homo'
'Saccharomyces'
'Escherichia'
save_entity_src_gen.gene_src_species.
_item_description.description
;
The species of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_species'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'sapiens'
'cerevisiae'
'coli'
save_entity_src_gen.gene_src_strain.
_item_description.description
;
The strain of the natural organism from which the gene was
obtained, if relevant.
;
_item.name '_entity_src_gen.gene_src_strain'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'DH5a'
'BMH 71-18'
save_entity_src_gen.gene_src_tissue.
_item_description.description
;
The tissue of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_tissue'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'heart'
'liver'
'eye lens'
save_entity_src_gen.gene_src_tissue_fraction.
_item_description.description
;
The sub-cellular fraction of the tissue of the natural organism
from which the gene was obtained.
;
_item.name '_entity_src_gen.gene_src_tissue_fraction'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'mitochondria'
'nucleus'
'membrane'
save_entity_src_gen.host_org_common_name.
_item_description.description
;
The common name of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_common_name'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'yeast'
'bacteria'
save_entity_src_gen.host_org_details.
_item_description.description
;
A description of special aspects of the organism that served as
host for the production of the entity.
;
_item.name '_entity_src_gen.host_org_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_entity_src_gen.host_org_genus.
_item_description.description
;
The genus of the organism that served as host for the production
of the entity.
;
_item.name '_entity_src_gen.host_org_genus'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Saccharomyces'
'Escherichia'
save_entity_src_gen.host_org_species.
_item_description.description
;
The species of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_species'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'cerevisiae'
'coli'
save_entity_src_gen.host_org_strain.
_item_description.description
;
The strain of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_strain'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'DH5a'
'BMH 71-18'
save_entity_src_gen.plasmid_details.
_item_description.description
;
A description of special aspects of the plasmid that produced the
entity in the host organism.
;
_item.name '_entity_src_gen.plasmid_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_entity_src_gen.plasmid_name.
_item_description.description
;
The name of the plasmid that produced the entity in the host
organism.
;
_item.name '_entity_src_gen.plasmid_name'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'pET3C'
'pT123sab'
_category.description
;
Data items in the ENTITY_SRC_NAT category records details of
the source from which the entity was obtained, in those cases
where the entity was isolated directly from a natural tissue.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_entity_src_nat.entity_id'
loop_
_category_group.id
'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_entity_src_nat.entity_id
_entity_src_nat.common_name
_entity_src_nat.genus
_entity_src_nat.species
_entity_src_nat.details
2 'bacteria' 'Actinomycetes' '?'
; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture
University, and provided to us by Dr. Ben Dunn, University of Florida,
and Dr. J. Kay, University of Wales.
;
;
save_entity_src_nat.common_name.
_item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.common_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'man' 'yeast' 'bacteria'
_item_description.description
;
A description of special aspects of the organism from which the
entity was isolated.
;
_item.name '_entity_src_nat.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
save_entity_src_nat.entity_id.
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.genus' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia'
_item_description.description ; The species of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.species' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli'
_item_description.description ; The strain of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.strain' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'DH5a' 'BMH 71-18'
_item_description.description ; The tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'heart' 'liver' 'eye lens'
save_entity_src_nat.tissue_fraction.
_item_description.description
;
The sub-cellular fraction of the tissue of the organism from
which the entity was isolated.
;
_item.name '_entity_src_nat.tissue_fraction'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'mitochondria'
'nucleus'
'membrane'
_category.description
;
Data items in the EXPTL category record details about the
growth of the crystal, and about experimental measurements on
the crystal, such as shape, size, density, and so on.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_exptl.block_id'
loop_
_category_group.id
'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_exptl.absorpt_coefficient_mu 0.59
_exptl.absorpt_correction_type 'shelx76 gaussian'
_exptl.absorpt_correction_T_min .933
_exptl.absorpt_correction_T_max .824
;
save_exptl.absorpt_coefficient_mu.
_item_description.description
;
The absorption coefficient mu calculated from atomic content of
the cell, the density and the radiation wavelength.
;
_item.name '_exptl.absorpt_coefficient_mu'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_coefficient_mu'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'reciprocal_millimetres'
save_exptl.absorpt_correction_T_max.
_item_description.description
;
The maximum transmission factors for the crystal and radiation.
These factors are also referred to as the absorption correction
A or 1/A*.
;
_item.name '_exptl.absorpt_correction_T_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_correction_T_max'
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
save_exptl.absorpt_correction_T_min.
_item_description.description
;
The minimum transmission factors for the crystal and radiation.
These factors are also referred to as the absorption correction
A or 1/A*.
;
_item.name '_exptl.absorpt_correction_T_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_correction_T_min'
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
save_exptl.absorpt_correction_type.
_item_description.description ; The absorption correction type and method. ; _item.name '_exptl.absorpt_correction_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_type' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail analytical 'analytical from crystal shape' integration 'integration from crystal shape' empirical 'empirical from diffraction data' refdelf 'refined from delta-F' sphere 'spherical' cylinder 'cylindrical' none 'no absorption correction applied'
save_exptl.absorpt_process_details.
_item_description.description ; Description of the absorption process applied to the data. ; _item.name '_exptl.absorpt_process_details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_process_details' _item_type.code char _item_examples.case 'Tompa analytical'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The total number of crystals used in the data measurement. ; _item.name '_exptl.crystals_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystals_number' _item_range.maximum ? _item_range.minimum 1 _item_type.code int
_item_description.description
;
Any special information about the experimental work prior to the
diffraction measurement. See also _exptl.crystal_preparation.
;
_item.name '_exptl.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_special_details'
_item_type.code char
_category.description
;
Data items in the EXPTL_CRYSTAL category record details about
experimental measurements on the crystal or crystals used,
such as shape, size, density, and so on.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_exptl_crystal.id'
loop_
_category_group.id
'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_exptl_crystal.description prism
_exptl_crystal.colour colourless
_exptl_crystal.size_max 0.32
_exptl_crystal.size_mid 0.27
_exptl_crystal.size_min 0.10
_exptl_crystal.density_diffrn 1.146
_exptl_crystal.density_meas ?
_exptl_crystal.F_000 656
;
_item_description.description ; The colour of the crystal. ; _item.name '_exptl_crystal.colour' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_colour' _item_type.code char _item_examples.case 'Dark green'
save_exptl_crystal.density_diffrn.
_item_description.description
;
Density values calculated from crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
;
_item.name '_exptl_crystal.density_diffrn'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_density_diffrn'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_exptl_crystal.density_meas.
_item_description.description
;
Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
_item.name '_exptl_crystal.density_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_density_meas'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_exptl_crystal.density_meas_temp.
_item_description.description
;
Temperature in degrees Kelvin at which
_exptl_crystal.density_meas was determined.
;
_item.name '_exptl_crystal.density_meas_temp'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_density_meas_temp'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'kelvin'
save_exptl_crystal.density_method.
_item_description.description ; The method used to measure _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_method' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_method' _item_type.code char
save_exptl_crystal.density_percent_sol.
_item_description.description
;
Density value calculated from crystal cell and contents,
expressed as percent solvent.
P = 1 - (1.23 * N * Mmass) / V
where N is the number of molecules in the unit cell
Mmass is the molecular mass of each molecule (gm/mole)
V is the volume of the unit cell (A^3)
and 1.23 is the product of:
(0.74 cm^3/gm^3) * (10^24 A^3/cm^3) / (6.02*10^23) moles/molecule
where 0.74 is an assumed value for the partial specific volume
of the molecule
;
_item.name '_exptl_crystal.density_percent_sol'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_exptl_crystal.description.
_item_description.description
;
A description of the crystal quality and habit. Dimensional data
is better placed in the _exptl_crystal.face_ data items.
;
_item.name '_exptl_crystal.description'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_description'
_item_type.code char
_item_description.description
;
The effective number of electrons in the crystal unit cell
contributing to F(000). It may contain dispersion contributions.
;
_item.name '_exptl_crystal.F_000'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_F_000'
_item_range.maximum ?
_item_range.minimum 1
_item_type.code int
_item_description.description
;
The value of _exptl_crystal.id must uniquely identify a record in
the EXPTL_CRYSTAL list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_exptl_crystal.id'
exptl_crystal
yes
'_exptl_crystal_grow.crystal_id'
exptl_crystal
yes
'_diffrn_refln.crystal_id'
diffrn_refln
yes
'_refln.crystal_id'
refln
yes
_item_aliases.alias_name '_exptl_crystal_id'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.crystal_id'
'_exptl_crystal.id'
'_exptl_crystal_grow.crystal_id'
'_exptl_crystal.id'
'_refln.crystal_id'
'_exptl_crystal.id'
_item_type.code char
_item_description.description
;
The value of _exptl_crystal.id must uniquely identify a record in
the EXPTL_CRYSTAL list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_exptl_crystal.id'
exptl_crystal
yes
'_exptl_crystal_grow.crystal_id'
exptl_crystal
yes
'_diffrn_refln.crystal_id'
diffrn_refln
yes
'_refln.crystal_id'
refln
yes
_item_aliases.alias_name '_exptl_crystal_id'
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.crystal_id'
'_exptl_crystal.id'
'_exptl_crystal_grow.crystal_id'
'_exptl_crystal.id'
'_refln.crystal_id'
'_exptl_crystal.id'
_item_type.code char
save_exptl_crystal.preparation.
_item_description.description
;
Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the diffraction measurements.
;
_item.name '_exptl_crystal.preparation'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_preparation'
_item_type.code char
_item_examples.case 'mounted in an argon-filled quartz capillary'
_item_description.description
;
The maximum dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals used in the
experiment.
;
_item.name '_exptl_crystal.size_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_max'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
_item_description.description
;
The medial dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals used in the
experiment.
;
_item.name '_exptl_crystal.size_mid'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_mid'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
_item_description.description
;
The minimum dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals used in the
experiment.
;
_item.name '_exptl_crystal.size_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_min'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
_item_description.description
;
The radius of the crystal, If the crystal is a sphere or a
cylinder. This item may appear in a list with _exptl_crystal.id
if multiple crystals used in the experiment.
;
_item.name '_exptl_crystal.size_rad'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_rad'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
_category.description
;
Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_k'
'_exptl_crystal_face.index_l'
loop_
_category_group.id
'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on
;
;
Need Example 2
;
save_exptl_crystal_face.diffr_chi.
_item_description.description
;
The chi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_chi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_chi'
_item_type.code float
_item_units.code 'degrees'
save_exptl_crystal_face.diffr_kappa.
_item_description.description
;
The kappa diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_kappa'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_kappa'
_item_type.code float
_item_units.code 'degrees'
save_exptl_crystal_face.diffr_phi.
_item_description.description
;
The phi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_phi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_phi'
_item_type.code float
_item_units.code 'degrees'
save_exptl_crystal_face.diffr_psi.
_item_description.description
;
The psi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_psi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_psi'
_item_type.code float
_item_units.code 'degrees'
save_exptl_crystal_face.index_h.
_item_description.description
;
Miller index h of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_exptl_crystal_face_index_h'
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_k'
'_exptl_crystal_face.index_l'
_item_type.code int
save_exptl_crystal_face.index_k.
_item_description.description
;
Miller index k of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_exptl_crystal_face_index_k'
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_l'
_item_type.code int
save_exptl_crystal_face.index_l.
_item_description.description
;
Miller index l of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_exptl_crystal_face_index_l'
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_k'
_item_type.code int
save_exptl_crystal_face.perp_dist.
_item_description.description
;
The perpendicular distance of the face to centre of rotation of
the crystal.
;
_item.name '_exptl_crystal_face.perp_dist'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_perp_dist'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'millimetres'
_category.description
;
Data items in the EXPTL_CRYSTAL_GROW category record details
about the conditions and methods used to grow the crystal.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_exptl_crystal_grow.crystal_id'
loop_
_category_group.id
'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'hanging drop'
_exptl_crystal_grow.apparatus 'Linbro plates'
_exptl_crystal_grow.atmosphere 'room air'
_exptl_crystal_grow.pH 4.7
_exptl_crystal_grow.temp 18(3)
_exptl_crystal_grow.time 'approximately 2 days'
;
save_exptl_crystal_grow.apparatus.
_item_description.description ; The physical apparatus in which the crystal was grown. ; _item.name '_exptl_crystal_grow.apparatus' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'Linbro plate' 'sandwich box' 'ACA plates'
save_exptl_crystal_grow.atmosphere.
_item_description.description
;
The nature of the gas or gas mixture in which the crystal was
grown.
;
_item.name '_exptl_crystal_grow.atmosphere'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'room air'
'nitrogen'
'argon'
save_exptl_crystal_grow.crystal_id.
_item_description.description
;
This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
save_exptl_crystal_grow.details.
_item_description.description ; A description of special aspects of the crystal growth. ; _item.name '_exptl_crystal_grow.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. ; ; Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. ; ; The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. ;
save_exptl_crystal_grow.method.
_item_description.description ; The method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'batch precipitation' 'batch dialysis' 'hanging drop vapor diffusion' 'sitting drop vapor diffusion'
save_exptl_crystal_grow.method_ref.
_item_description.description
;
A literature reference that describes the method used to grow
the crystals.
;
_item.name '_exptl_crystal_grow.method_ref'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'McPherson et al., 1988'
_item_description.description
;
The pH at which the crystal was grown. If more than one pH was
employed during the crystallization process, the final pH should
be noted here and the protocol involving multiple pH values
should be described in _exptl_crystal_grow.details.
;
_item.name '_exptl_crystal_grow.pH'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
loop_
_item_examples.case
7.4
7.6
4.3
save_exptl_crystal_grow.pressure.
_item_description.description
;
The ambient pressure in kilopascals at which the crystal was
grown.
;
_item.name '_exptl_crystal_grow.pressure'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kilopascals'
save_exptl_crystal_grow.pressure_esd.
_item_description.description ; The estimated standard deviation of _exptl_crystal_grow.pressure. ; _item.name '_exptl_crystal_grow.pressure_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kilopascals'
save_exptl_crystal_grow.seeding.
_item_description.description
;
A description of the protocol used for seeding the crystal
growth.
;
_item.name '_exptl_crystal_grow.seeding'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'macroseeding'
;
Microcrystals were introduced from a previous
crystal growth experiment by transfer with a
human hair.
;
save_exptl_crystal_grow.seeding_ref.
_item_description.description
;
A literature reference that describes the protocol used to seed
the crystal.
;
_item.name '_exptl_crystal_grow.seeding_ref'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'Stura et al., 19xx'
_item_description.description
;
The temperature in degress Kelvin at which the crystal was grown.
If more than one temperature was employed during the
crystallization process, the final temperature should be noted
here and the protocol involving multiple temperatures should be
described in _exptl_crystal_grow.details.
;
_item.name '_exptl_crystal_grow.temp'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'kelvin'
save_exptl_crystal_grow.temp_esd.
_item_description.description ; The estimated standard deviation of _exptl_crystal_grow.temp. ; _item.name '_exptl_crystal_grow.temp_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'kelvin'
_item_description.description
;
The approximate time that the crystal took to grow to the size
used for data collection.
;
_item.name '_exptl_crystal_grow.time'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'overnight'
'2-4 days'
'6 months'
_category.description
;
Data items in the EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
(by whatever means) to produce the crystal.
In general, solution 1 will be the solution that contains the
molecule to be crystallized and solution 2 will be the solution
that contains the precipitant. However, the number of solutions
required to describe the crystallization protocol is not limited
to 2.
Details of the crystallization protocol should be described in
EXPTL_CRYSTAL_GROW_DETAILS, using the solutions described in
EXPTL_CRYSTAL_GROW_COMP.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_exptl_crystal_grow_comp.id'
loop_
_category_group.id
'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
_exptl_crystal_grow_comp.volume
_exptl_crystal_grow_comp.conc
_exptl_crystal_grow_comp.details
1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml'
; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/
MES buffer, pH 7.5, 3 mM NaAzide
;
2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide'
3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide'
4 2 'Na Acetate' '0.053 ml' '100 mM'
; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7
according to a ratio calculated from the pKa. The actual pH of solution 2
was not measured.
;
5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide'
;
save_exptl_crystal_grow_comp.conc.
_item_description.description ; The concentration of the solution component. ; _item.name '_exptl_crystal_grow_comp.conc' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '200 \ml' '0.1 ml'
save_exptl_crystal_grow_comp.details.
_item_description.description
;
A description of any special aspects of the solution component.
When the solution component is the one that contains the
macromolecule, this could be the specification of the buffer in
which the macromolecule was stored. When the solution component
is a buffer component, this could be the methods (or formula)
used to achieve a desired pH.
;
_item.name '_exptl_crystal_grow_comp.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'in 3 mM NaAzide'
;
The protein solution was in a buffer
containing 25 mM NaCl, 100 mM NaMES/MES
buffer, pH 7.5, 3 mM NaAzide
;
;
in 3 mM NaAzide. Buffer components were mixed
to produce a pH of 4.7 according to a ratio
calculated from the pKa. The actual pH of
solution 2 was not measured.
;
save_exptl_crystal_grow_comp.id.
_item_description.description
;
The value of _exptl_crystal_grow_comp.id must uniquely identify
each item in the EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_exptl_crystal_grow_comp.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
1
A
'protein in buffer'
save_exptl_crystal_grow_comp.name.
_item_description.description ; A common name for the component of the solution. ; _item.name '_exptl_crystal_grow_comp.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'protein in buffer' 'acetic acid'
save_exptl_crystal_grow_comp.sol_id.
_item_description.description
;
An identifier for the solution to which the given solution
component belongs.
;
_item.name '_exptl_crystal_grow_comp.sol_id'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
1
'well solution'
'solution A'
save_exptl_crystal_grow_comp.volume.
_item_description.description ; The volume of the solution component. ; _item.name '_exptl_crystal_grow_comp.volume' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case '200 \ml' '0.1 ml'
_category.description
;
Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT and GEOM_TORSION) categories
record details about the molecular and crystal geometry, as
calculated from the contents of the ATOM, CELL, and
SYMMETRY data.
Geometry data are therefore redundant, in that they can be
calculated from other more fundamental quantities in the CIF.
They serve, however, the dual purpose of providing a check on
the correctness of both sets of data, and of enabling the most
important geometric data to be identified for publication by
setting the appropriate publication flag.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_geom.block_id'
loop_
_category_group.id
'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
The description of geometrical information not covered by the
existing GEOM data names, such as least-squares planes.
;
_item.name '_geom.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_special_details'
_item_type.code char
_category.description
;
Data items in the GEOM_ANGLE category record details about the
molecular and crystal angles, as calculated from the contents
of the ATOM, CELL, and SYMMETRY data.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_geom_angle.atom_site_label_1'
'_geom_angle.atom_site_label_2'
'_geom_angle.atom_site_label_3'
'_geom_angle.site_symmetry_1'
'_geom_angle.site_symmetry_2'
'_geom_angle.site_symmetry_3'
loop_
_category_group.id
'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_geom_angle.atom_site_label_1
_geom_angle.atom_site_label_2
_geom_angle.atom_site_label_3
_geom_angle.value
_geom_angle.site_symmetry_1
_geom_angle.site_symmetry_2
_geom_angle.site_symmetry_3
_geom_angle.publ_flag
C2 O1 C5 111.6(2) 1_555 1_555 1_555 yes
O1 C2 C3 110.9(2) 1_555 1_555 1_555 yes
O1 C2 O21 122.2(3) 1_555 1_555 1_555 yes
C3 C2 O21 127.0(3) 1_555 1_555 1_555 yes
C2 C3 N4 101.3(2) 1_555 1_555 1_555 yes
C2 C3 C31 111.3(2) 1_555 1_555 1_555 yes
C2 C3 H3 107(1) 1_555 1_555 1_555 ?
N4 C3 C31 116.7(2) 1_555 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
save_geom_angle.atom_site_label_1.
_item_description.description
;
The label of the first of the three atom sites that define the
angle specified by _geom_angle.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_angle_atom_site_label_1'
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_label_2'
'_geom_angle.atom_site_label_3'
save_geom_angle.atom_site_label_2.
_item_description.description
;
The label of the second of the three atom sites that define the
angle specified by _geom_angle. The second atom is taken to be
the apex of the angle.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_angle_atom_site_label_2'
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_label_1'
'_geom_angle.atom_site_label_3'
save_geom_angle.atom_site_label_3.
_item_description.description
;
The label of the third of the three atom sites that define the
angle specified by _geom_angle.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_angle_atom_site_label_3'
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_label_1'
'_geom_angle.atom_site_label_2'
_item_description.description
;
This code signals if the angle is referred to in a publication or
should be placed in a table of significant angles.
;
_item.name '_geom_angle.publ_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle_publ_flag'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
no
'do not include angle in special list'
n
'abbreviation for "no"'
yes
'do include angle in special list'
y
'abbreviation for "yes"'
save_geom_angle.site_symmetry_1.
_item_description.description
;
The symmetry code of the first of the three atom sites that
define the angle specified by _geom_angle.
;
_item.name '_geom_angle.site_symmetry_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle_site_symmetry_1'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_angle.site_symmetry_2.
_item_description.description
;
The symmetry code of the second of the three atom sites that
define the angle specified by _geom_angle.
;
_item.name '_geom_angle.site_symmetry_2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle_site_symmetry_2'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_angle.site_symmetry_3.
_item_description.description
;
The symmetry code of the third of the three atom sites that
define the angle specified by _geom_angle.
;
_item.name '_geom_angle.site_symmetry_3'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle_site_symmetry_3'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_item_description.description
;
Angle in degrees bounded by the _geom_angle.atom_site_label_1,
_geom_angle.atom_site_label__2 and
_geom_angle.atom_site_label__3.
;
_item.name '_geom_angle.value'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _geom_angle.value. ; _item.name '_geom_angle.value_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees'
_category.description
;
Data items in the GEOM_BOND category record details about
molecular and crystal bonds, as calculated from the contents
of the ATOM, CELL, and SYMMETRY data.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_geom_bond.atom_site_label_1'
'_geom_bond.atom_site_label_2'
'_geom_bond.site_symmetry_1'
'_geom_bond.site_symmetry_2'
loop_
_category_group.id
'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_geom_bond.atom_site_label_1
_geom_bond.atom_site_label_2
_geom_bond.distance
_geom_bond.site_symmetry_1
_geom_bond.site_symmetry_2
_geom_bond.publ_flag
O1 C2 1.342(4) 1_555 1_555 yes
O1 C5 1.439(3) 1_555 1_555 yes
C2 C3 1.512(4) 1_555 1_555 yes
C2 O21 1.199(4) 1_555 1_555 yes
C3 N4 1.465(3) 1_555 1_555 yes
C3 C31 1.537(4) 1_555 1_555 yes
C3 H3 1.00(3) 1_555 1_555 ?
N4 C5 1.472(3) 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
save_geom_bond.atom_site_label_1.
_item_description.description
;
The label of the first of the two atom sites that define the
bond specified by _geom_bond.distance.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_bond_atom_site_label_1'
_item_dependent.dependent_name '_geom_bond.atom_site_label_2'
save_geom_bond.atom_site_label_2.
_item_description.description
;
The label of the second of the two atom sites that define the
bond specified by _geom_bond.distance.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_bond_atom_site_label_2'
_item_dependent.dependent_name '_geom_bond.atom_site_label_1'
_item_description.description ; The intramolecular bond distance. ; _item.name '_geom_bond.distance' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_bond_distance' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_type_conditions.code esd _item_units.code 'angstroms'
_item_description.description ; The estimated standard deviation of _geom_bond.distance. ; _item.name '_geom_bond.distance_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
Signals if the bond distance is referred to in a publication
or should be placed in a list of special bond distances.
;
_item.name '_geom_bond.publ_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_bond_publ_flag'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
no
'do not include bond in special list'
n
'abbreviation for "no"'
yes
'do include bond in special list'
y
'abbreviation for "yes"'
save_geom_bond.site_symmetry_1.
_item_description.description
;
The symmetry code of the first of the two atom sites that
define the bond specified by _geom_bond.distance.
;
_item.name '_geom_bond.site_symmetry_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_bond_site_symmetry_1'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_bond.site_symmetry_2.
_item_description.description
;
The symmetry code of the second of the two atom sites that
define the bond specified by _geom_bond.distance.
;
_item.name '_geom_bond.site_symmetry_2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_bond_site_symmetry_2'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_category.description
;
Data items in the GEOM_CONTACT category record details about
molecular and crystal contacts, as calculated from the contents
of the ATOM, CELL, and SYMMETRY data.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_geom_contact.atom_site_label_1'
'_geom_contact.atom_site_label_2'
'_geom_contact.site_symmetry_1'
'_geom_contact.site_symmetry_2'
loop_
_category_group.id
'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
(1991). Acta Cryst. C48, 2262-2264].
;
;
loop_
_geom_contact.atom_site_label_1
_geom_contact.atom_site_label_2
_geom_contact.distance
_geom_contact.site_symmetry_1
_geom_contact.site_symmetry_2
_geom_contact.publ_flag
O(1) O(2) 2.735(3) . . yes
H(O1) O(2) 1.82 . . no
;
save_geom_contact.atom_site_label_1.
_item_description.description
;
The label of the first of the two atom sites that define the
contact specified by _geom_contact.distance.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_contact_atom_site_label_1'
_item_dependent.dependent_name '_geom_contact.atom_site_label_2'
save_geom_contact.atom_site_label_2.
_item_description.description
;
The label of the second of the two atom sites that define the
contact specified by _geom_contact.distance.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_contact_atom_site_label_2'
_item_dependent.dependent_name '_geom_contact.atom_site_label_1'
_item_description.description ; The estimated standard deviation of _geom_contact.distance. ; _item.name '_geom_contact.distance' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
Signals if the contact distance is referred to in a publication
or should be placed in a list of special contact distances.
;
_item.name '_geom_contact.publ_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_contact_publ_flag'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
no
'do not include distance in special list'
n
'abbreviation for "no"'
yes
'do include distance in special list'
y
'abbreviation for "yes"'
save_geom_contact.site_symmetry_1.
_item_description.description
;
The symmetry code of the first of the two atom sites that
define the contact specified by _geom_contact.distance.
;
_item.name '_geom_contact.site_symmetry_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_contact_site_symmetry_1'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_contact.site_symmetry_2.
_item_description.description
;
The symmetry code of the second of the two atom sites that
define the contact specified by _geom_contact.distance.
;
_item.name '_geom_contact.site_symmetry_2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_contact_site_symmetry_2'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_category.description
;
Data items in the GEOM_TORSION category record details about
molecular and crystal torsion angles, as calculated from the
contents of the ATOM, CELL, and SYMMETRY data.
The torsion angle definition should be that of Klyne, W. and
Prelog, V. (1960). Endeavour, 16, 521-528. The vector direction
_geom_torsion.atom_site_label_2 to
_geom_torsion.atom_site_label_3 is the viewing direction, and the
torsion angle is the angle of twist required to superimpose the
projection of the vector site2-site1 onto the projection of the
vector site3-site4. Clockwise torsions are positive,
anticlockwise torsions are negative.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_geom_torsion.atom_site_label_1'
'_geom_torsion.atom_site_label_2'
'_geom_torsion.atom_site_label_3'
'_geom_torsion.atom_site_label_4'
'_geom_torsion.site_symmetry_1'
'_geom_torsion.site_symmetry_2'
'_geom_torsion.site_symmetry_3'
'_geom_torsion.site_symmetry_4'
loop_
_category_group.id
'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[(1991). Acta Cryst. C48, 2262-2264].
;
;
loop_
_geom_torsion.atom_site_label_1
_geom_torsion.atom_site_label_2
_geom_torsion.atom_site_label_3
_geom_torsion.atom_site_label_4
_geom_torsion
_geom_torsion.site_symmetry_1
_geom_torsion.site_symmetry_2
_geom_torsion.site_symmetry_3
_geom_torsion.site_symmetry_4
_geom_torsion.publ_flag
C(9) O(2) C(7) C(2) 71.8(2) . . . . yes
C(7) O(2) C(9) C(10) -168.0(3) . . . 2_666 yes
C(10) O(3) C(8) C(6) -167.7(3) . . . . yes
C(8) O(3) C(10) C(9) -69.7(2) . . . 2_666 yes
O(1) C(1) C(2) C(3) -179.5(4) . . . . no
O(1) C(1) C(2) C(7) -0.6(1) . . . . no
;
save_geom_torsion.atom_site_label_1.
_item_description.description
;
The label of the first of the four atom sites that define the
torsion angle specified by _geom_torsion.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_torsion_atom_site_label_1'
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_label_2'
'_geom_torsion.atom_site_label_3'
'_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_2.
_item_description.description
;
The label of the second of the four atom sites that define the
torsion angle specified by _geom_torsion.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_torsion_atom_site_label_2'
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_label_1'
'_geom_torsion.atom_site_label_3'
'_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_3.
_item_description.description
;
The label of the third of the four atom sites that define the
torsion angle specified by _geom_torsion.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_torsion_atom_site_label_3'
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_label_1'
'_geom_torsion.atom_site_label_2'
'_geom_torsion.atom_site_label_4'
save_geom_torsion.atom_site_label_4.
_item_description.description
;
The label of the fourth of the four atom sites that define the
torsion angle specified by _geom_torsion.
This data item is a pointer to _atom_site.label in the ATOM_SITE
category.
;
_item_aliases.alias_name '_geom_torsion_atom_site_label_4'
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_label_1'
'_geom_torsion.atom_site_label_2'
'_geom_torsion.atom_site_label_3'
_item_description.description
;
This code signals if the angle is referred to in a publication or
should be placed in a table of significant angles.
;
_item.name '_geom_torsion.publ_flag'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_torsion_publ_flag'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
no
'do not include angle in special list'
n
'abbreviation for "no"'
yes
'do include angle in special list'
y
'abbreviation for "yes"'
save_geom_torsion.site_symmetry_1.
_item_description.description
;
The symmetry code of the first of the four atom sites that
define the torsion angle specified by _geom_torsion.
;
_item.name '_geom_torsion.site_symmetry_1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_torsion_site_symmetry_1'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_2.
_item_description.description
;
The symmetry code of the second of the four atom sites that
define the torsion angle specified by _geom_torsion.
;
_item.name '_geom_torsion.site_symmetry_2'
_item.category_id _item.category_id
_item_aliases.alias_name '_geom_torsion_site_symmetry_2'
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_3.
_item_description.description
;
The symmetry code of the third of the four atom sites that
define the torsion specified by _geom_torsion.
;
_item.name '_geom_torsion.site_symmetry_3'
_item.category_id _item.category_id
_item_aliases.alias_name '_geom_torsion_site_symmetry_3'
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_geom_torsion.site_symmetry_4.
_item_description.description
;
The symmetry code of the fourth of the four atom sites that
define the torsion angle specified by _geom_torsion.
;
_item.name '_geom_torsion.site_symmetry_4'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_geom_torsion_site_symmetry_4'
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_item_description.description ; The value of the torsion angle in degrees. ; _item.name '_geom_torsion.value' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_geom_torsion' _item_type.code float _item_type_conditions.code esd _item_units.code 'degrees'
_item_description.description ; The estimated standard deviation of _geom_torsion.value. ; _item.name '_geom_torsion.value_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'degrees'
_category.description
;
Data items in the JOURNAL category record details about the
book keeping entries used by the journal's staff when processing
a CIF submitted for publication.
Normally the creator of a CIF will not specify these data. The
data names are not defined in the dictionary because they are
for journal use only.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_journal.block_id'
loop_
_category_group.id
'inclusive_group'
'journal_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on Acta Cryst. file for entry HL0007 of Willis, Beckwith
& Tozer [(1991). Acta Cryst. C47, 2276-2277].
;
;
_journal.date_recd_electronic 91-04-15
_journal.date_from_coeditor 91-04-18
_journal.date_accepted 91-04-18
_journal.date_printers_first 91-08-07
_journal.date_proofs_out 91-08-07
_journal.coeditor_code HL0007
_journal.techeditor_code C910963
_journal.coden_ASTM ACSCEE
_journal.name_full 'Acta Crystallographica, Section C'
_journal.year 1991
_journal.volume 47
_journal.issue NOV91
_journal.page_first 2276
_journal.page_last 2277
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_ASTM' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coden_ASTM' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_Cambridge' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coden_Cambridge' _item_type.code char
save_journal.coeditor_address.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_address' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_address' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_code' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_code' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_email' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_fax' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_fax' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_name' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_notes' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_notes' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_phone' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_phone' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_accepted' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_accepted' _item_type.code char
save_journal.date_from_coeditor.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_from_coeditor' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_from_coeditor' _item_type.code char
save_journal.date_printers_final.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_final' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_final' _item_type.code char
save_journal.date_printers_first.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_first' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_first' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_in' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_in' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_out' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_out' _item_type.code char
save_journal.date_recd_copyright.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_copyright' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_copyright' _item_type.code char
save_journal.date_recd_electronic.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_electronic' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_electronic' _item_type.code char
save_journal.date_recd_hard_copy.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_hard_copy' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_hard_copy' _item_type.code char
save_journal.date_to_coeditor.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_to_coeditor' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_date_to_coeditor' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.issue' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_issue' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.name_full' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_name_full' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_first' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_page_first' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_last' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_page_last' _item_type.code char
save_journal.suppl_publ_number.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_number' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_number' _item_type.code char
save_journal.suppl_publ_pages.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_pages' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_pages' _item_type.code char
save_journal.techeditor_address.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_address' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_address' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_code' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_code' _item_type.code char
save_journal.techeditor_email.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_email' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_fax' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_fax' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_name' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_name' _item_type.code char
save_journal.techeditor_notes.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_notes' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_notes' _item_type.code char
save_journal.techeditor_phone.
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_phone' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_phone' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.volume' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_volume' _item_type.code char
_item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.year' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_journal_year' _item_type.code char
_category.description
;
Data items in the PHASING category record details about the
phasing of the structure, listing the various methods used in
the phasing process. The details about application of each
method are listed in the appropriate subcategories.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing.method'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - example is completely hypothetical
;
;
loop_
_phasing.method
'MIR'
'averaging'
;
_item_description.description
;
A listing of the method or methods applied to phase this
structure.
;
_item.name '_phasing.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
'averaging'
;
phase improvement by averaging over multiple
images of the structure
;
'isomorphous'
;
phasing begining with phases calculated from a
isomorphous structure
;
'MAD'
;
phasing by multiple-wavelength anomalous
dispersion
;
'MIR'
;
phasing by multiple isomorphous replacement
;
'MR'
;
phasing by molecular replacement
;
_category.description
;
Data items in the PHASING_AVERAGING category record details
about the phasing of the structure, when methods involving
averaging of multiple observations of the molecule in the
asymmetric unit are involved.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_averaging.block_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - example is completely hypothetical
;
;
_phasing_averaging.method
; Iterative 3-fold averaging alternating with phase extensions by 0.5
reciprocal lattice units per cycle according to the method described by
X and Y (ref).
;
_phasing_averaging.details
; The position of the 3-fold axis was redetermined every five cycles.
;
;
save_phasing_averaging.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_phasing_averaging.details.
_item_description.description
;
A description of special aspects of the averaging process.
;
_item.name '_phasing_averaging.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Position of the 3-fold axis was redetermined every
five cycles.
;
save_phasing_averaging.method.
_item_description.description
;
A description of the phase averaging phasing method applied to
phase this structure.
Note that this is not the computer program used, which is
described in _computing.phasing_averaging.
Rather this data item should be used to describe significant
methodological options used within the phase averaging program.
;
_item.name '_phasing_averaging.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Iterative 3-fold averaging alternating with phase
extension by 0.5 reciprocal lattice units per cycle
according to the method described by X and Y (ref).
;
_category.description
;
Data items in the PHASING_ISOMORPHOUS category record details
about the phasing of the structure, when a model isomorphous
to the structure being phased was used to generate initial
phases.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_isomorphous.block_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 4PHV and laboratory records for the
structure corresponding to PDB entry 4PHV
;
;
_phasing_isomorphous.parent 'PDB entry 5HVP'
_phasing_isomorphous.details
; The inhibitor and all solvent atoms were removed from the parent structure
before beginning refinement. All static disorder present in the parent
structure was also removed.
;
;
save_phasing_isomorphous.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_phasing_isomorphous.details.
_item_description.description
;
A description of special aspects of the isomorphous phasing.
;
_item.name '_phasing_isomorphous.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Residues 13-18 were eliminated from the starting
model as it was anticipated that binding of the
inhibitor would cause a structural rearrangement
in this part of the structure.
;
save_phasing_isomorphous.method.
_item_description.description
;
A description of the isomorphous phasing method applied to
phase this structure.
Note that this is not the computer program used, which is
described in the _computing. data items.
Rather this data item should be used to describe significant
methodological options used within the isomorphous phasing
program.
;
_item.name '_phasing_isomorphous.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Iterative 3-fold averaging alternating with phase
extension by 0.5 reciprocal lattice units per cycle
according to the method described by X and Y (ref).
;
save_phasing_isomorphous.parent.
_item_description.description
;
Reference to the structure used to generate starting phases
if the structure referenced in this data block was phased
by virtue of being isomorphous to a known structure (e.g.,
a mutant that crystallizes in the same space group as the
wild type protein.)
;
_item.name '_phasing_isomorphous.parent'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the PHASING_MAD category record details about
the phasing of the structure, when methods involving multiple
anomalous dispersion techniques are involved.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_MAD.block_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of special aspects of the MAD phasing. ; _item.name '_phasing_MAD.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description
;
A description of the MAD phasing method applied to phase
this structure.
Note that this is not the computer program used, which is
described in _computing.phasing_MAD.
Rather this data item should be used to describe significant
methodological options used within the MAD phasing program.
;
_item.name '_phasing_MAD.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the PHASING_MIR category record details about
the phasing of the structure, when methods involving isomorphous
replacement are involved.
All isomorphous based techniques are subsumed in this category,
including single isomorphous replacement (SIR), multiple
isomorphous replacement (MIR), single or multiple isomorphous
replacement plus anomalous scattering (SIRAS, MIRAS).
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_MIR.block_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
;
;
_phasing_MIR.method
; Standard phase refinement (Blow and Crick, 1959)
;
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; A description of special aspects of the isomorphous phasing. ; _item.name '_phasing_MIR.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
_item_description.description
;
A description of the MIR phasing method applied to phase this
structure.
Note that this is not the computer program used, which is
described in _computing.phasing_MIR.
Rather this data item should be used to describe significant
methodological options used within the MIR phasing program.
;
_item.name '_phasing_MIR.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the PHASING_MIR_DER category record details
about individual derivatives used in the phasing of the
structure when methods involving isomorphous replacement are
involved.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_MIR_der.id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
;
;
loop_
_phasing_MIR_der.id
_phasing_MIR_der.number_of_sites
_phasing_MIR_der.details
KAu(CN)2 3 'major site interpreted in difference Patterson'
K2HgI4 6 'sites found in cross-difference Fourier'
K3IrCl6 2 'sites found in cross-difference Fourier'
All 11 'data for all three derivatives combined'
;
_item_description.description
;
A description of special aspects of this derivative, its data,
its solution, or its use in phasing.
;
_item.name '_phasing_MIR_der.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_description.description
;
The value of _phasing_MIR_der.id must uniquely identify
a record in the PHASING_MIR_DER list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_MIR_der.id'
phasing_MIR_der
yes
'_phasing_MIR_refln.der_id'
phasing_MIR_refln
yes
'_phasing_MIR_site.der_id'
phasing_MIR_site
yes
'_phasing_MIR_der_shell.der_id'
phasing_MIR_der_shell
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_MIR_refln.der_id'
'_phasing_MIR_der.id'
'_phasing_MIR_site.der_id'
'_phasing_MIR_der.id'
'_phasing_MIR_der_shell.der_id'
'_phasing_MIR_der.id'
_item_type.code char
loop_
_item_examples.case
'KAu(CN)2'
K2HgI4
save_phasing_MIR_der.number_of_sites.
_item_description.description ; The number of heavy atom sites in this derivative. ; _item.name '_phasing_MIR_der.number_of_sites' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int
save_phasing_MIR_der.reflns_criteria.
_item_description.description
;
Criteria used to limit the reflections used in the phasing
calculations.
;
_item.name '_phasing_MIR_der.reflns_criteria'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '> 4 \s(I)'
_category.description
;
Data items in the PHASING_MIR_DER_SHELL category record details
for each derivative, broken down into shells of resolution,
when the phasing method involves isomorphous replacement.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_phasing_MIR_der_shell.der_id'
'_phasing_MIR_der_shell.d_res_low'
'_phasing_MIR_der_shell.d_res_high'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
made up arbitrary low-resolution limit
;
;
loop_
_phasing_MIR_der_shell.der_id
_phasing_MIR_der_shell.d_res_low
_phasing_MIR_der_shell.d_res_high
_phasing_MIR_der_shell.ha_ampl
_phasing_MIR_der_shell.loc
KAu(CN)2 15.0 8.3 54 26
KAu(CN)2 8.3 6.4 54 20
KAu(CN)2 6.4 5.2 50 20
KAu(CN)2 5.2 4.4 44 23
KAu(CN)2 4.4 3.8 39 23
KAu(CN)2 3.8 3.4 33 21
KAu(CN)2 3.4 3.0 28 17
KAu(CN)2 15.0 3.0 38 21
K2HgI4 15.0 8.3 149 87
K2HgI4 8.3 6.4 121 73
K2HgI4 6.4 5.2 95 61
K2HgI4 5.2 4.4 80 60
K2HgI4 4.4 3.8 73 63
K2HgI4 3.8 3.4 68 57
K2HgI4 3.4 3.0 63 46
K2HgI4 15.0 3.0 79 58
K3IrCl6 15.0 8.3 33 27
K3IrCl6 8.3 6.4 40 23
K3IrCl6 6.4 5.2 31 22
K3IrCl6 5.2 4.4 27 23
K3IrCl6 4.4 3.8 22 23
K3IrCl6 3.8 3.4 19 20
K3IrCl6 3.4 3.0 16 20
K3IrCl6 15.0 3.0 23 21
;
save_phasing_MIR_der_shell.d_res_high.
_item_description.description
;
The highest resolution for the interplanar spacing in the
reflection data for this derivative in this shell. This is the
smallest d value.
;
_item.name '_phasing_MIR_der_shell.d_res_high'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_phasing_MIR_der_shell.d_res_low.
_item_description.description
;
The lowest resolution for the interplanar spacing in the
reflection data for this derivative in this shell. This is the
highest d value.
;
_item.name '_phasing_MIR_der_shell.d_res_low'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_phasing_MIR_der_shell.der_id.
_item_description.description
;
This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
save_phasing_MIR_der_shell.fom.
_item_description.description
;
The mean value of the figure of merit m for reflections for this
derivative in this shell.
int P(a) exp(ia) da
m = -------------------
int P(a) da
where P(a) is the probability that phase angle a is correct
and the integrals are taken over the range a = 0 to 2 pi.
;
_item.name '_phasing_MIR_der_shell.fom'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.ha_ampl.
_item_description.description
;
The mean heavy-atom amplitude for reflections in this
derivative in this shell.
;
_item.name '_phasing_MIR_der_shell.ha_ampl'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.loc.
_item_description.description
;
The mean lack-of-closure error for reflections in this
derivative in this shell.
Lack-of-closure = Sum |F~ph~(obs) - F~ph~(calc)|
where F~ph~(obs) and F~ph~(calc) are the observed and calculated
structure factor amplitudes of the derivative.
;
_item.name '_phasing_MIR_der_shell.loc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.phase.
_item_description.description
;
The mean of the phase values for reflections in this
derivative in this shell.
;
_item.name '_phasing_MIR_der_shell.phase'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_phasing_MIR_der_shell.power.
_item_description.description
;
The mean phasing power for reflections in this derivative
in this shell.
{ Sum F~h~(calc)^2^ }^1/2^
Phasing power = { --------------------------------- }
{ Sum |F~ph~(obs) - F~ph~(calc)|^2^ }
where F~h~(calc) is the calculated structure factor amplitude of
the heavy atom and F~ph~(obs) and F~ph~(calc) are the observed
and calculated structure factor amplitudes of the derivative.
;
_item.name '_phasing_MIR_der_shell.power'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.R_Cullis.
_item_description.description
;
The R-factor for centric reflections in this derivative in this
shell.
R-Cullis: Sum ||F~ph~(obs)+/-F~p~(obs)|-F~h~(calc)|
/ Sum | F~ph~(obs)-F~p~(obs)|
where F~p~(obs) is the observed structure factor amplitude of the
parent molecule, F~h~(calc) is the calculated structure factor
amplitude of the heavy atom and F~ph~(obs) is the observed
structure factor amplitude of the derivative.
Cullis A F, Muirhead H, Perutz M F, Rossmann M G and North A C T
(1961) Proc. Roy. Soc. A265, 15-38.
;
_item.name '_phasing_MIR_der_shell.R_Cullis'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.R_Kraut.
_item_description.description
;
The R-factor for general reflections in this derivative in this
shell.
Sum |F~ph~(obs)-F~ph~(calc)|
R-Kraut = ----------------------------
Sum |F~ph~(obs)|
where F~ph~(obs) and F~ph~(calc) are the observed and calculated
structure factor amplitudes of the derivative.
Kraut, J., Sieker, L.C., High, D.F. and Freer, S.T. (1962).
Proc. Natl. Acad. Sci. USA, Vol 48, p. 1417.
;
_item.name '_phasing_MIR_der_shell.R_Kraut'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_der_shell.reflns.
_item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_der_shell.reflns' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_category.description
;
Data items in the PHASING_MIR_REFLN category record details about
the reflection data used in an MIR experiment.
This category of data items is provided so that derivative
intensity and phase information can be stored in the same data
block as the native information. However, no provision is made
for the storage of all of the details of obtaining those data;
to store such detailed information a separate data block should
be used for each derivative.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_phasing_MIR_refln.index_h'
'_phasing_MIR_refln.index_k'
'_phasing_MIR_refln.index_l'
'_phasing_MIR_refln.der_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
;
;
Need Example 1
;
save_phasing_MIR_refln.A_calc.
_item_description.description
;
The calculated value of structure-factor component A for this
derivative, in electrons.
A = |F|cos(phase)
;
_item.name '_phasing_MIR_refln.A_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.A_meas.
_item_description.description
;
The measured value of structure-factor component A for this
derivative, in electrons.
A = |F|cos(phase)
;
_item.name '_phasing_MIR_refln.A_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.B_calc.
_item_description.description
;
The calculated value of structure-factor component B for this
derivative, in electrons.
B = |F|sin(phase)
;
_item.name '_phasing_MIR_refln.B_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.B_meas.
_item_description.description
;
The measured value of structure-factor component B for this
derivative, in electrons.
B = |F|sin(phase)
;
_item.name '_phasing_MIR_refln.B_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.der_id.
_item_description.description
;
This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
save_phasing_MIR_refln.F_calc.
_item_description.description
;
The calculated value of the structure factor for this derivative,
in electrons.
;
_item.name '_phasing_MIR_refln.F_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.F_meas.
_item_description.description
;
The measured value of the structure factor for this derivative,
in electrons.
;
_item.name '_phasing_MIR_refln.F_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.F_sigma.
_item_description.description
;
The standard deviation (derived from the measured value) of the
structure factor for this derivative, in electrons.
;
_item.name '_phasing_MIR_refln.F_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'electrons'
save_phasing_MIR_refln.HL_A_iso.
_item_description.description
;
The isomorphous Hendrickson-Lattman coefficient Aiso for this
reflection for this derivative.
-2.0 * (Fp^2 + Fh^2 - Fph^2) * Fp * cos(alphah)
Aiso = ----------------------------------------------
E^2
where
Fp = the structure factor amplitude of the native
Fph = the structure factor amplitude of the derivative
Fh = the structure factor amplitude calculated from the
heavy atom model
alphah = the phase calculated from the heavy atom model
E = ((Fph - Fp) - Fh)^2 for centric reflections
= ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections
;
_item.name '_phasing_MIR_refln.HL_A_iso'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_phasing_MIR_refln.HL_B_iso.
_item_description.description
;
The isomorphous Hendrickson-Lattman coefficient Biso for this
reflection for this derivative.
-2.0 * (Fp^2 + Fh^2 - Fph^2) * Fp * sin(alphah)
Biso = ----------------------------------------------
E^2
where
Fp = the structure factor amplitude of the native
Fph = the structure factor amplitude of the derivative
Fh = the structure factor amplitude calculated from the
heavy atom model
alphah = the phase calculated from the heavy atom model
E = ((Fph - Fp) - Fh)^2 for centric reflections
= ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections
;
_item.name '_phasing_MIR_refln.HL_B_iso'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_phasing_MIR_refln.HL_C_iso.
_item_description.description
;
The isomorphous Hendrickson-Lattman coefficient Ciso for this
reflection for this derivative.
-Fp^2 * (sin(alphah)^2 - cos(alphah)^2)
Ciso = ---------------------------------------
E^2
where
Fp = the structure factor amplitude of the native
Fph = the structure factor amplitude of the derivative
Fh = the structure factor amplitude calculated from the
heavy atom model
alphah = the phase calculated from the heavy atom model
E = ((Fph - Fp) - Fh)^2 for centric reflections
= ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections
;
_item.name '_phasing_MIR_refln.HL_C_iso'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_phasing_MIR_refln.HL_D_iso.
_item_description.description
;
The isomorphous Hendrickson-Lattman coefficient Diso for this
reflection for this derivative.
-2.0 * Fp^2 * sin(alphah)^2 * cos(alphah)^2
Diso = -------------------------------------------
E^2
where
Fp = the structure factor amplitude of the native
Fph = the structure factor amplitude of the derivative
Fh = the structure factor amplitude calculated from the
heavy atom model
alphah = the phase calculated from the heavy atom model
E = ((Fph - Fp) - Fh)^2 for centric reflections
= ((Fph - Fp) *2^1/2 - Fh)^2 for acentric reflections
;
_item.name '_phasing_MIR_refln.HL_D_iso'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_phasing_MIR_refln.index_h.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_h' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_k' '_phasing_MIR_refln.index_l' _item_type.code int
save_phasing_MIR_refln.index_k.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_k' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_h' '_phasing_MIR_refln.index_l' _item_type.code int
save_phasing_MIR_refln.index_l.
_item_description.description ; Miller index h of the reflection. ; _item.name '_phasing_MIR_refln.index_l' _item.category_id _item.category_id _item.mandatory_code yes _item.sub_category_id 'miller_index' loop_ _item_dependent.dependent_name '_phasing_MIR_refln.index_h' '_phasing_MIR_refln.index_k' _item_type.code int
save_phasing_MIR_refln.phase_calc.
_item_description.description
;
The calculated value of the structure-factor phase for this
derivative, in degrees.
;
_item.name '_phasing_MIR_refln.phase_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
save_phasing_MIR_refln.phase_meas.
_item_description.description
;
The measured value of the structure-factor phase for this
derivative, in degrees.
;
_item.name '_phasing_MIR_refln.phase_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_category.description
;
Data items in the PHASING_MIR_SHELL category record details
broken down into shells of resolution, when the phasing method
involves isomorphous replacement.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_phasing_MIR_shell.d_res_low'
'_phasing_MIR_shell.d_res_high'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
made up arbitrary low-resolution limit
;
;
loop_
_phasing_MIR_shell.d_res_low
_phasing_MIR_shell.d_res_high
_phasing_MIR_shell.reflns
_phasing_MIR_shell.fom
15.0 8.3 80 0.69
8.3 6.4 184 0.73
6.4 5.2 288 0.72
5.2 4.4 406 0.65
4.4 3.8 554 0.54
3.8 3.4 730 0.53
3.4 3.0 939 0.50
;
save_phasing_MIR_shell.d_res_high.
_item_description.description
;
The highest resolution for the interplanar spacing in the
reflection data in this shell. This is the smallest d value.
Note that the resolution limits of shells in the items
_phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low
are independent of the resolution limits of shells in the items
_reflns_shell.d_res_high and _reflns_shell.d_res_low.
;
_item.name '_phasing_MIR_shell.d_res_high'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_phasing_MIR_shell.d_res_low.
_item_description.description
;
The lowest resolution for the interplanar spacing in the
reflection data in this shell. This is the largest d value.
Note that the resolution limits of shells in the items
_phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low
are independent of the resolution limits of shells in the items
_reflns_shell.d_res_high and _reflns_shell.d_res_low.
;
_item.name '_phasing_MIR_shell.d_res_low'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
The mean value of the figure of merit m for reflections in this
shell.
int P(a) exp(ia) da
m = -------------------
int P(a) da
where P(a) is the probability that phase angle a is correct
and the integrals are taken over the range a = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.fom'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_description.description
;
The mean lack-of-closure error for reflections in this shell.
Lack-of-closure = Sum |F~ph~(obs) - F~ph~(calc)|
where F~ph~(obs) and F~ph~(calc) are the observed and calculated
structure factor amplitudes of the derivative.
;
_item.name '_phasing_MIR_shell.loc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_shell.mean_phase.
_item_description.description ; The mean of the phase values for all reflections in this shell. ; _item.name '_phasing_MIR_shell.mean_phase' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float
_item_description.description
;
The mean phasing power for reflections in this shell.
{ Sum F~h~(calc)^2^ }^1/2^
Phasing power = { --------------------------------- }
{ Sum |F~ph~(obs) - F~ph~(calc)|^2^ }
where F~h~(calc) is the calculated structure factor amplitude of
the heavy atom and F~ph~(obs) and F~ph~(calc) are the observed
and calculated structure factor amplitudes of the derivative.
;
_item.name '_phasing_MIR_shell.power'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_shell.R_Cullis.
_item_description.description
;
The R-factor for centric reflections in this shell.
R-Cullis: Sum ||F~ph~(obs)+/-F~p~(obs)|-F~h~(calc)|
/ Sum | F~ph~(obs)-F~p~(obs)|
where F~p~(obs) is the observed structure factor amplitude of the
parent molecule, F~h~(calc) is the calculated structure factor
amplitude of the heavy atom and F~ph~(obs) is the observed
structure factor amplitude of the derivative.
Cullis et al. (1961) Proc. Roy. Soc. A265, 15-??.
;
_item.name '_phasing_MIR_shell.R_Cullis'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_shell.R_Kraut.
_item_description.description
;
The R-factor for general reflections in this shell.
Sum |F~ph~(obs)-F~ph~(calc)|
R-Kraut = ----------------------------
Sum |F~ph~(obs)|
where F~ph~(obs) and F~ph~(calc) are the observed and calculated
structure factor amplitudes of the derivative.
Kraut, J., Sieker, L.C., High, D.F. and Freer, S.T. (1962).
Proc. Natl. Acad. Sci. USA, Vol 48, p. 1417.
;
_item.name '_phasing_MIR_shell.R_Kraut'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_phasing_MIR_shell.reflns.
_item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
_category.description
;
Data items in the PHASING_MIR_SITE category record details
about the heavy-atom sites, when the phasing method involves
isomorphous replacement.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_phasing_MIR_site.der_id'
'_phasing_MIR_site.id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on Zanotti et al., JBC 268: 10728-10738 (1993)
with occupancies converted from electrons to fractional
;
;
loop_
_phasing_MIR_site.der_id
_phasing_MIR_site.id
_phasing_MIR_site.atom_type_symbol
_phasing_MIR_site.occupancy
_phasing_MIR_site.fract_x
_phasing_MIR_site.fract_y
_phasing_MIR_site.fract_z
_phasing_MIR_site.B_iso
KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0
KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9
KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7
K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7
K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7
K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2
K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7
K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4
K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9
K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8
K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9
;
save_phasing_MIR_site.atom_type_symbol.
_item_description.description
;
This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
The scattering factors referenced via this data item should be
those used in the refinement of the heavy atom data; in some
cases this will be the scattering factor to the single heavy
atom, in others it will be scattering factors for an atomic
cluster.
;
_item_description.description
;
Isotropic temperature factor for this heavy-atom site in this
derivative.
;
_item.name '_phasing_MIR_site.B_iso'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
_esd_default 0.0
save_phasing_MIR_site.B_iso_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.B_iso. ; _item.name '_phasing_MIR_site.B_iso_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_x.
_item_description.description
;
The x coordinate of this heavy-atom position in this derivative
specified as orthogonal Angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.cartn_transform_axes.
;
_item.name '_phasing_MIR_site.cartn_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.cartn_y'
'_phasing_MIR_site.cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_phasing_MIR_site.cartn_x_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_x. ; _item.name '_phasing_MIR_site.cartn_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_y_esd' '_phasing_MIR_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_y.
_item_description.description
;
The y coordinate of this heavy-atom position in this derivative
specified as orthogonal Angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.cartn_transform_axes.
;
_item.name '_phasing_MIR_site.cartn_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.cartn_x'
'_phasing_MIR_site.cartn_z'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_phasing_MIR_site.cartn_y_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_y. ; _item.name '_phasing_MIR_site.cartn_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x_esd' '_phasing_MIR_site.cartn_z_esd' _item_type.code float _item_units.code 'angstroms'
save_phasing_MIR_site.cartn_z.
_item_description.description
;
The z coordinate of this heavy-atom position in this derivative
specified as orthogonal Angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.cartn_transform_axes.
;
_item.name '_phasing_MIR_site.cartn_z'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'cartesian_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.cartn_x'
'_phasing_MIR_site.cartn_y'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'angstroms'
save_phasing_MIR_site.cartn_z_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.cartn_z. ; _item.name '_phasing_MIR_site.cartn_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'cartesian_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.cartn_x_esd' '_phasing_MIR_site.cartn_y_esd' _item_type.code float _item_units.code 'angstroms'
_item_description.description
;
This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
save_phasing_MIR_site.details.
_item_description.description ; A description of special aspects of the derivative site. ; _item.name '_phasing_MIR_site.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'binds to His 117' 'minor site obtained from difference Fourier' 'same as site 2 in the K2HgI4 derivative'
save_phasing_MIR_site.fract_x.
_item_description.description
;
The x coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_a.
;
_item.name '_phasing_MIR_site.fract_x'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.fract_y'
'_phasing_MIR_site.fract_z'
_item_type.code float
_item_type_conditions.code esd
save_phasing_MIR_site.fract_x_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_x. ; _item.name '_phasing_MIR_site.fract_x_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_y_esd' '_phasing_MIR_site.fract_z_esd' _item_type.code float
save_phasing_MIR_site.fract_y.
_item_description.description
;
The y coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_b.
;
_item.name '_phasing_MIR_site.fract_y'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.fract_x'
'_phasing_MIR_site.fract_z'
_item_type.code float
_item_type_conditions.code esd
save_phasing_MIR_site.fract_y_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_y. ; _item.name '_phasing_MIR_site.fract_y_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x_esd' '_phasing_MIR_site.fract_z_esd' _item_type.code float
save_phasing_MIR_site.fract_z.
_item_description.description
;
The z coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_c.
;
_item.name '_phasing_MIR_site.fract_z'
_item.category_id _item.category_id
_item.mandatory_code no
_item.sub_category_id 'fractional_coordinate'
loop_
_item_dependent.dependent_name
'_phasing_MIR_site.fract_x'
'_phasing_MIR_site.fract_y'
_item_type.code float
_item_type_conditions.code esd
save_phasing_MIR_site.fract_z_esd.
_item_description.description ; The estimated standard deviation of _phasing_MIR_site.fract_z. ; _item.name '_phasing_MIR_site.fract_z_esd' _item.category_id _item.category_id _item.mandatory_code no _item.sub_category_id 'fractional_coordinate_esd' _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_site.fract_x_esd' '_phasing_MIR_site.fract_y_esd' _item_type.code float
_item_description.description
;
The value of _phasing_MIR_site.id must uniquely identify each
site in each derivative in the PHASING_MIR_SITE list.
The atom identifiers need not be unique over all sites in all
derivatives; they need only be unique for each site in each
derivative.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_phasing_MIR_site.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
save_phasing_MIR_site.occupancy.
_item_description.description
;
The fraction of the atom type present at this heavy-atom site
in a given derivative. The sum of the occupancies of all the
atom types at this site may not significantly exceed 1.0 unless
it is a dummy site.
;
_item.name '_phasing_MIR_site.occupancy'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 1.0
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_category.description
;
Data items in the PHASING_MR category record details about
the phasing of the structure, when methods involving molecular
replacement are involved.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_phasing_MR.block_id'
loop_
_category_group.id
'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
A description of the molecular replacement phasing method
applied to phase this structure.
Note that this is not the computer program used, which is
described in _computing.phasing_MR.
Rather this data item should be used to describe significant
methodological options used within the molecular replacement
phasing program.
;
_item.name '_phasing_MR.method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the PUBL category are used when submitting a
manuscript for publication.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_publ.block_id'
loop_
_category_group.id
'inclusive_group'
'publ_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_publ.section_title
;
trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one
;
_publ.section_abstract
; The oxazolidinone ring is a shallow envelope conformation with the
tert-butyl and iso-butyl groups occupying trans-positions with
respect to the ring. The angles at the N atom sum to 356.2\%,
indicating a very small degree of pyramidalization at this atom.
This is consistent with electron delocalization between the N atom
and the carbonyl centre [N-C=O = 1.374(3)\%A].
;
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
The name and address of the author submitting the manuscript and
CIF. This is the person contacted by the journal editorial staff.
;
_item.name '_publ.contact_author'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author'
_item_type.code char
_item_examples.case
;
Professor Dr. J.U. Blogs
Department of Structural Chemistry
RRDD Institute of Technology
Building #6-M57
Highho Street
Citytown 64664
COUNTRYHERE
;
save_publ.contact_author_email.
_item_description.description ; Email address in a form recognisable to international networks. ; _item.name '_publ.contact_author_email' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_email' _item_type.code char loop_ _item_examples.case [email protected] [email protected]
_item_description.description
;
Facsimile telephone number with international code in
parentheses.
;
_item.name '_publ.contact_author_fax'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_fax'
_item_type.code char
_item_examples.case '(12) 34 947 7334'
save_publ.contact_author_phone.
_item_description.description
;
Telephone number with international code in parentheses and any
extension number preceded by 'ext'.
;
_item.name '_publ.contact_author_phone'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_phone'
_item_type.code char
_item_examples.case '(12) 34 947 7330 ext 5543'
_item_description.description ; A letter submitted to the journal editor by the contact author. ; _item.name '_publ.contact_letter' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_contact_letter' _item_type.code char
save_publ.manuscript_creation.
_item_description.description
;
A description of the wordprocessor package and computer used to
create the word processed manuscript stored as
_publ_manuscript_processed.
;
_item.name '_publ.manuscript_creation'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_creation'
_item_type.code char
_item_examples.case 'Tex file created by FrameMaker on a Sun 3/280'
save_publ.manuscript_processed.
_item_description.description
;
The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item _publ_manuscript_creation.
;
_item.name '_publ.manuscript_processed'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_processed'
_item_type.code char
_item_description.description
;
The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
;
_item.name '_publ.manuscript_text'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_text'
_item_type.code char
save_publ.requested_coeditor_name.
_item_description.description
;
The Co-editor's name requested to process the submitted
manuscript.
;
_item.name '_publ.requested_coeditor_name'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_requested_coeditor_name'
_item_type.code char
_item_description.description ; The journal's name requested for publication. ; _item.name '_publ.requested_journal' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_publ_requested_journal' _item_type.code char
_item_description.description
;
The abstract section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_abstract'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_abstract'
_item_type.code char
save_publ.section_acknowledgements.
_item_description.description
;
The acknowledgements section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_acknowledgements'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_acknowledgements'
_item_type.code char
_item_description.description
;
The comment section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_comment'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_comment'
_item_type.code char
_item_description.description
;
The discussion section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_discussion'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_discussion'
_item_type.code char
save_publ.section_experimental.
_item_description.description
;
The experimental section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
The _publ.section_exptl_prep and _publ.section_exptl_refinement
items are preferred for separating the chemical preparation and
refinement aspects of the experimental description.
;
_item.name '_publ.section_experimental'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_experimental'
_item_type.code char
_item_description.description
;
The experimental preparation section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ_manuscript_processed.
;
_item.name '_publ.section_exptl_prep'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_exptl_prep'
_item_type.code char
save_publ.section_exptl_refinement.
_item_description.description
;
The experimental refinement section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ_manuscript_processed.
;
_item.name '_publ.section_exptl_refinement'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_exptl_refinement'
_item_type.code char
save_publ.section_figure_captions.
_item_description.description
;
The figure captions section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_figure_captions'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_figure_captions'
_item_type.code char
save_publ.section_introduction.
_item_description.description
;
The introduction section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_introduction'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_introduction'
_item_type.code char
_item_description.description
;
The references section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ_manuscript_processed.
;
_item.name '_publ.section_references'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_references'
_item_type.code char
save_publ.section_table_legends.
_item_description.description
;
The table legends captions section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ_manuscript_processed.
;
_item.name '_publ.section_table_legends'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_table_legends'
_item_type.code char
_item_description.description
;
The title section of a manuscript if the manuscript is submitted
in parts. As an alternative see _publ.manuscript_text and
_publ_manuscript_processed.
;
_item.name '_publ.section_title'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_title'
_item_type.code char
_category.description
;
Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_publ_author.name'
loop_
_category_group.id
'inclusive_group'
'publ_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_publ_author.name
_publ_author.address
'Willis, Anthony C.'
; Research School of Chemistry
Australian National University
GPO Box 4
Canberra, A.C.T.
Australia 2601
;
;
_item_description.description
;
The address of a publication author. If there is more than one
author this will be looped with _publ_author_name.
;
_item.name '_publ_author.address'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_author_address'
_item_type.code char
_item_examples.case
;
Department
Institute
Street
City and postcode
COUNTRY
;
_item_description.description
;
The name of a publication author. If there are multiple authors
they will be looped with _publ_author_address. The family name(s)
followed by a comma, precedes the first names or initials.
;
_item.name '_publ_author.name'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_author_name'
_item_type.code char
loop_
_item_examples.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
_category.description
;
Data items in the PUBL_MANUSCRIPT_INCL category allow
the authors of a manuscript submitted for publication to list
data names that should be added to the standard request list
employed by journal printing software.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_publ_manuscript_incl.block_id'
loop_
_category_group.id
'inclusive_group'
'publ_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 2 - Example is completely hypothetical.
;
;
loop_
_publ_manuscript_incl.extra_item
_publ_manuscript_incl.extra_info
_publ_manuscript_incl.extra_defn
'_atom_site_symmetry_multiplicity' 'to emphasise very special sites' yes
'_chemical_compound_source' 'rare material from unusual source' yes
'_reflns_d_resolution_high' 'the limited data is a problem here' yes
'_crystal_magnetic_permeability' 'a new data quantity needed here' no
;
save_publ_manuscript_incl.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_publ_manuscript_incl.extra_defn.
_item_description.description
;
Specifies whether or not the extra information being included
into a manuscript is a standard definition.
;
_item.name '_publ_manuscript_incl.extra_defn'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_defn'
_item_type.code char
loop_
_item_examples.case
yes
no
save_publ_manuscript_incl.extra_info.
_item_description.description
;
Specifies the reason for including extra information into a
manuscript.
;
_item.name '_publ_manuscript_incl.extra_info'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_info'
_item_type.code char
loop_
_item_examples.case
'to emphasise very special sites'
'rare material from unusual source'
'the limited data is a problem here'
'a new data quantity needed here'
save_publ_manuscript_incl.extra_item.
_item_description.description
;
Specifies the name of a data item used to include extra
information into a manuscript. Note that
_publ_manuscript_incl.extra_item names MUST be enclosed in single
quotes.
;
_item.name '_publ_manuscript_incl.extra_item'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_item'
_item_type.code char
loop_
_item_examples.case
'_atom_site_symmetry_multiplicity'
'_chemical_compound_source'
'_reflns_d_resolution_high'
'_crystal_magnetic_permeability'
_category.description
;
Data items in the REFINE category record details about the
structure refinement parameters.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_refine.block_id'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_refine.ls_number_reflns_obs 12901
_refine.ls_number_restraints 6609
_refine.ls_number_parameters 7032
_refine.ls_R_Factor_obs 0.176
_refine.ls_weighting_scheme calc
_refine.ls_weighting_details
; Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at the beginning of refinement.
Afsig = 15.5, Bfsig = -50.0 at the end of refinement.
;
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_refine.details sfls:_F_calc_weight_full_matrix
_refine.ls_structure_factor_coef F
_refine.ls_matrix_type full
_refine.ls_weighting_scheme 'calc w=1/(\s^2^(F)+0.0004F^2^)'
_refine.ls_hydrogen_treatment 'refxyz except H332B noref'
_refine.ls_extinction_method Zachariasen
_refine.ls_extinction_coef 3514(42)
_refine.ls_extinction_expression
'equ(22) p292 "Crystallographic Computing" (1970)'
_refine.ls_abs_structure_details
; The absolute configuration was assigned to agree with the known
chirality at C3 arising from its precursor l-leucine.
;
_refine.ls_abs_structure_Flack 0
_refine.ls_number_reflns_obs 1408
_refine.ls_number_parameters 272
_refine.ls_number_restraints 0
_refine.ls_number_constraints 0
_refine.ls_R_factor_all .038
_refine.ls_R_factor_obs .034
_refine.ls_wR_factor_all .044
_refine.ls_wR_factor_obs .042
_refine.ls_goodness_of_fit_all 1.462
_refine.ls_goodness_of_fit_obs 1.515
_refine.ls_shift/esd_max .535
_refine.ls_shift/esd_mean .044
_refine.diff_density_min -.108
_refine.diff_density_max .131
;
_item_description.description
;
The maximum value for isotropic B value (temperature factors)
found in the coordinate set.
;
_item.name '_refine.B_iso_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms_squared'
_item_description.description
;
The minimum value for isotropic B value (temperature factors)
found in the coordinate set.
;
_item.name '_refine.B_iso_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms_squared'
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Description of special aspects of the refinement process. ; _item.name '_refine.details' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_special_details' _item_type.code char
_item_description.description
;
The maximum value of the electron density in the final difference
Fourier map.
;
_item.name '_refine.diff_density_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_max'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_max_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_max. ; _item.name '_refine.diff_density_max_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
_item_description.description
;
The minimum value of the electron density in the final difference
Fourier map.
;
_item.name '_refine.diff_density_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_min'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_min_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_min. ; _item.name '_refine.diff_density_min_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
_item_description.description
;
The root-mean-square-deviation of the electron density in the
final difference Fourier map. This value is measured with respect
to the arithmetic mean density, and is derived from summations
over each grid point in the asymmetric unit of the cell. This
quantity is useful for assessing the significance of the values
of _refine.diff_density_min and _refine.diff_density_max, and
also for defining suitable contour levels.
;
_item.name '_refine.diff_density_rms'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_rms'
_item_type.code float
_item_type_conditions.code esd
_item_units.code 'electrons_per_angstroms_cubed'
save_refine.diff_density_rms_esd.
_item_description.description ; The estimated standard deviation of _refine.diff_density_rms. ; _item.name '_refine.diff_density_rms_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float _item_units.code 'electrons_per_angstroms_cubed'
save_refine.ls_abs_structure_details.
_item_description.description
;
The nature of the absolute structure and how it was determined.
For example, to describe the nature of the Friedel data used.
;
_item.name '_refine.ls_abs_structure_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_details'
_item_type.code char
save_refine.ls_abs_structure_Flack.
_item_description.description
;
This measure of absolute structure (enantiomorph or polarity) is
defined in the paper by Flack, H. D. (1983). Acta Cryst. A39,
876-881. The value must be between 0. and 1. with an e.s.d.
;
_item.name '_refine.ls_abs_structure_Flack'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_Flack'
_item_type.code float
_item_type_conditions.code esd
save_refine.ls_abs_structure_Flack_esd.
_item_description.description
;
The estimated standard deviation of
_refine.ls_abs_structure_Flack.
;
_item.name '_refine.ls_abs_structure_Flack_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_refine.ls_abs_structure_Rogers.
_item_description.description
;
This measure of absolute structure (enantiomorph or polarity) is
defined in the paper by Rogers, D. (1981). Acta Cryst. A37,
734-741.
;
_item.name '_refine.ls_abs_structure_Rogers'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_Rogers'
_item_type.code float
_item_type_conditions.code esd
save_refine.ls_abs_structure_Rogers_esd.
_item_description.description
;
The estimated standard deviation of
_refine.ls_abs_structure_Rogers.
;
_item.name '_refine.ls_abs_structure_Rogers_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_refine.ls_extinction_coef.
_item_description.description
;
The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine.ls_extinction_expression & _refine.ls_extinction_method.
For the 'Zachariasen' method it will be the r* value; for the
'B-C type 1 isotropic' method it is the 'g' value, and for 'B-C
type 2 isotropic' corrections it is the 'rho' value. Note that
the magnitude of these values is usually of the order of 10000.
;
_item.name '_refine.ls_extinction_coef'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_extinction_coef'
_item_type.code float
_item_type_conditions.code esd
_item_examples.case 3472(52)
_item_examples.detail 'Zachariasen coefficient r* = 0.347(5) E04'
save_refine.ls_extinction_coef_esd.
_item_description.description ; The estimated standard deviation of _refine.ls_extinction_coef. ; _item.name '_refine.ls_extinction_coef_esd' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 0.0 _item_type.code float
save_refine.ls_extinction_expression.
_item_description.description
;
A description or reference of the extinction correction equation
used to apply the data item _refine.ls_extinction_coef. This
information must be sufficient to reproduce the extinction
correction factors applied to the structure factors.
;
_item.name '_refine.ls_extinction_expression'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Equation (22) p292 "Crystallographic
Computing" Munksgaard 1970
;
save_refine.ls_extinction_method.
_item_description.description
;
A description of the extinction correction method applied with
the data item _refine.ls_extinction_coef. This description should
include information about the correction method 'Becker-Coppens'
[Becker, P.J. & Coppens, P. (1974) Acta Cryst. A30, 129-153]
or 'Zachariasen' [Zachariasen, W.H. (1967) Acta Cryst. 23, 558-
564]. The latter is sometimes referred to as the 'Larson' method
[Larson, A.C. (1967) Acta Cryst. 23, 664-665] even though it
employs Zachariasen's formula. The Becker-Coppens procedure is
referred to as 'type 1' when correcting secondary extinction
dominated by the mosaic spread; as 'type 2' when secondary
extinction is dominated by particle size and includes a primary
extinction component; and as 'mixed' when there is a mixture of
types 1 and 2. For the B-C method it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian'; and
the nature of the extinction as 'isotropic' or 'anisotropic'.
Note that if either the 'mixed' or 'anisotropic' corrections
are applied the multiple coefficients cannot be contained in
*_extinction_coef and must be listed in _refine.details.
;
_item.name '_refine.ls_extinction_method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_extinction_method'
_item_default.value 'Zachariasen'
_item_type.code char
_item_examples.case 'B-C type 2 Gaussian isotropic'
save_refine.ls_goodness_of_fit_all.
_item_description.description
;
The least-squares goodness-of-fit parameter S for all data,
after the final cycle of refinement. Ideally, account should be
taken of parameters restrained in the least squares.
S = [sum(w|Ym-Yc|^2^) / (Nref-Nparam)]^1/2^
where the sum is over the specified reflection data; Nref is the
number of reflections used in the refinement; Nparam is the
number of refined parameters; Ym and Yc are the measured and
calculated coefficients specified in
_refine.ls_structure_factor_coef; and w is the least-squares
weight [1/(e.s.d. squared)]. See also the definition of
_refine.ls_restrained_S_all.
;
_item.name '_refine.ls_goodness_of_fit_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_goodness_of_fit_all'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
save_refine.ls_goodness_of_fit_all_esd.
_item_description.description
;
The estimated standard deviation of
_refine.ls_goodness_of_fit_all.
;
_item.name '_refine.ls_goodness_of_fit_all_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_refine.ls_goodness_of_fit_obs.
_item_description.description
;
The least-squares goodness-of-fit parameter S for reflection data
classified as 'observed' (see _reflns_observed_criterion), after
the final cycle of refinement. Ideally, account should be taken
of parameters restrained in the least squares.
S = [sum(w|Ym-Yc|^2^) / (Nref-Nparam)]^1/2^
where the sum is over the specified reflection data; Nref is the
number of reflections used in the refinement; Nparam is the
number of refined parameters; Ym and Yc are the measured and
calculated coefficients specified in
_refine.ls_structure_factor_coef; and w is the least-squares
weight [1/(e.s.d. squared)]. See also the definition of
_refine.ls_restrained_S_obs.
;
_item.name '_refine.ls_goodness_of_fit_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_goodness_of_fit_obs'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_type_conditions.code esd
save_refine.ls_goodness_of_fit_obs_esd.
_item_description.description
;
The estimated standard deviation of
_refine.ls_goodness_of_fit_obs.
;
_item.name '_refine.ls_goodness_of_fit_obs_esd'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_refine.ls_hydrogen_treatment.
_item_description.description ; Treatment of hydrogen atoms in the least-squares refinement. ; _item.name '_refine.ls_hydrogen_treatment' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_hydrogen_treatment' _item_default.value undef _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail refall 'refined all H parameters' refxyz 'refined H coordinates only' refU 'refined H U only' noref 'no refinement of H parameters' undef 'not defined'
_item_description.description ; Type of matrix used to accumulate the least-squares derivatives. ; _item.name '_refine.ls_matrix_type' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refine_ls_matrix_type' _item_default.value full _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only'
save_refine.ls_number_constraints.
_item_description.description
;
The number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site.constraints and _atom_site_refinement_flags. A general
description of constraints may appear in _refine.details.
;
_item.name '_refine.ls_number_constraints'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_constraints'
_item_default.value 0
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine.ls_number_parameters.
_item_description.description
;
The number of parameters refined in the least-squares process.
If possible this number should include some contribution from the
restrained parameters.The restrained parameters are distinct from
the constrained parameters (where one or more parameters are
linearly dependent on the refined value of another). Least-
squares restraints often depend on geometry or energy consider-
ations and this makes their direct contribution to this number,
and to the goodness-of-fit calculation, difficult to assess.
;
_item.name '_refine.ls_number_parameters'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_parameters'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine.ls_number_reflns_all.
_item_description.description
;
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low.
;
_item.name '_refine.ls_number_reflns_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine.ls_number_reflns_obs.
_item_description.description
;
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low,
that were flagged as observed (see _reflns.observed_criterion),
and that were included in the refinement.
;
_item.name '_refine.ls_number_reflns_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_reflns'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine.ls_number_restraints.
_item_description.description
;
The number of restrained parameters. These are parameters which
are not directly dependent on another refined parameter. Often
restrained parameters involve geometry or energy dependencies.
See also _atom_site.constraints and _atom_site_refinement_flags.
A general description of refinement constraints may appear in
_refine.details.
;
_item.name '_refine.ls_number_restraints'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_restraints'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_item_description.description
;
Residual factor R for all reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|];
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine.ls_R_factor_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_factor_all'
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_wR_factor_all'
'alternate'
_item_type.code float
_item_description.description
;
Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low, that were flagged as observed (see
_reflns.observed_criterion), and that were included in the
refinement.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|]
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine.ls_R_factor_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_factor_obs'
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_wR_factor_obs'
'alternate'
_item_type.code float
save_refine.ls_R_factor_R_free.
_item_description.description
;
Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low, that were flagged as observed (see
_reflns.observed_criterion), but that were excluded from
refinement (see _reflns.R_free_details) so as to be included in
the calculation of a "free" R-factor.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|]
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine.ls_R_factor_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_wR_factor_R_free'
'alternate'
_item_type.code float
save_refine.ls_restrained_S_all.
_item_description.description
;
The least-squares goodness-of-fit parameter S' for all reflection
data, after the final cycle of least squares. This parameter
explicitly includes the restraints applied in the least-squares
process.
S' = {[sum(w|Ym-Yc|^2^) + sumr(wr|Pc-Pt|^2^)]
/ (Nref+Nrestr-Nparam)}^1/2^
where the sum is over the specified reflection data; sumr is over
the restraint data; Nref is the number of reflections used in the
refinement (see _refine.ls_number_reflns); Nparam is the number
of refined parameters (see _refine.ls_number_parameters); Nrestr
is the number of restraints (see _refine.ls_number_restraints);
Ym and Yc are the measured and calculated coefficients specified
in _refine.ls_structure_factor_coef; Pc and Pt are the calculated
and target restraint values; w is the least-squares reflection
weight [1/(e.s.d. squared)] and wr is the restraint weight.
See also the definition of _refine.ls_goodness_of_fit_all.
;
_item.name '_refine.ls_restrained_S_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_restrained_S_all'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_refine.ls_restrained_S_obs.
_item_description.description
;
The least-squares goodness-of-fit parameter S' for reflection
data classified as observed (see _reflns_observed_criterion)
after the final cycle of least squares. This parameter explicitly
includes the restraints applied in the least-squares process.
S' = {[sum(w|Ym-Yc|^2^) + sumr(wr|Pc-Pt|^2^)]
/ (Nref+Nrestr-Nparam)}^1/2^
where the sum is over the specified reflection data; sumr is over
the restraint data; Nref is the number of reflections used in the
refinement (see _refine.ls_number_reflns); Nparam is the number
of refined parameters (see _refine.ls_number_parameters); Nrestr
is the number of restraints (see _refine.ls_number_restraints);
Ym and Yc are the measured and calculated coefficients specified
in _refine.ls_structure_factor_coef; Pc and Pt are the calculated
and target restraint values; w is the least-squares reflection
weight [1/(e.s.d. squared)] and wr is the restraint weight.
See also the definition of _refine.ls_goodness_of_fit_obs.
;
_item.name '_refine.ls_restrained_S_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_restrained_S_obs'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_description.description
;
The largest ratio of the final least-squares parameter shift
divided by the final estimated standard deviation
;
_item.name '_refine.ls_shift/esd_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_shift/esd_max'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_refine.ls_shift/esd_mean.
_item_description.description
;
The average ratio of the final least-squares parameter shift
divided by the final estimated standard deviation
;
_item.name '_refine.ls_shift/esd_mean'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_shift/esd_mean'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_refine.ls_structure_factor_coef.
_item_description.description
;
Structure-factor coefficient |F|, F^2^ or I, used in the least-
squares refinement process.
;
_item.name '_refine.ls_structure_factor_coef'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_structure_factor_coef'
_item_default.value F
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
Inet
'net intensity'
Fsqd
'structure factor squared'
F
'structure factor magnitude'
save_refine.ls_weighting_details.
_item_description.description
;
A description of special aspects of the weighting scheme used
in least-squares refinement. Used to describe the weighting
when the value of _refine.ls_weighting_scheme is specified
as 'calc'.
;
_item.name '_refine.ls_weighting_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Sigdel model of Konnert-Hendrickson:
Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0 at the end of refinement.
;
save_refine.ls_weighting_scheme.
_item_description.description
;
The weighting scheme applied in the least-squares process. The
standard code may be followed by a description of the weight.
;
_item.name '_refine.ls_weighting_scheme'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_weighting_scheme'
_item_default.value sigma
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
sigma
"based on measured e.s.d.'s"
unit
'unit or no weights applied'
calc
'calculated weights applied'
_item_description.description
;
Weighted residual factor wR for all reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine.ls_wR_factor_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_wR_factor_all'
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_R_factor_all'
_item_type.code float
_item_description.description
;
Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low, that were flagged as observed (see
_reflns.observed_criterion), and that were included in the
refinement.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine.ls_wR_factor_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_wR_factor_obs'
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_R_factor_obs'
'alternate'
_item_type.code float
save_refine.ls_wR_factor_R_free.
_item_description.description
;
Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low, that were flagged as observed (see
_reflns.observed_criterion), but that were excluded from
refinement (see _reflns.R_free_details) so as to be included in
the calculation of a "free" R-factor.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine.ls_wR_factor_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine.ls_R_factor_R_free'
'alternate'
_item_type.code float
_item_description.description ; The maximum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_max' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
_item_description.description ; The minimum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_min' _item.category_id _item.category_id _item.mandatory_code no _item_default.value 1.0 _item_range.maximum 1.0 _item_range.minimum 0.0 _item_type.code float
_category.description
;
Data items in the REFINE_B_ISO category record details about
the treatment of isotropic B (temperature) factors during
refinement.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_refine_b_iso.class'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_refine_b_iso.class
_refine_b_iso.treatment
'protein' isotropic
'solvent' isotropic
'inhibitor' isotropic
;
_item_description.description
;
A class of atoms treated similarly for isotropic B (temperature)
factor refinement.
;
_item.name '_refine_b_iso.class'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'all'
'protein'
'solvent'
'sugar-phosphate backbone'
_item_description.description
;
A description of special aspects of the isotropic B (temperature)
factor refinement for the class of atoms described in
_refine_b_iso.class.
;
_item.name '_refine_b_iso.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The temperature factors of atoms in the side
chain of Arg 92 were held fixed due to
unstable behavior in refinement.
;
_item_description.description
;
The treatment of isotropic B (temperature) factor refinement for
a class of atoms defined in _refine_b_iso.class.
;
_item.name '_refine_b_iso.treatment'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
fixed
isotropic
anisotropic
_item_description.description
;
The value of the isotropic B (temperature) factor assigned to a
class of atoms defined in _refine_b_iso.class. Meaningful only
for atoms with fixed isotropic B (temperature) factors.
;
_item.name '_refine_b_iso.value'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms_squared'
_category.description
;
Data items in the REFINE category record details about the
various steps along the way in the refinement of the structure.
These data items are not meant to be as thorough as description
of the refinement as is provided for the final model in other
categories; rather, these data items provide a mechanism for
sketching out the progress of the refinement, supported by a
small set of representative statistics.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_refine_hist.cycle_id'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
_item_description.description
;
The value of refine_hist.cycle_id must uniquely identify a record
in the REFINE_HIST list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_refine_hist.cycle_id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
_item_description.description
;
The highest resolution for the interplanar spacing in the
reflection data for this cycle of refinement.
;
_item.name '_refine_hist.d_res_high'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
The lowest resolution for the interplanar spacing in the
reflection data for this cycle of refinement.
;
_item.name '_refine_hist.d_res_low'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
Description of special aspects of this cycle of the refinement
process.
;
_item.name '_refine_hist.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Residues 13-17 fit and added to model;
substantinal rebuilding of loop containing
residues 43-48; addition of first atoms to
solvent model; ten cycles of Prolsq
refinement.
;
save_refine_hist.number_atoms_solvent.
_item_description.description
;
The number of solvent atoms that were included in the model at
this cycle of the refinement.
;
_item.name '_refine_hist.number_atoms_solvent'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine_hist.number_atoms_total.
_item_description.description
;
The total number of atoms that were included in the model at
this cycle of the refinement.
;
_item.name '_refine_hist.number_atoms_total'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine_hist.number_reflns_obs.
_item_description.description
;
The number of reflections that were included in this cycle of
the refinement.
;
_item.name '_refine_hist.number_reflns_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine_hist.R_factor_obs.
_item_description.description
;
Residual factor R for reflections that were included in the
this cycle of the refinement.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|]
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine_hist.R_factor_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_refine_ls.number_reflns_R_free.
_item_description.description
;
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low,
that were flagged as observed (see _reflns.observed_criterion),
but that were excluded from refinement (see
_reflns.R_free_details) so as to be included in the calculation
of a "free" R-factor.
;
_item.name '_refine_ls.number_reflns_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_category.description
;
Data items in the REFINE_LS_RESTR category record details about
the restraints applied to various classes of parameters during
least-squares refinement.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_refine_ls_restr.type'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.dev_ideal
_refine_ls_restr.number
_refine_ls_restr.criterion
_refine_ls_restr.rejects
'bond_d' 0.020 0.018 1654 '> 2\s' 22
'angle_d' 0.030 0.038 2246 '> 2\s' 139
'planar_d' 0.040 0.043 498 '> 2\s' 21
'planar' 0.020 0.015 270 '> 2\s' 1
'chiral' 0.150 0.177 278 '> 2\s' 2
'singtor_nbd' 0.500 0.216 582 '> 2\s' 0
'multtor_nbd' 0.500 0.207 419 '> 2\s' 0
'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0
'planar_tor' 3.0 2.6 203 '> 2\s' 9
'staggered_tor' 15.0 17.4 298 '> 2\s' 31
'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1
;
save_refine_ls_restr.criterion.
_item_description.description
;
A criterion used to define a parameter value that deviates
significantly from its ideal value in the model obtained by
restrained least-squares refinement.
;
_item.name '_refine_ls_restr.criterion'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case '> 3\s'
save_refine_ls_restr.dev_ideal.
_item_description.description
;
For the given parameter type, the root-mean-square deviation
between the ideal values used as restraints in the least-squares
refinement and the values obtained by refinement. For instance,
bond distances may deviate by 0.018 \%A (rms) from ideal values
in current model.
;
_item.name '_refine_ls_restr.dev_ideal'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_refine_ls_restr.dev_ideal_target.
_item_description.description
;
For the given parameter type, the target root-mean-square
deviation between the ideal values used as restraints in the
least-squares refinement and the values obtained by refinement.
;
_item.name '_refine_ls_restr.dev_ideal_target'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_description.description
;
The number parameters of this type subjected to restraint in
least-squares refinement.
;
_item.name '_refine_ls_restr.number'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_item_description.description
;
The number of parameters of this type that deviate from ideal
values by more than the amount defined in
_refine_ls_restr.criterion in the model obtained by restrained
least-squares refinement.
;
_item.name '_refine_ls_restr.rejects'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_item_description.description
;
The type of the parameter being restrained.
An explicit set of data values are provided for programs Protin/
Prolsq (beginning with p_) and X-plor (beginning with x_).
As computer programs will evolve, these data values are given
as examples, and not as an enumeration list. Computer programs
converting a CIF to a refinement table will expect the exact
form of the data values given here to be used.
;
_item.name '_refine_ls_restr.type'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
_item_examples.detail
'p_bond_d'
'bond distance'
'p_angle_d'
'bond angle expressed as a distance'
'p_planar_d'
'planar 1,4 distance'
'p_xhbond_d'
'x-h bond distance'
'p_xhangle_d'
'x-h bond angle expressed as a distance'
'p_hydrog_d'
'hydrogen distance'
'p_special_d'
'special distance'
'p_planar'
'planes'
'p_chiral'
'chiral centers'
'p_singtor_nbd'
'single-torsion non-bonded contact'
'p_multtor_nbd'
'multiple-torsion non-bonded contact'
'p_xyhbond_nbd'
'possible (x....y) hydrogen-bond'
'p_xhyhbond_nbd'
'possible (x-h..y) hydrogen-bond'
'p_special_tor'
'special torsion angle'
'p_planar_tor'
'planar torsion angle'
'p_staggered_tor'
'staggered torsion angle'
'p_orthonormal_tor'
'orthonormal torsion angle'
'p_mcbond_it'
'main-chain bond isotropic thermal factor'
'p_mcangle_it'
'main-chain angle isotropic thermal factor'
'p_scbond_it'
'side-chain bond isotropic thermal factor'
'p_scangle_it'
'side-chain angle isotropic thermal factor'
'p_xhbond_it'
'x-h bond isotropic thermal factor'
'p_xhangle_it'
'x-h angle isotropic thermal factor'
'p_special_it'
'special isotropic thermal factor'
_category.description
;
Data items in the REFINE_LS_SHELL category record details about
the results of least-squares refinement, broken out by shells of
resolution.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_refine_ls_shell.d_res_low'
'_refine_ls_shell.d_res_high'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_refine_ls_shell.d_res_low
_refine_ls_shell.d_res_high
_refine_ls_shell.reflns
_refine_ls_shell.R_factor_obs
8.00 4.51 1226 0.196
4.51 3.48 1679 0.146
3.48 2.94 2014 0.160
2.94 2.59 2147 0.182
2.59 2.34 2127 0.193
2.34 2.15 2061 0.203
2.15 2.00 1647 0.188
;
save_refine_ls_shell.d_res_high.
_item_description.description
;
The highest resolution for the interplanar spacing in the
reflection data in this shell. These is the largest d value.
;
_item.name '_refine_ls_shell.d_res_high'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_refine_ls_shell.d_res_low.
_item_description.description
;
The lowest resolution for the interplanar spacing in the
reflection data in this shell. This is the smallest d value.
;
_item.name '_refine_ls_shell.d_res_low'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_refine_ls_shell.number_reflns_all.
_item_description.description ; The total number of reflections in this shell. ; _item.name '_refine_ls_shell.number_reflns_all' _item.category_id _item.category_id _item.mandatory_code no _item_range.maximum ? _item_range.minimum 0 _item_type.code int
save_refine_ls_shell.number_reflns_obs.
_item_description.description
;
The number of reflections in this shell that were flagged as
observed (see _reflns.observed_criterion) and included in the
refinement.
;
_item.name '_refine_ls_shell.number_reflns_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine_ls_shell.number_reflns_R_free.
_item_description.description
;
The number of reflections in this shell that were flagged as
observed (see _reflns.observed_criterion) but excluded from
refinement (see _reflns.R_free_details) so as to be included in
the calculation of a "free" R-factor.
;
_item.name '_refine_ls_shell.number_reflns_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_refine_ls_shell.R_factor_all.
_item_description.description
;
Residual factor R for all reflections in this shell.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|];
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine_ls_shell.R_factor_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.wR_factor_all'
'alternate'
_item_type.code float
save_refine_ls_shell.R_factor_obs.
_item_description.description
;
Residual factor R for reflections in this shell that were flagged
as observed (see _reflns.observed_criterion) and included in the
refinement.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|]
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine_ls_shell.R_factor_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.wR_factor_obs'
'alternate'
_item_type.code float
save_refine_ls_shell.R_factor_R_free.
_item_description.description
;
Residual factor R for reflections in this shell that were flagged
as observed (see _reflns.observed_criterion) but excluded from
refinement (see _reflns.R_free_details) so as to be included in
the calculation of a "free" R-factor.
R = [sum||F~m~|-|F~c~|| / sum|F~m~|]
F~m~ and F~c~ are the measured and calculated structure factors.
This is the conventional R factor.
;
_item.name '_refine_ls_shell.R_factor_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.wR_factor_R_free'
'alternate'
_item_type.code float
save_refine_ls_shell.wR_factor_all.
_item_description.description
;
Weighted residual factor wR for all reflections in this shell.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine_ls_shell.wR_factor_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.R_factor_all'
'alternate'
_item_type.code float
save_refine_ls_shell.wR_factor_obs.
_item_description.description
;
Weighted residual factor wR for reflections in this shell that
were flagged as observed (see _reflns.observed_criterion) and
included in the refinement.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine_ls_shell.wR_factor_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.R_factor_obs'
'alternate'
_item_type.code float
save_refine_ls_shell.wR_factor_R_free.
_item_description.description
;
Weighted residual factor wR for reflections in this shell that
were flagged as observed (see _reflns.observed_criterion) but
excluded from refinement (see _reflns.R_free_details) so as to be
included in the calculation of a "free" R-factor.
wR = [sum(w|Y~m~-Y~c~|^2^) / sum(wY~m~^2^)]^1/2^
Y~m~ and Y~c~ are the measured and calculated coefficients
specified by _refine.ls_structure_factor_coef and w is the least
squares weight.
;
_item.name '_refine_ls_shell.wR_factor_R_free'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
loop_
_item_related.related_name
_item_related.function_code
'_refine_ls_shell.R_factor_R_free'
'alternate'
_item_type.code float
_category.description
;
Data items in the REFINE_OCCUPANCY category record details
about the treatment of atomic occupancies during refinement.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_refine_occupancy.class'
loop_
_category_group.id
'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_refine_occupancy.class
_refine_occupancy.treatment
_refine_occupancy.value
_refine_occupancy.details
'protein' fix 1.00 .
'solvent' fix 1.00 .
'inhibitor orientation 1' fix 0.65 .
'inhibitor orientation 2' fix 0.35
; The inhibitor binds to the enzyme in two alternative conformations. The
occupancy of each conformation was adjusted so as to result in
approximately equal mean thermal factors for the atoms in each
conformation.
;
;
_item_description.description ; The class of atoms treated similarly for occupancy refinement. ; _item.name '_refine_occupancy.class' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone'
save_refine_occupancy.details.
_item_description.description
;
A description of special aspects of the occupancy refinement for
a class of atoms described in _refine_occupancy.class.
;
_item.name '_refine_occupancy.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The inhibitor binds to the enzyme in two alternative
conformations. The occupancy of each conformation was
adjusted so as to result in approximately equal mean
thermal factors for the atoms in each conformation.
;
save_refine_occupancy.treatment.
_item_description.description
;
The treatment of occupancy refinement for a class of atoms
described in _refine_occupancy.class.
;
_item.name '_refine_occupancy.treatment'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
fix
fixed
ref
refined
_item_description.description
;
The value of occupancy assigned to a class of atoms defined in
_refine_occupancy.class. Meaningful only for atoms with fixed
occupancy.
;
_item.name '_refine_occupancy.value'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum 1.0
_item_range.minimum 0.0
_item_type.code float
loop_
_item_examples.case
1.0
0.41
_category.description
;
Data items in the REFLN category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in loop lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_refln.index_h'
'_refln.index_k'
'_refln.index_l'
loop_
_category_group.id
'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
;
Example 2 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[(1993). Acta Cryst. C49, 1352-1354].
;
;
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_squared_calc
_refln.F_squared_meas
_refln.F_squared_sigma
_refln.observed_status
2 0 0 85.57 58.90 1.45 o
3 0 0 15718.18 15631.06 30.40 o
4 0 0 55613.11 49840.09 61.86 o
5 0 0 246.85 241.86 10.02 o
6 0 0 82.16 69.97 1.93 o
7 0 0 1133.62 947.79 11.78 o
8 0 0 2558.04 2453.33 20.44 o
9 0 0 283.88 393.66 7.79 o
10 0 0 283.70 171.98 4.26 o
;
_item_description.description
;
The calculated value of structure-factor component A in
electrons.
A = |F|cos(phase)
;
_item.name '_refln.A_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_A_calc'
_item_type.code float
_item_units.code 'electrons'
_item_description.description
;
The measured value of structure-factor component A in electrons.
A = |F|cos(phase)
;
_item.name '_refln.A_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_A_meas'
_item_type.code float
_item_units.code 'electrons'
_item_description.description
;
The calculated value of structure-factor component B in
electrons.
B = |F|sin(phase)
;
_item.name '_refln.B_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_B_calc'
_item_type.code float
_item_units.code 'electrons'
_item_description.description
;
The measured value of structure-factor component B in electrons.
B = |F|sin(phase)
;
_item.name '_refln.B_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_B_meas'
_item_type.code float
_item_units.code 'electrons'
_item_description.description
;
This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item_aliases.alias_name '_refln_crystal_id'
_item_description.description ; The calculated value of the structure factor, in electrons. ; _item.name '_refln.F_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_calc' _item_type.code float _item_units.code 'electrons'
_item_description.description ; The measured value of the structure factor, in electrons. ; _item.name '_refln.F_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_F_meas' _item_type.code float _item_units.code 'electrons'
_item_description.description
;
The standard deviation (derived from measured value) of the
structure factor, in electrons.
;
_item.name '_refln.F_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_sigma'
_item_type.code float
_item_units.code 'electrons'
_item_description.description
;
The calculated value of the squared structure factor, in
electrons squared.
;
_item.name '_refln.F_squared_calc'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_calc'
_item_type.code float
_item_units.code 'electrons_squared'
_item_description.description
;
The measured value of the squared structure factor, in electrons
squared.
;
_item.name '_refln.F_squared_meas'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_meas'
_item_type.code float
_item_units.code 'electrons_squared'
_item_description.description
;
The estimated standard deviation of the squared structure
factor, in electrons squared.
;
_item.name '_refln.F_squared_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_sigma'
_item_type.code float
_item_units.code 'electrons_squared'
_item_description.description
;
For phasing experiments using MIR, the Hendrickson-Lattman
coefficient A.
A = please fill in Eleanor
where...
;
_item.name '_refln.HL_coeff_A'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description
;
Miller index h of the reflection.
The values of the Miller indices in the REFLN category must
correspond to the cell defined by cell lengths and cell angles
in the CELL category.
;
_item.name '_refln.index_h'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_refln_index_h'
loop_
_item_dependent.dependent_name
'_refln.index_k'
'_refln.index_l'
_item_type.code int
_item_description.description
;
Miller index k of the reflection.
The values of the Miller indices in the REFLN category must
correspond to the cell defined by cell lengths and cell angles
in the CELL category.
;
_item.name '_refln.index_k'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_refln_index_k'
loop_
_item_dependent.dependent_name
'_refln.index_h'
'_refln.index_l'
_item_type.code int
_item_description.description
;
Miller index l of the reflection.
The values of the Miller indices in the REFLN category must
correspond to the cell defined by cell lengths and cell angles
in the CELL category.
;
_item.name '_refln.index_l'
_item.category_id _item.category_id
_item.mandatory_code yes
_item.sub_category_id 'miller_index'
_item_aliases.alias_name '_refln_index_l'
loop_
_item_dependent.dependent_name
'_refln.index_h'
'_refln.index_k'
_item_type.code int
_item_description.description ; The calculated value of the intensity, in the measured units. ; _item.name '_refln.intensity_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_calc' _item_type.code float
_item_description.description ; The measured value of the intensity, in the measured units. ; _item.name '_refln.intensity_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_meas' _item_type.code float
_item_description.description
;
The standard deviation (derived from measured data) of the
intensity, in the measured units.
;
_item.name '_refln.intensity_sigma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_intensity_sigma'
_item_type.code float
save_refln.mean_path_length_tbar.
_item_description.description ; Mean path length through the crystal for this reflection. ; _item.name '_refln.mean_path_length_tbar' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_mean_path_length_tbar' _item_type.code float _item_units.code 'millimetres'
_item_description.description ; The calculated value of the structure-factor phase in degrees. ; _item.name '_refln.phase_calc' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_phase_calc' _item_type.code float _item_units.code 'degrees'
_item_description.description ; The measured value of the structure-factor phase in degrees. ; _item.name '_refln.phase_meas' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_phase_meas' _item_type.code float _item_units.code 'degrees'
_item_description.description ; Status of reflection in the structure refinement process. ; _item.name '_refln.refinement_status' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_refinement_status' _item_default.value incl _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction'
_item_description.description ; The (sin theta)/lambda for this reflection. ; _item.name '_refln.sint/lambda' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_refln_sint/lambda' _item_range.maximum ? _item_range.minimum 0.0 _item_type.code float _item_units.code 'reciprocal_angstroms'
_item_description.description
;
Classification of a reflection so at to indicate its status with
respect to inclusion in refinement and calculation of R-factors.
;
_item.name '_refln.status'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_observed_status'
_item_default.value o
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
o
;
satisfies _refine.d_res_high
satisfies _refine.d_res_low
observed by _reflns_observed_criterion
;
<
;
satisfies _refine.d_res_high
satisfies _refine.d_res_low
unobserved by _reflns_observed_criterion
;
-
'systematically absent reflection'
x
'unreliable measurement -- not used'
h
'does not satisfy _refine.d_res_high'
l
'does not satifsy _refine.d_res_low'
f
;
satisfies _refine.d_res_high
satisfies _refine.d_res_low
observed by _reflns_observed_criterion
excluded from refinement so as to be
included in calculation of "free" R-factor
;
_item_description.description
;
The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
space-group symmetry operations.
;
_item.name '_refln.symmetry_epsilon'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_symmetry_epsilon'
_item_range.maximum 32
_item_range.minimum 1
_item_type.code int
save_refln.symmetry_multiplicity.
_item_description.description
;
The number of symmetry-equivalent reflections. The equivalent
reflections have the same structure-factor value because of the
space-group symmetry and the Friedel relationship.
;
_item.name '_refln.symmetry_multiplicity'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_symmetry_multiplicity'
_item_range.maximum 24
_item_range.minimum 1
_item_type.code int
_item_description.description
;
The mean wavelength of radiation used to measure this reflection.
This is an important parameter for data collected using energy-
dispersive detectors or the Laue method.
;
_item.name '_refln.wavelength'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_refln_wavelength'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
This data item is a pointer to _diffrn_radiation.wavelength_id in
the DIFFRN_RADIATION category.
;
_item_aliases.alias_name '_refln_wavelength_id'
_category.description
;
Data items in the REFLNS category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_reflns.block_id'
loop_
_category_group.id
'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_reflns.data_reduction_method
; Xengen program scalei. Anomalous paris were merged. Scaling proceeded
in several passes, beginning with 1-parameter fit and ending with
3-parameter fit.
;
_reflns.data_reduction_details
; Merging and scaling based on only those reflections with I > \s(I).
;
_reflns.d_resolution_high 2.00
_reflns.d_resolution_low 8.00
_reflns.limit_h_max 22
_reflns.limit_h_min 0
_reflns.limit_k_max 46
_reflns.limit_k_min 0
_reflns.limit_l_max 57
_reflns.limit_l_min 0
_reflns.number_obs 7228
_reflns.observed_criterion '> 1 \s(I)'
_reflns.details none
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_reflns.limit_h_min 0
_reflns.limit_h_max 6
_reflns.limit_k_min 0
_reflns.limit_k_max 17
_reflns.limit_l_min 0
_reflns.limit_l_max 22
_reflns.number_all 1592
_reflns.number_obs 1408
_reflns.observed_criterion F_>_6.0_\s(F)
_reflns.d_resolution_high 0.8733
_reflns.d_resolution_low 11.9202
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
save_reflns.d_resolution_high.
_item_description.description
;
The highest resolution for the interplanar spacings in
the reflection data. This is the smallest d value.
;
_item.name '_reflns.d_resolution_high'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_d_resolution_high'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
The lowest resolution for the interplanar spacings in the
reflection data. This is the largest d value.
;
_item.name '_reflns.d_resolution_low'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_d_resolution_low'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_reflns.data_reduction_details.
_item_description.description
;
A description of special aspects of the data reduction
procedures.
;
_item.name '_reflns.data_reduction_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Merging and scaling based on only those reflections
with I > sig(I).
;
save_reflns.data_reduction_method.
_item_description.description
;
The method used in reducing the data.
Note that this is not the computer program used, which is
described in _computing.save_reduction.
Rather this data item should be used to describe significant
methodological options used within the data reduction programs.
;
_item.name '_reflns.data_reduction_method'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
Profile fitting by methods of Kabsch (19xx). Scaling
used spherical harmonic coefficients.
;
_item_description.description
;
A description of reflection data not covered by the other data
names. It should include details of the Friedel reflection data.
;
_item.name '_reflns.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_special_details'
_item_type.code char
_item_description.description
;
Maximum value of Miller index h for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_h_max.
;
_item.name '_reflns.limit_h_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_h_max'
_item_type.code int
_item_description.description
;
Minimum value of Miller index h for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_h_min.
;
_item.name '_reflns.limit_h_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_h_min'
_item_type.code int
_item_description.description
;
Maximum value of Miller index k for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_k_max.
;
_item.name '_reflns.limit_k_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_k_max'
_item_type.code int
_item_description.description
;
Minimum value of Miller index k for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_k_min.
;
_item.name '_reflns.limit_k_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_k_min'
_item_type.code int
_item_description.description
;
Maximum value of Miller index l for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_l_max.
;
_item.name '_reflns.limit_l_max'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_l_max'
_item_type.code int
_item_description.description
;
Minimum value of Miller index l for the reflection data. This
need not be have the same value as _diffrn_reflns.limit_l_min.
;
_item.name '_reflns.limit_l_min'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_l_min'
_item_type.code int
_item_description.description
;
The total number of reflections in the REFLN list (not the
DIFFRN_REFLN list). This number may contain Friedel equivalent
reflections according to the nature of the structure and the
procedures used. The item _reflns.details describes the
reflection data.
;
_item.name '_reflns.number_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_number_total'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
_item_description.description
;
The number of reflections in the REFLN list (not the DIFFRN_REFLN
list) classified as observed (see _reflns_observed_criterion).
This number may contain Friedel equivalent reflections according
to the nature of the structure and the procedures used.
;
_item.name '_reflns.number_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_number_observed'
_item_range.maximum ?
_item_range.minimum 0
_item_type.code int
save_reflns.observed_criterion.
_item_description.description
;
The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of an e.s.d. threshold.
;
_item.name '_reflns.observed_criterion'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_observed_criterion'
_item_type.code char
_item_examples.case '>2sigma(I)'
_item_description.description
;
A description of the method by which a subset of reflections was
selected for exclusion from refinement so as to be used in the
calculation of a "free" R-factor.
;
_item.name '_reflns.R_free_details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The data set was sorted with l varying most
rapidly and h varying least rapidly. Every
10th reflection is this sorted list was
excluded from refinement and included in the
calculation of a "free" R-factor.
;
_category.description
;
Data items in the REFLNS_SCALE category record details about
the structure factor scales. They are referenced from within
the REFLN list through _refln.scale_group_code.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_reflns_scale.group_code'
loop_
_category_group.id
'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
_item_description.description
;
The code identifying a scale _reflns_scale.meas_. These are
linked to the REFLN list by the _refln.scale_group_code.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_reflns_scale.group_code'
reflns_scale
yes
'_refln.scale_group_code'
refln
yes
_item_aliases.alias_name '_reflns_scale_group_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_refln.scale_group_code'
'_reflns_scale.group_code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
c1
c2
c3
_item_description.description
;
The code identifying a scale _reflns_scale.meas_. These are
linked to the REFLN list by the _refln.scale_group_code.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_reflns_scale.group_code'
reflns_scale
yes
'_refln.scale_group_code'
refln
yes
_item_aliases.alias_name '_reflns_scale_group_code'
loop_
_item_linked.child_name
_item_linked.parent_name
'_refln.scale_group_code'
'_reflns_scale.group_code'
_item_type.code char
loop_
_item_examples.case
1
2
3
s1
A
B
c1
c2
c3
_item_description.description
;
A scale associated with _reflns_scale.group_code. These codes
may not correspond to those in the DIFFRN_SCALE list.
;
_item.name '_reflns_scale.meas_F'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_F'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_scale.meas_F_squared.
_item_description.description
;
A scale associated with _reflns_scale.group_code. These codes
may not correspond to those in the DIFFRN_SCALE list.
;
_item.name '_reflns_scale.meas_F_squared'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_F_squared'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_scale.meas_intensity.
_item_description.description
;
A scale associated with _reflns_scale.group_code. These codes
may not correspond to those in the DIFFRN_SCALE list.
;
_item.name '_reflns_scale.meas_intensity'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_intensity'
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_category.description
;
Data items in the REFLNS_SHELL category record details about
the reflection data used to determine the ATOM_SITE data items,
as broken down by shells of resolution.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_reflns_shell.d_res_high'
'_reflns_shell.d_res_low'
loop_
_category_group.id
'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.meanI/sigI_obs
_reflns_shell.number_measured_obs
_reflns_shell.number_unique_obs
_reflns_shell.possible_%_obs
_reflns_shell.Rmerge_F_obs
31.38 3.82 69.8 9024 2540 96.8 1.98
3.82 3.03 26.1 7413 2364 95.1 3.85
3.03 2.65 10.5 5640 2123 86.2 6.37
2.65 2.41 6.4 4322 1882 76.8 8.01
2.41 2.23 4.3 3247 1714 70.4 9.86
2.23 2.10 3.1 1140 812 33.3 13.99
;
_item_description.description
;
The highest for the interplanar spacing in the reflection data in
this shell. This is the smallest d value.
;
_item.name '_reflns_shell.d_res_high'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
_item_description.description
;
The lowest resolution for the interplanar spacing in the
reflection data in this shell. This is the largest d value.
;
_item.name '_reflns_shell.d_res_low'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_item_units.code 'angstroms'
save_reflns_shell.meanI/sigI_all.
_item_description.description
;
The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard deviations of the
intensities of all reflections in the resolution shell.
;
_item.name '_reflns_shell.meanI/sigI_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_reflns_shell.meanI/sigI_obs.
_item_description.description
;
The ratio of the mean of the intensities of the reflections
classified as 'observed' (see _reflns_observed_criterion) in this
shell to the mean of the standard deviations of the intensities
of the 'observed' reflections in the resolution shell.
.
;
_item.name '_reflns_shell.meanI/sigI_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_reflns_shell.number_measured_all.
_item_description.description
;
The total number of diffraction reflections measured for this
resolution shell.
;
_item.name '_reflns_shell.number_measured_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_reflns_shell.number_measured_obs.
_item_description.description
;
The number of diffraction reflections classified as 'observed'
(see _reflns_observed_criterion) measured for this
resolution shell
;
_item.name '_reflns_shell.number_measured_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_reflns_shell.number_possible.
_item_description.description
;
The number of unique reflections it is possible to measure in
this reflection shell.
;
_item.name '_reflns_shell.number_possible'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code int
save_reflns_shell.number_unique_all.
_item_description.description
;
The total number of diffraction reflections which are
symmetrically unique after merging for this resolution shell.
;
_item.name '_reflns_shell.number_unique_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_reflns_shell.number_unique_obs.
_item_description.description
;
The total number of diffraction reflections classified as
'observed' (see _reflns_observed_criterion) which are
symmetrically unique after merging for this resolution shell.
;
_item.name '_reflns_shell.number_unique_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code int
save_reflns_shell.percent_possible_all.
_item_description.description
;
The percentage of geometrically possible diffraction reflections
represented by all diffraction reflections measured for this
resolution shell.
;
_item.name '_reflns_shell.percent_possible_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_shell.percent_possible_obs.
_item_description.description
;
The percentage of geometrically possible diffraction reflections
represented by diffraction reflections classified as
'observed' (see _reflns_observed_criterion) measured for this
resolution shell.
;
_item.name '_reflns_shell.percent_possible_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_shell.Rmerge_F_all.
_item_description.description
;
The value of Rmerge(F) for all reflections in a given shell.
Rmerge(F) = sum~i~ [sum~j~ |F~j~-|] / sum~i~ [sum~j~ ||]
were sum~i is taken over all reflections and
sum~j is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_F_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_shell.Rmerge_F_obs.
_item_description.description
;
The value of Rmerge(F) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
Rmerge(F) = sum~i~ [sum~j~ |F~j~-|] / sum~i~ [sum~j~ ||]
were sum~i is taken over all reflections and
sum~j is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_F_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_shell.Rmerge_I_all.
_item_description.description
;
The value of Rmerge(I) for all reflections in a given shell.
Rmerge(I) - sum~i~ [sum~j~ |I~j~-|] / sum~i~ [sum~j~ ||]
were sum~i is taken over all reflections and
sum~j is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_I_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
save_reflns_shell.Rmerge_I_obs.
_item_description.description
;
The value of Rmerge(I) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
Rmerge(I) - sum~i~ [sum~j~ |I~j~-|] / sum~i~ [sum~j~ ||]
were sum~i is taken over all reflections and
sum~j is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_I_obs'
_item.category_id _item.category_id
_item.mandatory_code no
_item_range.maximum ?
_item_range.minimum 0.0
_item_type.code float
_category.description
;
Data items in the STRUCT category record details about the
description of the crystallographic structure.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct.block_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_struct.title
; HIV-1 protease complex with acetyl-pepstatin
;
loop_ _struct.keywords
'enzyme-inhibitor complex'
'aspartyl protease'
'structure-based drug design'
'static disorder'
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; Keywords for the structure archived in the CIF. ; _item.name '_struct.keywords' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'serine protease' 'inhibited complex' 'high resolution refinement'
_item_description.description
;
A title for the CIF. The author should attempt to convey the
essence of the structure archived in the CIF in the title, and
to distinguish this structural result from others.
;
_item.name '_struct.title'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
"5'-D(*(I)CP*CP*GP*G)-3"
'T4 lysozyme mutant - S32A'
'hen egg white lysozyme at -30 degrees C'
'quail egg white lysozyme at 2 atmospheres'
_category.description
;
Data items in the STRUCT_ASYM category record details about the
structural elements in the asymmetric unit.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_asym.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'one monomer of the dimeric enzyme'
B 1 'one monomer of the dimeric enzyme'
C 2 'one partially occupied position for the inhibitor'
D 2 'one partially occupied position for the inhibitor'
;
_item_description.description
;
A description of special aspects of this portion of the contents
of the asymmetric unit.
;
_item.name '_struct_asym.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is
roughly twofold symmetric to biological unit (2).
Disorder in the protein chain indicated with alternative
id 2 should be used with this biological unit.
;
_item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ;
_item_description.description
;
The value of _struct_asym.id must uniquely identify a record in
the STRUCT_ASYM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_asym.id'
struct_asym
yes
'_atom_site.label_asym_id'
atom_site
yes
'_struct_biol_gen.asym_id'
struct_biol_gen
yes
'_struct_conf.beg_label_asym_id'
struct_conf
yes
'_struct_conf.end_label_asym_id'
struct_conf
yes
'_struct_conn.ptnr1_label_asym_id'
struct_conn
yes
'_struct_conn.ptnr2_label_asym_id'
struct_conn
yes
'_struct_mon_nucl.label_asym_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_asym_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_asym_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_asym_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_asym_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_asym_id'
struct_site
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_asym_id'
'_struct_asym.id'
'_struct_biol_gen.asym_id'
'_struct_asym.id'
'_struct_conf.beg_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conf.end_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conn.ptnr1_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conn.ptnr2_label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_nucl.label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_prot.label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_prot_cis.label_asym_id'
'_atom_site.label_asym_id'
'_struct_ncs_dom_gen.beg_label_asym_id'
'_atom_site.label_asym_id'
'_struct_ncs_dom_gen.end_label_asym_id'
'_atom_site.label_asym_id'
'_struct_site_gen.label_asym_id'
'_atom_site.label_asym_id'
_item_type.code char
loop_
_item_examples.case
1
A
2B3
_item_description.description
;
The value of _struct_asym.id must uniquely identify a record in
the STRUCT_ASYM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_asym.id'
struct_asym
yes
'_atom_site.label_asym_id'
atom_site
yes
'_struct_biol_gen.asym_id'
struct_biol_gen
yes
'_struct_conf.beg_label_asym_id'
struct_conf
yes
'_struct_conf.end_label_asym_id'
struct_conf
yes
'_struct_conn.ptnr1_label_asym_id'
struct_conn
yes
'_struct_conn.ptnr2_label_asym_id'
struct_conn
yes
'_struct_mon_nucl.label_asym_id'
struct_mon_nucl
yes
'_struct_mon_prot.label_asym_id'
struct_mon_prot
yes
'_struct_mon_prot_cis.label_asym_id'
struct_mon_prot_cis
yes
'_struct_ncs_dom_gen.beg_label_asym_id'
struct_ncs_dom_gen
yes
'_struct_ncs_dom_gen.end_label_asym_id'
struct_ncs_dom_gen
yes
'_struct_site_gen.label_asym_id'
struct_site
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_asym_id'
'_struct_asym.id'
'_struct_biol_gen.asym_id'
'_struct_asym.id'
'_struct_conf.beg_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conf.end_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conn.ptnr1_label_asym_id'
'_atom_site.label_asym_id'
'_struct_conn.ptnr2_label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_nucl.label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_prot.label_asym_id'
'_atom_site.label_asym_id'
'_struct_mon_prot_cis.label_asym_id'
'_atom_site.label_asym_id'
'_struct_ncs_dom_gen.beg_label_asym_id'
'_atom_site.label_asym_id'
'_struct_ncs_dom_gen.end_label_asym_id'
'_atom_site.label_asym_id'
'_struct_site_gen.label_asym_id'
'_atom_site.label_asym_id'
_item_type.code char
loop_
_item_examples.case
1
A
2B3
_category.description
;
Data items in the STRUCT_BIOL category record details about
the structural elements that form each structure of biological
significance.
A given crystal structure may contain many different biological
structures. A given structural component in the asymmetric
unit may be part of more than one biological unit. A given
biological structure may involve crystallographic symmetry.
For instance, in a structure of a lysozyme-FAB structure, the
light and heavy chain components of the FAB could be one
biological unit, while the two chains of the FAB and the lysozyme
could constitute a second biological unit.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_biol.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_biol.id
_struct_biol.details
1
; significant deviations from twofold symmetry exist in this dimeric
enzyme
;
2
; The drug binds to this enzyme in two roughly twofold symmetric modes.
Hence this biological unit (2) is roughly twofold symmetric to biological
unit (3). Disorder in the protein chain indicated with alternative
id 1 should be used with this biological unit.
;
3
; The drug binds to this enzyme in two roughly twofold symmetric modes.
Hence this biological unit (3) is roughly twofold symmetric to biological
unit (2). Disorder in the protein chain indicated with alternative
id 2 should be used with this biological unit.
;
;
_item_description.description
;
A description of special aspects of the biological unit.
;
_item.name '_struct_biol.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is
roughly twofold symmetric to biological unit (2).
Disorder in the protein chain indicated with alternative
id 2 should be used with this biological unit.
;
_item_description.description
;
The value of _struct_biol.id must uniquely identify a record in
the STRUCT_BIOL list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_biol.id'
struct_biol
yes
'_struct_biol_gen.biol_id'
struct_biol_gen
yes
'_struct_biol_keywords.biol_id'
struct_biol_keywords
yes
'_struct_biol_view.biol_id'
struct_biol_view
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_biol_gen.biol_id'
'_struct_biol.id'
'_struct_biol_keywords.biol_id'
'_struct_biol.id'
'_struct_biol_view.biol_id'
'_struct_biol.id'
_item_type.code char
_category.description
;
Data items in the STRUCT_BIOL_GEN category record details about
the generation of each biological unit. The STRUCT_BIOL_GEN
data items provide the specifications of the components that
constitute that biological unit, which may include symmetry
elements.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_biol_gen.biol_id'
'_struct_biol_gen.asym_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_biol_gen.biol_id
_struct_biol_gen.asym_id
_struct_biol_gen.symmetry
1 A 1_555
1 B 1_555
2 A 1_555
2 B 1_555
2 C 1_555
3 A 1_555
3 B 1_555
3 D 1_555
;
_item_description.description
;
This data item is a pointer to _struct_asym.id in the STRUCT_ASYM
category.
;
_item_description.description
;
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
_item_description.description
;
A description of special aspects of the symmetry generation of
this portion of the biological structure.
;
_item.name '_struct_biol_gen.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The zinc atom lies on a special position; application
of symmetry elements to generate the insulin hexamer
will generate excess zinc atoms, which must be removed
by hand.
;
save_struct_biol_gen.symmetry.
_item_description.description
;
Describes the symmetry operation that should be applied to the
atom set specified by _struct_biol_gen.asym_id to generate a
portion of the biological structure.
;
_item.name '_struct_biol_gen.symmetry'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_category.description
;
Data items in the STRUCT_BIOL_KEYWORDS category record details
about keywords that describe each biological unit.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_biol_keywords.biol_id'
'_struct_biol_keywords.text'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_biol_keywords.biol_id
_struct_biol_keywords.text
1 'aspartyl-protease'
1 'aspartic-protease'
1 'acid-protease'
1 'aspartyl-proteinase'
1 'aspartic-proteinase'
1 'acid-proteinase'
1 'enzyme'
1 'protease'
1 'proteinase'
1 'dimer'
2 'drug-enzyme complex'
2 'inhibitor-enzyme complex'
2 'drug-protease complex'
2 'inhibitor-protease complex'
3 'drug-enzyme complex'
3 'inhibitor-enzyme complex'
3 'drug-protease complex'
3 'inhibitor-protease complex'
;
save_struct_biol_keywords.biol_id.
_item_description.description
;
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
save_struct_biol_keywords.text.
_item_description.description ; Keywords describing this biological entity. ; _item.name '_struct_biol_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case antibody antigen enzyme cytokine tRNA
_category.description
;
Data items in the STRUCT_BIOL_VIEW category record details
about how to draw and annotate a useful didactic view of the
biological structure.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_biol_view.biol_id'
'_struct_biol_view.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
save_struct_biol_view.biol_id.
_item_description.description
;
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
save_struct_biol_view.details.
_item_description.description
;
A description of special aspects of this view of the biological
structure.
This data item can be used as a figure legend, if desired.
;
_item.name '_struct_biol_view.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
;
The enzyme has been oriented with the molecular
twofold axis aligned with the horizontal axis
of the figure.
;
_item_description.description
;
The value of _struct_biol_view.id must uniquely identify a
record in the STRUCT_BIOL_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_biol_view.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Figure 1'
'unliganded enzyme'
'view down enzyme active site'
save_struct_biol_view.rot_matrix.
_item_description.description
;
The matrix used to rotate the subset of the Cartesian coordinates
in the ATOM_SITE category identified in the STRUCT_BIOL_VIEW_GEN
category to a view useful for describing the structure. The
conventions used in the rotation are described in
_struct_site_view_details.
|11 12 13| x x'
|21 22 23| ( y ) Cartesian = ( y' ) reoriented Cartesian
|31 32 33| z z'
;
_item.name '_struct_biol_view.rot_matrix'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
_category.description
;
Data items in the STRUCT_CONF category record details about
the backbone conformation of a segment of polymer.
The STRUCT_CONF_TYPE records define the criteria used to
identify the backbone conformations.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_conf.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_conf.id
_struct_conf.conf_type_id
_struct_conf.beg_label_res_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.end_label_res_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.details
HELX1 HELX-RHAL ARG A 87 GLN A 92 .
HELX2 HELX-RHAL ARG B 287 GLN B 292 .
STRN1 STRN PRO A 1 LEU A 5 .
STRN2 STRN CYS B 295 PHE B 299 .
STRN3 STRN CYS A 95 PHE A 299 .
STRN4 STRN PRO B 201 LEU B 205 .
# - - - - data truncated for brevity - - - -
TURN1 TURN-TY1P ILE A 15 GLN A 18 .
TURN2 TURN-TY2 GLY A 49 GLY A 52 .
TURN3 TURN-TY1P ILE A 55 HIS A 69 .
TURN4 TURN-TY1 THR A 91 GLY A 94 .
# - - - - data truncated for brevity - - - -
;
save_struct_conf.beg_label_asym_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _struct_asym.id in the STRUCT_ASYM
category.
;
save_struct_conf.beg_label_res_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_conf.beg_label_seq_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item_description.description ; A description of special aspects of the conformation assignment. ; _item.name '_struct_conf.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char
save_struct_conf.end_label_asym_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_conf.end_label_res_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_conf.end_label_seq_id.
_item_description.description
;
A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item_description.description
;
The value of _struct_conf.id must uniquely identify a record in
the STRUCT_CONF list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_conf.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
_category.description
;
Data items in the STRUCT_CONF_TYPE category record details
about the criteria used to identify backbone conformations of a
segment of polymer.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_conf_type.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_conf_type.id
_struct_conf_type.criteria
_struct_conf_type.reference
HELX-RHAL 'author judgement' .
STRN 'author judgement' .
TURN-TY1 'author judgement' .
TURN-TY1P 'author judgement' .
TURN-TY2 'author judgement' .
TURN-TY2P 'author judgement' .
;
save_struct_conf_type.criteria.
_item_description.description ; The criteria used to assign this conformation type. ; _item.name '_struct_conf_type.criteria' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'author judgement' 'phi=54-74, psi=30-50'
_item_description.description
;
The descriptor that categorizes type of the conformation of the
backbone of the polymer (whether protein or nucleic acid).
Explicit values for the torsions angles that define each
conformation are not given here, but it is expected that the
author would provide such information in either the
_struct_conf_type.criteria or _struct_conf_type.reference data
items, or both.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_conf_type.id'
struct_conf_type
yes
'_struct_conf.conf_type_id'
struct_conf
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conf.conf_type_id'
'_struct_conf_type.id'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
HELX-RHAL
'right-handed alpha helix (protein)'
HELX-RHGA
'right-handed gamma helix (protein)'
HELX-RHOM
'right-handed omega helix (protein)'
HELX-RHPI
'right-handed pi helix (protein)'
HELX-RH3T
'right-handed 3-10 helix (protein)'
HELX-LHAL
'left-handed alpha helix (protein)'
HELX-LHGA
'left-handed gamma helix (protein)'
HELX-LHOM
'left-handed omega helix (protein)'
HELX-LHPI
'left-handed pi helix (protein)'
HELX-LH3T
'left-handed 3-10 helix (protein)'
HELX-PPRO
'polyproline (protein)'
HELX-OTHR
'helix other (protein)'
HELX-RHA
'right-handed A helix (nucleic acid)'
HELX-RHB
'right-handed B helix (nucleic acid)'
HELX-RHZ
'right-handed Z helix (nucleic acid)'
HELX-RHO
'right-handed other helix (nucleic acid)'
HELX-LHA
'left-handed A helix (nucleic acid)'
HELX-LHB
'left-handed B helix (nucleic acid)'
HELX-LHZ
'left-handed Z helix (nucleic acid)'
HELX-LHO
'left-handed other helix (nucleic acid)'
TURN-TY1
'type I turn (protein)'
TURN-TY1P
'type 1 prime turn (protein)'
TURN-TY2
'type II turn (protein)'
TURN-TY2P
'type II prime turn (protein)'
TURN-TY3
'type III turn (protein)'
TURN-TY3P
'type III prime turn (protein)'
TURN-OTHR
'turn other (protein)'
STRN
'beta strand (protein)'
_item_description.description
;
The descriptor that categorizes type of the conformation of the
backbone of the polymer (whether protein or nucleic acid).
Explicit values for the torsions angles that define each
conformation are not given here, but it is expected that the
author would provide such information in either the
_struct_conf_type.criteria or _struct_conf_type.reference data
items, or both.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_conf_type.id'
struct_conf_type
yes
'_struct_conf.conf_type_id'
struct_conf
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conf.conf_type_id'
'_struct_conf_type.id'
_item_type.code char
loop_
_item_enumeration.value
_item_enumeration.detail
HELX-RHAL
'right-handed alpha helix (protein)'
HELX-RHGA
'right-handed gamma helix (protein)'
HELX-RHOM
'right-handed omega helix (protein)'
HELX-RHPI
'right-handed pi helix (protein)'
HELX-RH3T
'right-handed 3-10 helix (protein)'
HELX-LHAL
'left-handed alpha helix (protein)'
HELX-LHGA
'left-handed gamma helix (protein)'
HELX-LHOM
'left-handed omega helix (protein)'
HELX-LHPI
'left-handed pi helix (protein)'
HELX-LH3T
'left-handed 3-10 helix (protein)'
HELX-PPRO
'polyproline (protein)'
HELX-OTHR
'helix other (protein)'
HELX-RHA
'right-handed A helix (nucleic acid)'
HELX-RHB
'right-handed B helix (nucleic acid)'
HELX-RHZ
'right-handed Z helix (nucleic acid)'
HELX-RHO
'right-handed other helix (nucleic acid)'
HELX-LHA
'left-handed A helix (nucleic acid)'
HELX-LHB
'left-handed B helix (nucleic acid)'
HELX-LHZ
'left-handed Z helix (nucleic acid)'
HELX-LHO
'left-handed other helix (nucleic acid)'
TURN-TY1
'type I turn (protein)'
TURN-TY1P
'type 1 prime turn (protein)'
TURN-TY2
'type II turn (protein)'
TURN-TY2P
'type II prime turn (protein)'
TURN-TY3
'type III turn (protein)'
TURN-TY3P
'type III prime turn (protein)'
TURN-OTHR
'turn other (protein)'
STRN
'beta strand (protein)'
save_struct_conf_type.reference.
_item_description.description
;
A literature reference that defines the criteria used to assign
this conformation type and subtype.
;
_item.name '_struct_conf_type.reference'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case 'Kabsch and Sander, ref?'
_category.description
;
Data items in the STRUCT_CONN category record details about
the interactions between portions of structure. These can be
hydrogen bonds, salt bridges, disulfide bridges, and so on.
The STRUCT_CONN_TYPE records define the criteria used to
identify these contacts.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_conn.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_label_res_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_role
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_res_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_role
_struct_conn.ptnr2_symmetry
_struct_conn.details
C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1 negative 1_555
.
C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O acceptor 1_555
.
# - - - - data truncated for brevity - - - -
;
_item_description.description ; A description of special aspects of the connect item. ; _item.name '_struct_conn.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'disulfide bridge C-S-S-C is highly distorted' 'another example'
_item_description.description
;
The value of _struct_conn.id must uniquely identify a record in
the STRUCT_CONN list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_conn.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
save_struct_conn.ptnr1_label_alt_id.
_item_description.description
;
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_conn.ptnr1_label_asym_id.
_item_description.description
;
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_conn.ptnr1_label_atom_id.
_item_description.description
;
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
save_struct_conn.ptnr1_label_res_id.
_item_description.description
;
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_conn.ptnr1_label_seq_id.
_item_description.description
;
A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item_description.description
;
The chemical or structural role of the the first partner in
the structure connection.
;
_item.name '_struct_conn.ptnr1_role'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'donor'
'acceptor'
'negative'
'positive'
'metal'
'metal coordination'
save_struct_conn.ptnr1_symmetry.
_item_description.description
;
Describes the symmetry operation that should be applied to the
atom set specified by _struct_conn.ptnr1_label* to generate the
first partner in the structure connection.
;
_item.name '_struct_conn.ptnr1_symmetry'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
save_struct_conn.ptnr2_label_alt_id.
_item_description.description
;
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_conn.ptnr2_label_asym_id.
_item_description.description
;
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_conn.ptnr2_label_atom_id.
_item_description.description
;
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
save_struct_conn.ptnr2_label_res_id.
_item_description.description
;
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_conn.ptnr2_label_seq_id.
_item_description.description
;
A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item_description.description
;
The chemical or structural role of the the second partner in
the structure connnection.
;
_item.name '_struct_conn.ptnr2_role'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'donor'
'acceptor'
'negative'
'positive'
'metal'
'metal coordination'
save_struct_conn.ptnr2_symmetry.
_item_description.description
;
Describes the symmetry operation that should be applied to the
atom set specified by _struct_conn.ptnr2_label* to generate the
second partner in the structure connection.
;
_item.name '_struct_conn.ptnr2_symmetry'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_category.description
;
Data items in the STRUCT_CONN_TYPE category record details
about the criteria used to identify interactions between
portions of structure.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_conn_type.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
saltbr
'negative to positive distance > 2.5 \%A, < 3.2 \%A' .
hydrog
'N to O distance > 2.5 \%A, < 3.5 \%A, N O C angle < 120 degrees' .
;
save_struct_conn_type.criteria.
_item_description.description ; The criteria used to define the interaction. ; _item.name '_struct_conn_type.criteria' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case 'O to N distance > 2.5 \%A, < 3.2 \%A' 'authors judgement'
_item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction'
_item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code char loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction'
save_struct_conn_type.reference.
_item_description.description
;
A reference that specifies the criteria used to define the
interaction.
;
_item.name '_struct_conn_type.reference'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_category.description
;
Data items in the STRUCT_MON_CIS category record identify
monomers that have been found to have the peptide bond in the cis
conformation. The criterion used to select residues to be
designated as containing cis peptide bonds is given in
_struct_mon_details.prot_cis.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_mon_prot_cis.label_alt_id'
'_struct_mon_prot_cis.label_asym_id'
'_struct_mon_prot_cis.label_res_id'
'_struct_mon_prot_cis.label_seq_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
_category.description
;
Data items in the STRUCT_MON_DETAILS category record details
about specifics of calculations summaries in data items in the
STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can
include the coefficients used in various maps calculations,
the radii used for including points in a calculation, etc.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_mon_details.block_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
save_struct_mon_details.block_id.
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description
;
This data item describes the specifics of the calculations that
generated the values given in given in _struct_mon_prot.RSCC_all,
_struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for inclusion of map grid points
in the calculation.
;
_item.name '_struct_mon_details.RSCC'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item.examples.case
;
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Maps grid points within 1.5 A of the
designated atoms were included in the
calculation.
;
;
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure factor amplitudes
and phases, respectively, calculated from the
current model.
Maps grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
;
_item_description.description
;
This data item describes the specifics of the calculations that
generated the values given in given in _struct_mon_prot.RSR_all,
_struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for inclusion of map grid points
in the calculation.
;
_item.name '_struct_mon_details.RSR'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item.examples.case
;
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Maps grid points within 1.5 A of the
designated atoms were included in the
calculation.
;
;
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure factor amplitudes
and phases, respectively, calculated from the
current model.
Maps grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
;
_category.description . _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_mon_nucl.label_alt_id' '_struct_mon_nucl.label_asym_id' '_struct_mon_nucl.label_res_id' '_struct_mon_nucl.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case
_item_description.description
;
The value in degrees of the backbone torsion angle alpha
o3'_p_o5'_c5'.
;
_item.name '_struct_mon_nucl.alpha'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the backbone torsion angle beta
p_o5'_c5'_c4'.
;
_item.name '_struct_mon_nucl.beta'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar-base torsion angle chi
o4'_c1'_n1_c2.
;
_item.name '_struct_mon_nucl.chi1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar-base torsion angle chi
o4'_c1'_n9_c4.
;
_item.name '_struct_mon_nucl.chi2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the backbone torsion angle delta
c5'_c4'_c3'_o3'.
;
_item.name '_struct_mon_nucl.delta'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
A description of special aspects of the residue, its
conformation, behavior in refinement, or any other aspect that
requires annotation.
;
_item.name '_struct_mon_nucl.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item.examples.case
;
Part of the phosphodiester backbone not in
density.
;
_item_description.description
;
The value in degrees of the backbone torsion angle epsilon
c4'_c3'_o3'_p.
;
_item.name '_struct_mon_nucl.epsilon'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the backbone torsion angle gamma
o5'_c5'_c4'_c3'.
;
_item.name '_struct_mon_nucl.gamma'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
save_struct_mon_nucl.label_alt_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_mon_nucl.label_asym_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_mon_nucl.label_res_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_mon_nucl.label_seq_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
save_struct_mon_nucl.mean_B_all.
_item_description.description
;
The mean value of the isotropic temperature factor for all atoms
in the monomer.
;
_item.name '_struct_mon_nucl.mean_B_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.mean_B_base.
_item_description.description
;
The mean value of the isotropic temperature factor for atoms
in the base moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_base'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.mean_B_phos.
_item_description.description
;
The mean value of the isotropic temperature factor for atoms
in the phosphate moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_phos'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.mean_B_sugar.
_item_description.description
;
The mean value of the isotropic temperature factor for atoms
in the sugar moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_sugar'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description
;
The value in degrees of the sugar torsion angle nu0
c4'_o4'_c1'_c2'.
;
_item.name '_struct_mon_nucl.nu0'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar torsion angle nu1
o4'_c1'_c2'_c3'.
;
_item.name '_struct_mon_nucl.nu1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar torsion angle nu2
c1'_c2'_c3'_c4'.
;
_item.name '_struct_mon_nucl.nu2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar torsion angle nu3
c2'_c3'_c4'_o4'.
;
_item.name '_struct_mon_nucl.nu3'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the sugar torsion angle nu4
c3'_c4'_o4'_c1'.
;
_item.name '_struct_mon_nucl.nu4'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
save_struct_mon_nucl.RSCC_all.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
nucleic acid monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), < > indicates
an average and the sums are taken over all map grid points near
the relevant atoms.
;
_item.name '_struct_mon_nucl.RSCC_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSCC_base.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
base moiety of the nucleic acid monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), < > indicates
an average and the sums are taken over all map grid points near
the relevant atoms.
;
_item.name '_struct_mon_nucl.RSCC_base'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSCC_phos.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
phosphate moiety of the nucleic acid monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), < > indicates
an average and the sums are taken over all map grid points near
the relevant atoms.
;
_item.name '_struct_mon_nucl.RSCC_phosphodiester'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSCC_sugar.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
sugar moiety of the nucleic acid monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), < > indicates
an average and the sums are taken over all map grid points near
the relevant atoms.
;
_item.name '_struct_mon_nucl.RSCC_sugar'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the nucleic acid monomer.
RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)]
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), and the sums
are taken over all map grid points near the relevant atoms.
;
_item.name '_struct_mon_nucl.RSR_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSR_base.
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the base moiety of the nucleic acid monomer.
RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)]
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), and the sums
are taken over all map grid points near the relevant atoms.
;
_item.name '_struct_mon_nucl.RSR_base'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSR_phos.
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the phosphate moiety of the nucleic acid monomer.
RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)]
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), and the sums
are taken over all map grid points near the relevant atoms.
;
_item.name '_struct_mon_nucl.RSR_phosphodiester'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_nucl.RSR_sugar.
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the sugar moiety of the nucleic acid monomer.
RSR = SUM [p(o) - p(c)] / SUM [p(o) + p(c)]
where p(o) is the density in a map calculated with amplitude
F(o) and phase alpha(c), p(c) is the density in a map
calculated with amplitude F(c) and phase alpha(c), and the sums
are taken over all map grid points near the relevant atoms.
;
_item.name '_struct_mon_nucl.RSR_sugar'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description
;
The value in degrees of the backbone torsion angle zeta
c3'_o3'_p_o5'.
;
_item.name '_struct_mon_nucl.zeta'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_category.description
;
Data items in the STRUCT_MON_PROT category record details about
structural properties of a protein when analysed at the monomer
level. Analogous data items for nucleic acids are given in the
STRUCT_MON_NUCL category. For items where the value of the
property depends on the method employed to calculate it, the
details of the method of calculation are described in data items
in the STRUCT_MON_DETAILS category.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_mon_prot.label_alt_id'
'_struct_mon_prot.label_asym_id'
'_struct_mon_prot.label_res_id'
'_struct_mon_prot.label_seq_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
_item_description.description
;
The value in degrees of the side chain torsion angle chi1, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi1'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the side chain torsion angle chi2, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi2'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the side chain torsion angle chi3, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi3'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the side chain torsion angle chi4, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi4'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The value in degrees of the side chain torsion angle chi5, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi5'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
A description of special aspects of the residue, its
conformation, behavior in refinement, or any other aspect that
requires annotation.
;
_item.name '_struct_mon_prot.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
loop_
_item.examples.case
'very poor density'
;
The side chain of this density may occupy
alternative conformations, but alternative
conformations were not fit in this model
;
;
This residue has a close contact with the
bound inhibitor, which may account for
the non-standard conformation of the side
chain.
;
save_struct_mon_prot.label_alt_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_mon_prot.label_asym_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_mon_prot.label_res_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_mon_prot.label_seq_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
save_struct_mon_prot.mean_B_all.
_item_description.description
;
The mean value of the isotropic temperature factor for all atoms
in the monomer.
;
_item.name '_struct_mon_prot.mean_B_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.mean_B_main.
_item_description.description
;
The mean value of the isotropic temperature factor for atoms
in the main chain of the monomer.
;
_item.name '_struct_mon_prot.mean_B_main'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.mean_B_side.
_item_description.description
;
The mean value of the isotropic temperature factor for atoms
in the side chain of the monomer.
;
_item.name '_struct_mon_prot.mean_B_side'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description ; The value in degrees of the main chain torsion angle omega. ; _item.name '_struct_mon_prot.omega' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the main chain torsion angle phi. ; _item.name '_struct_mon_prot.phi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description ; The value in degrees of the main chain torsion angle psi. ; _item.name '_struct_mon_prot.psi' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
save_struct_mon_prot.RSCC_all.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSCC.
< > indicates an average and the sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon.details_RSCC.
;
_item.name '_struct_mon_prot.RSCC_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.RSCC_main.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
main chain of the monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSCC.
< > indicates an average and the sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon.details_RSCC.
;
_item.name '_struct_mon_prot.RSCC_main'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.RSCC_side.
_item_description.description
;
The real-space (linear) correlation coefficient RSCC, as
described by T.A. Jones, J.Y. Zou, S.W. Cowan and M. Kjeldgaard,
Acta Cryst. A47, 110-119 (1991) evaluated over all atoms in the
side chain of the monomer.
SUM [p(o) - ] * SUM [p(c) - ]
RSCC = ------------------------------------------------------
SQRT {SUM[(p(o) - )^2] * SUM[(p(c) - )^2]}
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSCC.
< > indicates an average and the sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon.details_RSCC.
;
_item.name '_struct_mon_prot.RSCC_side'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the monomer.
SUM [p(o) - p(c)]
RSR = -----------------
SUM [p(o) + p(c)]
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSR.
The sums are taken over all map grid points near the relevant
atoms. The radius for including grid points in the calculation
should also be given in _struct_mon.details_RSR.
;
_item.name '_struct_mon_prot.RSR_all'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.RSR_main.
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the main chain of the monomer.
SUM [p(o) - p(c)]
RSR = -----------------
SUM [p(o) + p(c)]
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSR.
The sums are taken over all map grid points near the relevant
atoms. The radius for including grid points in the calculation
should also be given in _struct_mon.details_RSR.
;
_item.name '_struct_mon_prot.RSR_main'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot.RSR_side.
_item_description.description
;
The real-space residual RSR, as described by C.I. Branden and
T.A. Jones, Nature 343, 687-689 (1990) evaluated over all atoms
in the main chain of the monomer.
SUM [p(o) - p(c)]
RSR = -----------------
SUM [p(o) + p(c)]
where p(o) is the density in an "experimental" map and p(c) is
the density in a "calculated" map. The details of how these maps
were calculated should be described in _struct_mon_details.RSR.
The sums are taken over all map grid points near the relevant
atoms. The radius for including grid points in the calculation
should also be given in _struct_mon.details_RSR.
;
_item.name '_struct_mon_prot.RSR_side'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
save_struct_mon_prot_cis.label_alt_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_mon_prot_cis.label_asym_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_mon_prot_cis.label_res_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_mon_prot_cis.label_seq_id.
_item_description.description
;
A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_category.description
;
Data items in the STRUCT_NCS_DOM record information about the
domains in an ensemble of domains related by non-crystallographic
symmetry. A domain need not correponds to a poly-peptide chains
- it can be composed of segments of a single chain, or segments
of more than one chain.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_ncs_dom.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
_item_description.description
;
A description of special aspects of the structural elements that
comprise a domain in an emsemble of domains related by non-
crystallographic symmetry.
;
_item.name '_struct_ncs_dom.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
;
The loop between residues 18 and 23 in this
domain interacts with a symmetry related
molecule, and thus deviates significantly from
the non-crystallographic 3-fold.
;
_item_description.description
;
The value of _struct_ncs_dom.id must uniquely identify a
record in the STRUCT_NCS_DOM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_dom.id'
struct_ncs_dom
yes
'_struct_ncs_ens_gen.dom_id_1'
struct_ncs_ens_gen
yes
'_struct_ncs_ens_gen.dom_id_2'
struct_ncs_ens_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.dom_id_1'
'_struct_ncs_dom.id'
'_struct_ncs_ens_gen.dom_id_2'
'_struct_ncs_dom.id'
_item_type.code char
_item_description.description
;
The value of _struct_ncs_dom.id must uniquely identify a
record in the STRUCT_NCS_DOM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_dom.id'
struct_ncs_dom
yes
'_struct_ncs_ens_gen.dom_id_1'
struct_ncs_ens_gen
yes
'_struct_ncs_ens_gen.dom_id_2'
struct_ncs_ens_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.dom_id_1'
'_struct_ncs_dom.id'
'_struct_ncs_ens_gen.dom_id_2'
'_struct_ncs_dom.id'
_item_type.code char
_item_description.description
;
The value of _struct_ncs_dom.id must uniquely identify a
record in the STRUCT_NCS_DOM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_dom.id'
struct_ncs_dom
yes
'_struct_ncs_ens_gen.dom_id_1'
struct_ncs_ens_gen
yes
'_struct_ncs_ens_gen.dom_id_2'
struct_ncs_ens_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.dom_id_1'
'_struct_ncs_dom.id'
'_struct_ncs_ens_gen.dom_id_2'
'_struct_ncs_dom.id'
_item_type.code char
_category.description
;
Data items in the STRUCT_NCS_DOM_GEN category identify the
structural elements thats comprise a domain in an ensemble
of domains related by non-crystallographic symmetry.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_ncs_dom_gen.dom_id'
'_struct_ncs_dom_gen.beg_label_alt_id'
'_struct_ncs_dom_gen.beg_label_asym_id'
'_struct_ncs_dom_gen.beg_label_res_id'
'_struct_ncs_dom_gen.beg_label_seq_id'
'_struct_ncs_dom_gen.end_label_alt_id'
'_struct_ncs_dom_gen.end_label_asym_id'
'_struct_ncs_dom_gen.end_label_res_id'
'_struct_ncs_dom_gen.end_label_seq_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
save_struct_ncs_dom_gen.beg_label_alt_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_ncs_dom_gen.beg_label_asym_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_ncs_dom_gen.beg_label_res_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_ncs_dom_gen.beg_label_seq_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
save_struct_ncs_dom_gen.dom_id.
_item_description.description
;
This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
save_struct_ncs_dom_gen.end_label_alt_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_ncs_dom_gen.end_label_asym_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_ncs_dom_gen.end_label_res_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_ncs_dom_gen.end_label_seq_id.
_item_description.description
;
A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_category.description
;
Data items in the STRUCT_NCS_ENS category record information
about ensembles of structural element related by non-
crystallographic symmetry (ncs), such as the point group of the
ensemble when taken as a whole, and any special aspects of it
that require description.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_ncs_ens.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
_item_description.description ; A description of special aspects of the connect item. ; _item.name '_struct_ncs_ens.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 ;
_item_description.description
;
The value of _struct_ncs_ens.id must uniquely identify a
record in the STRUCT_NCS_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_ens.id'
struct_ncs_ensemble
yes
'_struct_ncs_ens_gen.ens_id'
struct_ncs_ens_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.ens_id'
'_struct_ncs_ens.id'
_item_type.code char
_item_description.description
;
The value of _struct_ncs_ens.id must uniquely identify a
record in the STRUCT_NCS_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_ens.id'
struct_ncs_ensemble
yes
'_struct_ncs_ens_gen.ens_id'
struct_ncs_ens_gen
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.ens_id'
'_struct_ncs_ens.id'
_item_type.code char
save_struct_ncs_ens.point_group.
_item_description.description
;
The point group of the ensemble of structural elements related by
non crystallographic symmetry. The relationships need not be
precise; this data items is intended to give a rough description
of the non-crystallographic symmetry relationships.
;
_item.name '_struct_ncs_ens.point_group'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
loop_
_item_examples.case
'3'
'422'
'non-proper'
_category.description
;
Data items in the STRUCT_NCS_ENS_GEN category describe the
operations that result in the superposition of one domain in
an ensembled of domains related by non-crystallographic
symmetry upon a second domain in the ensemble.
%%%
%%% Note - I have only added data items for the polar angles that describe
%%% the operation - we are probably going to need some vector component to
%%% this as well, and this will take some thought and consultation
%%%
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_ncs_ens_oper.ens_id'
'_struct_ncs_ens_oper.dom_id_1'
'_struct_ncs_ens_oper.dom_id_2'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
Need example 1
;
save_struct_ncs_ens_oper.details.
_item_description.description ; A description of special aspects of the transformation operation. ; _item.name '_struct_ncs_ens_oper.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char loop_ _item_examples.case ; The operation is given a precise threefold rotation, despite the fact the the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 angles and a translation of 0.13 angstroms. ;
save_struct_ncs_ens_oper.dom_id_1.
_item_description.description
;
The identifier for the domain that will remain unchanged by the
transformation operator.
This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
save_struct_ncs_ens_oper.dom_id_2.
_item_description.description
;
The identifier for the domain that will be transformed by
application of the transformation operator.
This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
save_struct_ncs_ens_oper.ens_id.
_item_description.description
;
This data item is a pointer to _struct_ncs_ens.id in the
STRUCT_NCS_ENS category.
;
save_struct_ncs_ens_oper.kappa.
_item_description.description ; The rotation in degrees about the symmetry axis. %%% %%% Need more precise definition here. %%% ; _item.name '_struct_ncs_ens_oper.kappa' _item.category_id _item.category_id _item.mandatory_code no _item_type.code float _item_units.code 'degrees'
_item_description.description
;
The angle that the symmetry axis makes with the xz plane of
the refence coordinate system.
%%%
%%% Need more precise definition here.
%%%
;
_item.name '_struct_ncs_ens_oper.phi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_description.description
;
The angle that the symmetry axis makes with the z axis of
the refence coordinate system.
%%%
%%% Need more precise definition here.
%%%
;
_item.name '_struct_ncs_ens_oper.psi'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_category.description
;
Data items in the STRUCT_SITE category record details about
portions of structure that contribute to certain structurally
relevant sites (i.e., active sites, substrate-binding subsites,
metal-coordination sites).
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_site.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_site.id
_struct_site.details
'P2 site C'
; residues with a contact < 3.7 \%A to an atom in the P2 moiety of the
inhibitor in the conformation with _struct_asym.id = C
;
'P2 site D'
; residues with a contact < 3.7 \%A to an atom in the P1 moiety of the
inhibitor in the conformation with _struct_asym.id = D)
;
;
_item_description.description ; A description of special aspects of the structural site. ; _item.name '_struct_site.details' _item.category_id _item.category_id _item.mandatory_code no _item_type.code char _item_examples.case ; ??? ;
_item_description.description
;
The value of _struct_site.id must uniquely identify a record in
the STRUCT_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_site.id'
struct_site
yes
'_struct_site_gen.site_id'
struct_site_gen
yes
'_struct_site_keywords.site_id'
struct_site_keywords
yes
'_struct_site_view.site_id'
struct_site_view
yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_site_gen.site_id'
'_struct_site.id'
'_struct_site_keywords.site_id'
'_struct_site.id'
'_struct_site_view.site_id'
'_struct_site.id'
_item_type.code char
_category.description
;
Data items in the STRUCT_SITE_GEN category record details about
the generation of portions of structure that contribute to
structurally relevant sites.
;
_category.id _category.id
_category.mandatory_code no
loop_
_category_key.name
'_struct_site_gen.id'
'_struct_site_gen.site_id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.label_res_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 1 VAL A 32 1_555 .
2 1 ILE A 47 1_555 .
3 1 VAL A 82 1_555 .
4 1 ILE A 84 1_555 .
5 2 VAL B 232 1_555 .
6 2 ILE B 247 1_555 .
7 2 VAL B 282 1_555 .
8 2 ILE B 284 1_555 .
;
_item_description.description
;
A description of special aspects of the symmetry generation of
this portion of the structural site.
;
_item.name '_struct_site_gen.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The zinc atom lies on a special position; application
of symmetry elements to generate the insulin hexamer
will generate excess zinc atoms, which must be removed
by hand.
;
_item_description.description
;
The value of _struct_site_gen.id must uniquely identify a record
in the STRUCT_SITE_GEN list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_site_gen.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
save_struct_site_gen.label_alt_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
save_struct_site_gen.label_asym_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
save_struct_site_gen.label_atom_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _entity_mon_atom.atom_id in the
ENTITY_MON_ATOM category.
;
save_struct_site_gen.label_res_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _entity_mon.id in the ENTITY_MON
category.
;
save_struct_site_gen.label_seq_id.
_item_description.description
;
A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item_description.description
;
This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
save_struct_site_gen.symmetry.
_item_description.description
;
Describes the symmetry operation that should be applied to the
atom set specified by _struct_site_gen.label* to generate a
portion of the structure site.
;
_item.name '_struct_site_gen.symmetry'
_item.category_id _item.category_id
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail
.
'no symmetry or translation to site'
4
'4th symmetry operation applied'
7_645
'7th symm. posn.; +a on x; -b on y'
_category.description ; Data items in the STRUCT_SITE_KEYWORDS category... ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_struct_site_keywords.site_id' '_struct_site_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _struct_site_keywords.site_id _struct_site_keywords.text 'P2 site C' 'binding site' 'P2 site C' 'binding pocket' 'P2 site C' 'P2 site' 'P2 site C' 'P2 pocket' 'P2 site D' 'binding site' 'P2 site D' 'binding pocket' 'P2 site D' 'P2 site' 'P2 site D' 'P2 pocket' ;
save_struct_site_keywords.site_id.
_item_description.description
;
This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
save_struct_site_keywords.text.
_item_description.description ; Keywords describing this structural site. ; _item.name '_struct_site_keywords.text' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code char loop_ _item_examples.case 'active site' 'binding pocket' 'Ca coordination'
_category.description
;
Data items in the STRUCT_SITE_VIEW category record details
about how to draw and annotate a useful didactic view of the
structural site.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_struct_site_view.id'
loop_
_category_group.id
'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on
;
;
Need Example 1
;
save_struct_site_view.details.
_item_description.description
;
A description of special aspects of this view of the structural
site. This data item can be used as a figure legend, if desired.
;
_item.name '_struct_site_view.details'
_item.category_id _item.category_id
_item.mandatory_code no
_item_type.code char
_item_examples.case
;
The active site has been oriented with the specificity
pocket on the right and the active site machinery on
the left.
;
_item_description.description
;
The value of _struct_site_view.id must uniquely identify a
record in the STRUCT_SITE_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_site_view.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
loop_
_item_examples.case
'Figure 1'
'unliganded enzyme'
'view down enzyme active site'
save_struct_site_view.rot_matrix.
_item_description.description
;
The matrix used to rotate the subset of the Cartesian coordinates
in the ATOM_SITE category identified in the STRUCT_SITE_VIEW_GEN
category to a view useful for describing the structural site. The
conventions used in the rotation are described in
_struct_site_view.details.
|11 12 13| x x'
|21 22 23| ( y ) Cartesian = ( y' ) reoriented Cartesian
|31 32 33| z z'
;
_item.name '_struct_site_view.rot_matrix'
_item.category_id _item.category_id
_item.mandatory_code no
_item_structure.code 'matrix3x3'
_item_structure.organization 'rowwise'
_item_type.code float
save_struct_site_view.site_id.
_item_description.description
;
This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
_category.description
;
Data items in the SYMMETRY category record details about the
space-group symmetry.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_symmetry.block_id'
loop_
_category_group.id
'inclusive_group'
'symmetry_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_symmetry.cell_setting orthorhombic
_symmetry.Int_Tables_number 18
_symmetry.space_group_name_H-M 'P 21 21 2'
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_symmetry.cell_setting orthorhombic
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.space_group_name_Hall P_2ac_2ab
;
_item_description.description ; This data item is a pointer to _block.id in the BLOCK category. ;
_item_description.description ; The cell settings for this space-group symmetry. ; _item.name '_symmetry.cell_setting' _item.category_id _item.category_id _item.mandatory_code no _item_aliases.alias_name '_symmetry_cell_setting' _item_type.code char loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic
save_symmetry.Int_Tables_number.
_item_description.description
;
Space-group number from International Tables for Crystallography,
Vol. A (1987).
;
_item.name '_symmetry.Int_Tables_number'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_Int_Tables_number'
_item_type.code int
save_symmetry.space_group_name_H-M.
_item_description.description
;
Hermann-Mauguin space-group symbol. Note that the H-M symbol does
not necessarily contain complete information about the symmetry
and the space-group origin. If used always supply the FULL symbol
from International Tables for Crystallography, Vol. A (1987) and
indicate the origin and the setting if it is not implicit. If
there is any doubt that the equivalent positions can be uniquely
deduced from this symbol specify the _symmetry.equiv_pos_as_xyz
or _symmetry.space_group_name_Hall data items as well. Leave
spaces between symbols referring to different axes.
;
_item.name '_symmetry.space_group_name_H-M'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_space_group_name_H-M'
_item_type.code char
loop_
_item_examples.case
'P 1 21/m 1'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'
save_symmetry.space_group_name_Hall.
_item_description.description
;
Hall space-group symbol [Hall, S. R. (1981). Acta Cryst. A37,
517-525]. This symbol gives the space-group setting explicitly.
Leave spaces between the separate components of the symbol.
;
_item.name '_symmetry.space_group_name_Hall'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_space_group_name_Hall'
_item_type.code char
loop_
_item_examples.case
'-P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
_category.description
;
Data items in the SYMMETRY_EQUIV category list the
symmetry equivalent positions for the space group.
;
_category.id _category.id
_category.mandatory_code no
_category_key.name '_symmetry_equiv.id'
loop_
_category_group.id
'inclusive_group'
'symmetry_group'
loop_
_category_examples.detail
_category_examples.case
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
1 '+x,+y,+z'
2 '-x,-y,z'
3 '1/2+x,1/2-y,-z'
4 '1/2-x,1/2+y,-z'
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_symmetry_equiv.pos_as_xyz
+x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z
;
_item_description.description
;
The value of _symmetry_equiv.id must uniquely identify
a record in the SYMMETRY_EQUIV category.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_symmetry_equiv.id'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code char
save_symmetry_equiv.pos_as_xyz.
_item_description.description
;
Symmetry equivalent position in the 'xyz' representation. Except
for the space group P1, this data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography, Vol. A. (1987). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
_item.name '_symmetry_equiv.pos_as_xyz'
_item.category_id _item.category_id
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_equiv_pos_as_xyz'
_item_type.code char
_item_examples.case -y+x,-y,1/3+z