[Date Prev][Date Next][Date Index]
(50) Call for approval of CIF Core dictionary version 2.0
- To: COMCIFS@iucr.ac.uk
- Subject: (50) Call for approval of CIF Core dictionary version 2.0
- From: bm
- Date: Wed, 2 Oct 1996 16:50:01 +0100
Dear Colleagues
I call for closure and approval of release of version 2.0 of the CIF Core
dictionary. All full members of COMCIFS are required to submit their assent
for the release of the dictionary sent out with the last circular, and
modified as indicated below.
There follows a summary of comments made since the last mailing (S> flags
comments by Syd, D> by David and G> by Gotzon). Note carefully the
recommendation in D50.8.
D44.2 Disorder
--------------
S> I agree with your proposed action, which seems to be sensible.
D45.7 _audit_link_block_code
----------------------------
S> Similarly with D45.7, what you suggest may not be
S> the final answer but is a good and sensible approach...let's go for it.
G> _audit_block_code seems to substitute finally the former _block_id
G> introduced in the drafts corresponding to the powder, ms and symm
G> dictionaries. However each of those _block_id's were realized to force
G> a reasonably high degree of uniqueness. Could the definitions of the
G> _block_id's be preserved as recommendations in each dictionary extension?
G> Furthermore, could the definition of _audit_block_code include an
G> additional sentence as: "Recommendations about how this code should be
G> constructed for specific applications can be found in the appropriate
G> dictionary extensions"?. I guess some problems (dictionary extensions are
G> not yet official) but it could be of great utility.
Obviously this needs some more work. I think the current definition in
the dictionary gives us a mechanism that we must constrain somehow. The
possibility of specifying constraints on a dictionary by dictionary basis is
reasonably attractive.
D45.8 Inheritance across data blocks
------------------------------------
S> D45.8 comments will receive my standard reply. If you want this sort
S> of scope outside of a data block then save frames must be used. There
S> will be no changes to the STAR scoping rules.
We were discussing the possibility of adopting CIF conventions
(application-specific rules, if you will) to bypass the strict scoping rules
of STAR, but David identifies some problems even in doing so:
D> I have one comment on inheritance (D45.8). It is true that the use of the
D> _audit_link fields allows us to include all the listed blocks in the scope
D> of the file, thus allowing inheritance across data blocks. However, as no
D> doubt Syd will be quick to point out, the scoping rules are intimately
D> tied to the rule that a data name should only appear once in a data block.
D> If we have three linked data blocks, the parent data name might appear in
D> all three blocks. Which one should be used? We could of course require
D> that a parent name that occurs in the same data block as the child will
D> take precedence over any others, and that if the parent does not appear in
D> the block, then it should be sought in one of the linked blocks. But
D> which block? If the parent occurs in more than one of the other linked
D> blocks it is necessary to establish some hierarchy among the blocks, like
D> the paths defined in the autoexec file of a computer. We cannot use the
D> order in which the blocks are defined in the _audit_link loop for this
D> purpose since the order of data items in a cif is not defined, so an
D> additional hierarchy field is necessary. How essential is it that we
D> include these links in the current dictionary? Would it not be better to
D> exclude them in this round until we have had a chance to think through the
D> implications for the scoping rules more carefully?
I certainly accept that we should exclude these ideas from the current
dictionary. It will be useful, though, to seek volunteers willing to explore
the implications of extending the CIF syntax to the full STAR rule set in
the near future.
D48.1 DIFFRN categories
-----------------------
S> I did look carefully at the _diffrn_ definitions (printed them
S> out separately) as this is important for the area detector data for
S> Section C next year. The duplication of essentially the same data is of
S> concern and I think that we must "relate" these in the longer term.
Agreed. In the longer term.
=====================================
Gotzon had some additional comments:
D50.1 Completeness of including units in definitions
----------------------------------------------------
G> A new list of minor suggestions concerning the Core.
G>
G> As far as I remember you wanted to include the units of the data items
G> in their definitions. I have checked this point along the new draft and I
G> have discovered some definitions in which the units are missing.
G>
G> _atom_type_scat_length_neutron
G> _exptl_crystal_size_
G> _geom_hbond_distance_
G> _refine_ls_d_res_high
G> _refine_ls_d_res_low
G> _reflns_shell_d_res_high
G> _reflns_shell_d_res_low
G>
G> Also (this is strictly cosmetic) in the definitions of the next items,
G> units appear abbreviated (mA, kW, kV)
G>
G> _diffrn_source_current
G> _diffrn_source_power
G> _diffrn_source_voltage
I have added all the missing ones and expanded the abbreviated ones for
consistency.
D50.2 Relations between equivalent B's and U's
----------------------------------------------
G> The pairs (_atom_site_B_equiv_geom, _atom_site_B_iso_or_equiv) and
G> (_atom_site_U_equiv_geom, _atom_site_U_iso_or_equiv) are considered
G> (correctly) as alternate, however there is an additional relationship
G> (they are proportional) between _atom_site_B_equiv_geom and
G> _atom_site_U_equiv_geom and _atom_site_B_iso_or_equiv and
G> _atom_site_U_iso_or_equiv. I think that the corresponding
G>
G> _related_function conversion
G>
G> should appear in their corresponding dictionary entries.
Done.
D50.3 Additional abbreviations
------------------------------
G> citation_coordinate_linkage and publ_manuscript_incl_extra_defn,
G> should include in their _enumeration lists 'n' and 'y' as abbreviation
G> for 'no' and 'yes' respectively.
Sounds sensible. Done.
D50.4 _list_mandatory/_list_reference
-------------------------------------
G> There are some questions concerning the use of _list_mandatory.
G> Sometimes I am not sure about the use of this item and _list_reference.
G> For example, _cell_id should be _list_mandatory, but not
G> _atom_site_aniso_label. The problem is that there is not a category
G> ATOM_SITE_ANISO and therefore _atom_site_aniso_label becomes redundant
G> with _atom_site_label. The same happens with _atom_site_aniso_type_symbol.
G> Did ATOM_SITE_ANISO exist in the past as a separate category?.
The _atom_site_aniso_ items have a very long and chequered history, which I
won't go into here (but is accessible if you're very patient through the old
COMCIFS mailings). However, I would be grateful if Syd would check the
examples you give for consistency.
D50.5 Examples for category descriptions
----------------------------------------
G> Some examples if they are still needed
G>
G> Category CELL_MEASUREMENT_REFLN
G> ...
G> Category DIFFRN_REFLN
These are very welcome and have been included as examples in the dictionary
(see below).
D50.6 Nomenclature clash
------------------------
Hans Wondratschek has carried out a detailed scrutiny of the data names in
the core and draft mmCIF dictionaries, and identified some cases where the
nomenclature we have used is ambiguous or clashes with the conventions of
International Tables. In the case of existing data names, there is nothing
that can be done, but his notes indicate areas where greater care should be
taken in future. I'll send these notes to the Chair of the mmCIF working
group for consideration in examining the aliases in the mmCIF dictionary,
and I'll also make them available to anyone else who is interested. David
has seen a copy of the letter and comments:
D> Hans Wondratschek's letter to you has raised some important
D> nomenclature points about which we have been altogether rather lax. I
D> have checked his list of problems, and most of the core ones we can do
D> nothing about as they are in the original core. However, I would like to
D> suggest that we accept his recommendation that _symmetry_equiv_pos_id be
D> replaced with _symmetry_equiv_pos_site_id. This change can still be
D> made and does not upset our other naming conventions.
I have implemented this change.
D50.7 Consistency of abbreviations
----------------------------------
D> I also like [Hans'] idea that we make a glossary of abbreviations so
D> that we are consistent in our use of abbreviations in constructing data
D> names. I will go through our current dictionaries and build such a
D> glossary. I have eyeballed the core extension and find only one glaring
D> problem, viz: _atom_site_U_equiv_geom. The geom stands for geometry in
D> other places, possibly geometric, but never geometric mean. I suggest
D> that we change this name to _atom_site_U_equiv_geom_mean.
Done.
D50.8 Long data names
---------------------
Scrutiny of the current dictionary reveals the following set of data names
which exceed the 32-character limit:
1 2 3 4
1234567890123456789012345678901234567890
_diffrn_measurement_device_details
_diffrn_measurement_specimen_support
_reflns_shell_meanI_over_sigI_all
_reflns_shell_meanI_over_sigI_obs
_reflns_shell_number_measured_all
_reflns_shell_number_measured_obs
_reflns_shell_percent_possible_all
_reflns_shell_percent_possible_obs
These might all be brought down to 32 characters or less by judicious
abbreviation, but there is the risk of collision with the principle of
maintaining consistent abbreviations (see D50.7 above). It has for some time
been implicit in our discussions that the 32-character limit should be
relaxed. I propose that we retain the existing data names and advertise the
relaxation in the limit to 74 characters (to allow data_stuff and
save__stuff block codes on the dictionaries to remain inside the
80-character line limit). Shout if you think this is being controversial!
===================================
Below I append a complete context diff listing between the dictionary
circulated last time and the most recent working draft. You should find that
it is not too difficult to follow, and there are very few changes other than
those I've identified above. I shall send you a complete copy of the current
working draft upon request.
Please register your approval of this version of the dictionary as soon as
possible.
Regards
Brian
===================================
*** c96.250996 Wed Oct 2 14:14:51 1996
--- cif_core.dic Wed Oct 2 15:48:51 1996
***************
*** 28,34 ****
data_on_this_dictionary
_dictionary_name cif_core.dic
_dictionary_version 2.0
! _dictionary_update 1996-09-25
_dictionary_history
;
1991-05-27 Created from CIF Dictionary text. SRH
--- 28,34 ----
data_on_this_dictionary
_dictionary_name cif_core.dic
_dictionary_version 2.0
! _dictionary_update 1996-10-02
_dictionary_history
;
1991-05-27 Created from CIF Dictionary text. SRH
***************
*** 173,180 ****
Introduced _diffrn_detector_dtime in the DIFFRN_DETECTOR
category and restored _diffrn_radiation_detector_dtime to
DIFFRN_RADIATION
! 1996-09-25 BMcM: Reworded definitions of _atom_site_disorder_assembly
! and *_group
;
###############
--- 173,200 ----
Introduced _diffrn_detector_dtime in the DIFFRN_DETECTOR
category and restored _diffrn_radiation_detector_dtime to
DIFFRN_RADIATION
! 1996-09-25 BMcM:
! Reworded definitions of _atom_site_disorder_assembly and *_group
! 1996-10-02 BMcM:
! Changed _symmetry_equiv_pos_id to _symmetry_equiv_pos_site_id
! in recognition of the technical meaning of 'position' in
! International Tables
! Addition of the names of the relevant units to definitions of
! _atom_type_scat_length_neutron, _exptl_crystal_size_,
! _geom_hbond_distance_, _refine_ls_d_res_high and *_low,
! _reflns_shell_d_res_high and *_low; and cosmetic expansion
! of units listed in the definitions for _diffrn_source_current,
! *_power and *_voltage
! Addition of '_related_function conversion' to
! _atom_site_B_equiv_geom and *_U_equiv_geom and
! _atom_site_B_iso_or_equiv and *_U_iso_or_equiv
! Examples for CELL_MEASUREMENT_REFLN and DIFFRN_REFLN from
! Gotzon Madariaga
! Renamed _atom_site_U_equiv_geom as _atom_site_U_equiv_geom_mean
! and likewise for *_B_* to increase the consistency of
! abbreviations, as suggested by I.D. Brown
! Added disorder example to the ATOM_SITE category description
!
;
###############
***************
*** 239,249 ****
C513 .074(2) .055(2) .075(2) .004(2) .001(2) -.010(2) C
# - - - - data truncated for brevity - - - -
;
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
loop_
_atom_site_label
--- 259,269 ----
C513 .074(2) .055(2) .075(2) .004(2) .001(2) -.010(2) C
# - - - - data truncated for brevity - - - -
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
***************
*** 263,268 ****
--- 283,309 ----
bin Shawkataly [(1996). Acta Cryst. C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ;
+ loop_
+ _atom_site_label # *_assembly 'M' is a disordered methyl
+ _atom_site_occupancy # with configurations 'A' and 'B':
+ _atom_site_disorder_assembly #
+ _atom_site_disorder_group # H11B H11A H13B
+ # . | .
+ C1 1 . . # . | .
+ H11A .5 M A # . | .
+ H12A .5 M A # C1 --------C2---
+ H13A .5 M A # / . \
+ H11B .5 M B # / . \
+ H12B .5 M B # / . \
+ H13B .5 M B # H12A H12B H13A
+
+ ;
+ ;
+ Example 4 - Hypothetical example to illustrate the description of a
+ disordered methyl group.
+ ;
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_SITE category record details about
the atom sites in a crystal structure, such as the positional
***************
*** 391,398 ****
calculated) are given.
;
! data_atom_site_B_equiv_geom
! _name '_atom_site_B_equiv_geom'
_category atom_site
_type numb
_type_conditions esd
--- 432,439 ----
calculated) are given.
;
! data_atom_site_B_equiv_geom_mean
! _name '_atom_site_B_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
***************
*** 399,406 ****
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! _related_item '_atom_site_B_iso_or_equiv'
! _related_function alternate
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 440,448 ----
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! loop_ _related_item
! _related_function '_atom_site_B_iso_or_equiv' alternate
! '_atom_site_U_equiv_geom_mean' conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 425,432 ****
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! _related_item '_atom_site_U_iso_or_equiv'
! _related_function conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 467,475 ----
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! loop_ _related_item
! _related_function '_atom_site_B_equiv_geom_mean' alternate
! '_atom_site_U_iso_or_equiv' conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 759,766 ****
_atom_site_label is used for this purpose. See _atom_type_symbol.
;
! data_atom_site_U_equiv_geom
! _name '_atom_site_U_equiv_geom'
_category atom_site
_type numb
_type_conditions esd
--- 802,809 ----
_atom_site_label is used for this purpose. See _atom_type_symbol.
;
! data_atom_site_U_equiv_geom_mean
! _name '_atom_site_U_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
***************
*** 767,774 ****
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! _related_item '_atom_site_U_iso_or_equiv'
! _related_function alternate
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 810,818 ----
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
! loop_ _related_item
! _related_function '_atom_site_U_iso_or_equiv' alternate
! '_atom_site_B_equiv_geom_mean' conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 789,796 ****
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:10.0
! _related_item '_atom_site_B_iso_or_equiv'
! _related_function conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 833,841 ----
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:10.0
! loop_ _related_item
! _related_function '_atom_site_U_equiv_geom_mean' alternate
! '_atom_site_B_iso_or_equiv' conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 1118,1125 ****
_units fm
_units_detail 'femtometres'
_definition
! ; The bound coherent scattering length for the atom type at
! the isotopic composition used for the diffraction
experiment.
;
--- 1163,1170 ----
_units fm
_units_detail 'femtometres'
_definition
! ; The bound coherent scattering length in femtometres for the
! atom type at the isotopic composition used for the diffraction
experiment.
;
***************
*** 1809,1818 ****
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! End of Example 1
;
;
! Example 1 - need example here
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
--- 1854,1877 ----
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! loop_
! _cell_measurement_refln_index_h
! _cell_measurement_refln_index_k
! _cell_measurement_refln_index_l
! _cell_measurement_refln_theta
! -2 4 1 8.67
! 0 3 2 9.45
! 3 0 2 9.46
! -3 4 1 8.93
! -2 1 -2 7.53
! 10 0 0 23.77
! 0 10 0 23.78
! -5 4 1 11.14
! # - - - - data truncated for brevity - - - -
;
;
! Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room
! temperature (not yet published).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
***************
*** 2516,2522 ****
_type char
_list yes
_list_reference '_citation_id'
! loop_ _enumeration yes no
_definition
; _citation_coordinate_linkage states whether or not this citation
is concerned with precisely the set of coordinates given in the
--- 2575,2584 ----
_type char
_list yes
_list_reference '_citation_id'
! loop_ _enumeration no 'citation unrelated to current coordinates'
! n 'abbreviation for "no"'
! yes 'citation related to current coordinates'
! y 'abbreviation for "yes"'
_definition
; _citation_coordinate_linkage states whether or not this citation
is concerned with precisely the set of coordinates given in the
***************
*** 3697,3706 ****
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! End of Example 1
;
;
! Example 1 - need example here
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
--- 3759,3797 ----
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! loop_
! _diffrn_refln_index_h
! _diffrn_refln_index_k
! _diffrn_refln_index_l
! _diffrn_refln_angle_chi
! _diffrn_refln_scan_rate
! _diffrn_refln_counts_bg_1
! _diffrn_refln_counts_total
! _diffrn_refln_counts_bg_2
! _diffrn_refln_angle_theta
! _diffrn_refln_angle_phi
! _diffrn_refln_angle_omega
! _diffrn_refln_angle_kappa
! _diffrn_refln_scan_width
! _diffrn_refln_elapsed_time
!
! 0 0 -16 0. 4.12 28 127 36 33.157 -75.846 16.404 50.170 1.516 19.43
! 0 0 -15 0. 4.12 38 143 28 30.847 -75.846 14.094 50.170 1.516 19.82
! 0 0 -14 0. 1.03 142 742 130 28.592 -75.846 11.839 50.170 1.516 21.32
! 0 0 -13 0. 4.12 26 120 37 26.384 -75.846 9.631 50.170 1.450 21.68
! 0 0 -12 0. 0.97 129 618 153 24.218 -75.846 7.464 50.170 1.450 23.20
! 0 0 -11 0. 4.12 33 107 38 22.087 -75.846 5.334 50.170 1.384 23.55
! 0 0 -10 0. 4.12 37 146 33 19.989 -75.846 3.235 50.170 1.384 23.90
! 0 0 -9 0. 4.12 50 179 49 17.918 -75.846 1.164 50.170 1.384 24.25
! # - - - - data truncated for brevity - - - -
! 3 4 -4 0. 1.03 69 459 73 30.726 -53.744 46.543 -47.552 1.516 2082.58
! 3 4 -5 0. 1.03 91 465 75 31.407 -54.811 45.519 -42.705 1.516 2084.07
! 3 14 -6 0. 1.03 84 560 79 32.228 -55.841 44.745 -38.092 1.516 2085.57
! # - - - - data truncated for brevity - - - -
;
;
! Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room
! temperature (not yet published).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
***************
*** 4192,4198 ****
_units mA
_units_detail 'milliamperes'
_definition
! ; The current in mA at which the radiation source was operated.
;
data_diffrn_source_details
--- 4283,4290 ----
_units mA
_units_detail 'milliamperes'
_definition
! ; The current in milliamperes at which the radiation source was
! operated.
;
data_diffrn_source_details
***************
*** 4213,4219 ****
_units kW
_units_detail 'kilowatts'
_definition
! ; The power in kW at which the radiation source was operated.
;
data_diffrn_source_size
--- 4305,4312 ----
_units kW
_units_detail 'kilowatts'
_definition
! ; The power in kilowatts at which the radiation source was
! operated.
;
data_diffrn_source_size
***************
*** 4267,4273 ****
_units kV
_units_detail 'kilovolts'
_definition
! ; The voltage in kV at which the radiation source was operated.
;
###########################
--- 4360,4367 ----
_units kV
_units_detail 'kilovolts'
_definition
! ; The voltage in kilovolts at which the radiation source was
! operated.
;
###########################
***************
*** 4679,4688 ****
_units mm
_units_detail 'millimetres'
_definition
! ; The maximum, medial and minimum dimensions of the crystal. If
! the crystal is a sphere or a cylinder then the *_rad item is
! the radius. These may appear in a list with _exptl_crystal_id
! if multiple crystals are used in the experiment.
;
--- 4773,4783 ----
_units mm
_units_detail 'millimetres'
_definition
! ; The maximum, medial and minimum dimensions in millimetres of
! the crystal. If the crystal is a sphere or a cylinder then
! the *_rad item is the radius. These may appear in a list
! with _exptl_crystal_id if multiple crystals are used in the
! experiment.
;
***************
*** 4930,4936 ****
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
--- 5025,5031 ----
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
***************
*** 5048,5054 ****
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
--- 5143,5149 ----
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
***************
*** 5158,5164 ****
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
--- 5253,5259 ----
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
***************
*** 5254,5262 ****
_units A
_units_detail 'Angstroms'
_definition
! ; Distances between the donor and hydrogen (*_DH), hydrogen
! and acceptor (*_HA) and donor and acceptor (*_DA) sites in
! a hydrogen bond.
;
data_geom_hbond_publ_flag
--- 5349,5357 ----
_units A
_units_detail 'Angstroms'
_definition
! ; Distances in angstroms between the donor and hydrogen (*_DH),
! hydrogen and acceptor (*_HA) and donor and acceptor (*_DA)
! sites in a hydrogen bond.
;
data_geom_hbond_publ_flag
***************
*** 5298,5304 ****
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
--- 5393,5399 ----
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
***************
*** 5433,5439 ****
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
--- 5528,5534 ----
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
! _symmetry_equiv_pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
***************
*** 6124,6130 ****
--- 6219,6227 ----
loop_ _enumeration
_enumeration_detail
no 'not a standard CIF data name'
+ n 'abbreviation for "no"'
yes 'a standard CIF data name'
+ y 'abbreviation for "yes"'
_enumeration_default yes
_definition
; Flags whether the corresponding data item marked for inclusion
***************
*** 6276,6283 ****
_units A
_units_detail 'Angstroms'
_definition
! ; The highest resolution for the interplanar spacing in the
! reflections used in refinement. This is the smallest
d value.
;
--- 6373,6380 ----
_units A
_units_detail 'Angstroms'
_definition
! ; The highest resolution in angstroms for the interplanar spacing
! in the reflections used in refinement. This is the smallest
d value.
;
***************
*** 6289,6296 ****
_units A
_units_detail 'Angstroms'
_definition
! ; The lowest resolution for the interplanar spacing in the
! reflections used in refinement. This is the highest
d value.
;
--- 6386,6393 ----
_units A
_units_detail 'Angstroms'
_definition
! ; The lowest resolution in angstroms for the interplanar spacing
! in the reflections used in refinement. This is the highest
d value.
;
***************
*** 7229,7236 ****
_units A
_units_detail 'Angstroms'
_definition
! ; The highest resolution for the interplanar spacing in the
! reflections in this shell. This is the smallest d value.
;
data_reflns_shell_d_res_low
--- 7326,7333 ----
_units A
_units_detail 'Angstroms'
_definition
! ; The highest resolution in angstroms for the interplanar spacing
! in the reflections in this shell. This is the smallest d value.
;
data_reflns_shell_d_res_low
***************
*** 7241,7248 ****
_units A
_units_detail 'Angstroms'
_definition
! ; The lowest resolution for the interplanar spacing in the
! reflections in this shell. This is the largest d value.
;
data_reflns_shell_meanI_over_sigI_all
--- 7338,7345 ----
_units A
_units_detail 'Angstroms'
_definition
! ; The lowest resolution in angstroms for the interplanar spacing
! in the reflections in this shell. This is the largest d value.
;
data_reflns_shell_meanI_over_sigI_all
***************
*** 7531,7537 ****
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
! _symmetry_equiv_pos_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
--- 7628,7634 ----
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
! _symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
***************
*** 7542,7548 ****
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277]. Formally the value of
! _symmetry_equiv_pos_id can be any unique character string;
it is recommended that it be assigned the sequence number of
the list of equivalent positions for compatibility with
older files in which it did not appear.
--- 7639,7645 ----
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277]. Formally the value of
! _symmetry_equiv_pos_site_id can be any unique character string;
it is recommended that it be assigned the sequence number of
the list of equivalent positions for compatibility with
older files in which it did not appear.
***************
*** 7553,7560 ****
symmetry equivalent positions for the space group.
;
! data_symmetry_equiv_pos_id
! _name '_symmetry_equiv_pos_id'
_category symmetry_equiv
_type numb
_list yes
--- 7650,7657 ----
symmetry equivalent positions for the space group.
;
! data_symmetry_equiv_pos_site_id
! _name '_symmetry_equiv_pos_site_id'
_category symmetry_equiv
_type numb
_list yes
===================================
- Prev by Date: (49) Remaining issues: block id, disorder, diffrn
- Next by Date: (51) Approval of extended Core - update
- Index(es):