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(46) A further round of changes to the submitted Core
- To: COMCIFS@iucr.ac.uk
- Subject: (46) A further round of changes to the submitted Core
- From: bm
- Date: Sun, 28 Jul 1996 13:40:14 +0100
Dear Colleagues
We're getting there...
At the end of this message I append a diff listing (for those who can read
such things) showing the latest round of significant changes to the working
version of the CIF core. If you prefer, you can retrieve the latest version
in its entirety from the COMCIFS ftp account.
D40.1 F(000)
------------
David Watkin has has asked for a revision to the new definition of F(000)
(which he supplied!):
DW> I think the definition is a bit more complicated - I make it
DW>
DW> F0 = sqrt( sum real**2 + sum imag**2), and this is true even for
DW>
DW> centro structures (when we used to publish structure factors, referees were
DW> sometimes surprised to see phases other than 0&180 for centrosymmetric
DW> structures - the only restriction is that phase(-h) = 180+phase(h) ).
DW> However, you should seek another opinion before commiting yourself to paper!
I am somewhat perturbed by how difficult it is to get hold of an
authoritative definition for this, and an appropriate formalism for
representing it. What I have at present is:
_definition
; The effective number of electrons in the crystal unit cell
contributing to F(000). It may contain dispersion contributions,
and is calculated as
F(000) = ( sum (f~r~^2^ + f~i~^2^) )^1/2^
f~r~ = real part of the scattering factors at theta = 0
f~i~ = imaginary part of the scattering factors at theta = 0
;
Further enlightenment will be welcome.
D40.3 Geometric formulation of U(equiv)
---------------------------------------
David requested "I would like to see a definition of this in terms of the
usual U(ij)'s that people report." I passed this comment to David Watkin
(who had been instrumental in opening this thread). For interest, his
response was:
DW> Its strange how things proceed! The next release of CRYSTALS has been
DW> modified so that the user can choose which definition of Uequiv they want!
DW> To avoid any confusion, I proposed to name the geometric mean Ugeom. Syd
DW> convinced me that re-definitions of established terms was more trouble
DW> than it was worth - and I can see that. There is no snappy definition
DW> of Ugeom in terms of Uij. In fact I asked Terry Willis why they (in Willis
DW> and Pryor) had chosen the arithmetic mean, and he said because it was
DW> easier to compute (at that time).
DW>
DW> In fact the geometric mean is more tricky than your expression shows -
DW> try making one of the Ui is negative. With proper handling, it gives a
DW> negative Ugeom - just the thing to draw the readers attention to the fact
DW> that something is seriously wrong. Uarith might look more or less ok. It
DW> turns out that Ugeom is a good diagnostic, while Uarith is what you need
DW> to get structure factors as close as possible to those computed from
DW> Uiso - perhaps not surprising that different definitions have different
DW> uses.
D44.3 _atom_type_scat_versus_stol_list
--------------------------------------
D> I think we should leave this field the way it is. Gotzon's
D> suggestion is interesting but too restrictive. In any case we would
D> need to define a new text field to hold the structured information since
D> the existing field can use any format. This might be worth doing, but I
D> doubt it, at least not now.
Summary: the field is left as a free-text field; the definition remains as
"This table should be well commented to indicate the items present. Regularly
formatted lists are strongly recommended." The possibility of introducing a
more formal presentation remains open for the future.
D44.6 _cell_* etc
-----------------
D> I agree with your analysis.
Summary: the proposed CELL and CELL_MEASUREMENT categories have been rolled
into one. CELL_MEASUREMENT_REFLN remains a separate category.
D44.11, 13 _diffrn_*
--------------------
D> When did we approve the addition of _diffrn_radiation_probe,
D> *_xray_symbol and *_xray_target?
They were discussed in circulars 25 and 26, and provoked no strong
resistance.
D> I am a little concerned about the
D> _diffrn_radiation_[] category. This is not needed for loops (except for
D> wavelengths). Will this restrict our freedom later? A source may have
D> several wavelengths, and different parts of an experiment may use
D> different sources, so *_wavelength perhaps should be considered as a
D> category of its own. I would hate to adopt ANYTHING new in this area
D> until we can review the whole field, unless it is absolutely essential
D> for the functioning of the core extension. Otherwise I agree with your
D> suggestions.
B> On the list of _diffrn_ fields to strike, I suggest keeping some
B> of the _details items. They will be needed, particularly until
B> we get the other fields coded. Of particular importance will be
B> _diffrn_radiation_source_details so that people who want to record
B> power/voltage etc will have a place to do so. I think that
B> _diffrn_measurement_details is also a good candidate to keep.
David has suggested to me that he might be willing, after Seattle, to
conduct a full analysis of the requirements for describing diffraction
apparatus, now and in the foreseeable future, and to recommend a coherent
strategy for extending the data names in this set. (But he might be willing
to concede the task to someone even more enthusiastic to undertake it!)
Summary: I have deleted _diffrn_measurement_device_details, *_specific,
*_type, _diffrn_radiation_detector_details, *_specific, *_type,
_diffrn_radiation_source_power, *_specific, *_target, *_type, leaving
the following entries in:
+ _diffrn_measurement_[]
+ _diffrn_measurement_details
. _diffrn_measurement_device
. _diffrn_measurement_method
+ _diffrn_radiation_[]
+ _diffrn_radiation_collimation
. _diffrn_radiation_detector
. _diffrn_radiation_detector_dtime
. _diffrn_radiation_filter_edge
. _diffrn_radiation_inhomogeneity
. _diffrn_radiation_monochromator
. _diffrn_radiation_polarisn_norm
. _diffrn_radiation_polarisn_ratio
+ _diffrn_radiation_probe
. _diffrn_radiation_source
+ _diffrn_radiation_source_details
. _diffrn_radiation_type
. _diffrn_radiation_wavelength
. _diffrn_radiation_wavelength_id
. _diffrn_radiation_wavelength_wt
+ _diffrn_radiation_xray_symbol
+ _diffrn_radiation_xray_target
The sharp-eyed among you will notice that I have left IN
_diffrn_radiation_collimation, though no-one has specifically referred to
it, because I see some benefit in having a text field to describe the
collimation; but I can be persuaded otherwise.
I haven't changed the category assignments across this collection of
datanames, but I do see David's point, and shall review this when my mind is
fresher. Additional input on this issue is welcome.
D45.3 _list
-----------
D> I agree with the analysis and proposals
Summary: the interpretation of _list yes as meaning "can only be declared in
a looped list" is to be enforced. _symmetry_equiv_pos_as_xyz should thus
have _list both to cater for the P1 case where there is only one value.
(This is really a defect of the original definition which stated "Except
for the space group P1, this data will be repeated in a loop." Formally,
a loop with only one value is perfectly OK - i.e. "loop_
_symmetry_equiv_pos_as_xyz x,y,z" makes perfect STAR sense.)
D45.4 _atom_site_B_equiv_geom
-----------------------------
D> I agree (in very small letters). Please let us distribute the
D> warning about B not being recommended as liberally as possible.
Added to dictionary.
D45.6 Addresses
---------------
D> Leave well alone.
Summary: do not introduce additional items for parts of addresses (_street,
_city etc.)
D45.7 _audit_link_block_code
----------------------------
D> Gotzon's suggestion seems like a good idea. There need be no
D> universal code for the _block_id, it could be left to different
D> applications, and could be redefined when files are copied. For example,
D> if Acta Cryst wanted to ensure all blocks had unique id's in their
D> archive, they could redefine the author's id using an appropriate
D> algorithm. The same would be true for any of the databases, even though
D> Brian T may like to publish the algorithm that should be used for powder
D> patterns submitted to ICDD.
D45.8 Inheritance across datablocks
-----------------------------------
D> Linked files were not envisaged when the parent/child links were
D> defined. Perhaps the definition could be changed to include all data
D> blocks listed in _audit_link_*, but isn't this outside the jurisdiction of
D> comcifs?
Yes, this is a STAR matter. Syd, Nick, please review - is there a way to
extend the STAR scoping rules to permit interconnected lists in different
data blocks?
D45.12 _diffrn_orient_refln_angle
---------------------------------
D> I agree.
Summary: Add *_theta and *_omega data names.
D45.13 _diffrn_refln_scan_mode
------------------------------
D> Add 'q' to the enumeration list. Let's not rush in to any
D> further specifications until we are clear that they are needed.
Done.
D45.14 _diffrn_reflns_number (also .23 _refine_ls_number_reflns)
----------------------------------------------------------------
D> As Syd suggests, these are only to give an idea of the numbers of
D> reflections measured and used. Detailed definitions are not needed.
D45.16 _diffrn_standards_decay_%
--------------------------------
D> Your proposed change in the definition is fine. Do not add
D> Gotzon's second sentence.
D45.22 _refine_ls_goodness_of_fit
---------------------------------
D> A standard uncertainty does seem a little strange for this
D> quantity which is in the nature of a standard uncertainty itself.
D> However, I see no reason to change, even if it were possible to do so.
D45.26 _symmetry_space_group_name_H-M
-------------------------------------
D> We should leave all changes here to the development of symcif.
D> There are problems, but the way to resolve them is not yet clear.
D45.28 _symmetry_equiv_pos_id
-----------------------------
D> It makes sense to restrict these to numbers, but it is not
D> essential that they be sequential. In fact, since the order of items in a
D> cif is undefined, they cannot be sequence numbers in any rigorous sense.
D> Some people may want to use names to indicate the nature of the operation
D> (e.g. mx, 2z, ay) but in this case it would be better to define a
D> _symmetry_equiv_pos_name. Leave this for symcif as well.
D45.31 Category names
---------------------
D> I prefer the use of capitals. Underlining is a feature of
D> datanames and should be restricted to datanames. We may have categories
D> that do not correspond to the first part of the dataname, and in this
D> case the underlining convention may be confusing.
New threads
===========
D46.1 (was D44.7) _citation_journal_coden_ASTM *_CAS
----------------------------------------------------
We had agreed to delete _citation_journal_coden_CAS as the same coden
scheme is now used by CAS and ASTM. However, on going to do this, I notice
that the definition reads "The Chemical Abstracts Service (CAS) abstract
identifier" - suggesting that the intent was to reference a specific
abstract, not a journal name. Hence I have renamed the dataname as
_citation_journal_abstract_id_CAS.
Paula: Was this the intention?
D46.2 _units missing from angles
--------------------------------
Quantities referring to angular measurement had no _units attributes.
Possibly this was due to some feeling that degrees, being dimensionless,
were not proper units; but I have felt it better to add in _units deg
where appropriate.
D46.3 Some comments on esd's
----------------------------
The following is for information only - I consider it COMCIFS' job to
supply a formalism for identifying an e.s.d. (s.u.!), but not to define it.
David Watkin writes:
DW> So - all that's bothering me about publication at the moment now is
DW> esds. Any physicist will tell you that a value without its esd is valueless,
DW> and in a way that is true. However, what is worse is a value with a guesd
DW> - a kind of semi-computerised guess, calculated from a horrendously
DW> approximate formula. Publication of a value for the esd gives it a kind of
DW> authority which it might not really have. Where esds are given, they
DW> must be computed reliably and in a well defined way - in fact, so should
DW> the derived parameter itself.
DW> I'm sure that you know that the current edition of Int Tab has THREE methods
DW> for computing best planes, likely to give different answers, and esds.
DW>
DW> If the author does not give an esd, the reader can make an informed
DW> guess (see for example Carpenter Acta A35 (1979) 248-250), if a value is
DW> given the gullible reader might be misled.
DW>
DW> So, in a round about way we come to what should be in parenthesis
DW> after Uequiv! If the esd on Uii is .001, the esd on Uarith or Ugeom
DW> will be about .001 using propagation of error from the variance covariance
DW> matrix. Not much use if U1=.1, U2=.05 and U3=.001. An rms deviation would be
DW> more informative, and give a real clue about the underlying unsatisfactory
DW> nature of the refinement.
DW>
DW> As always with maths, the problem is to decide what is the 'most
DW> useful' calculation, and that will depend upon what you are tring to
DW> demonstrate.
I also had an email a few weeks ago from George Sheldrick (I'm sorry I
didn't reply George - please accept this as acknowledgement and response):
G> I seem to have run into a problem about how many significant figures should
G> be written to the CIF file.
>>
>> [The new] SHELXL gives too many figures (in some cases) for bond lengths
>> and angles. A recent iodine compound, e.g., had C-C such as 1.4567(234).
>> Acta now insists that no esd can exceed 19. Fair enough; it's not too much
>> trouble to edit the few affected values (most of them don't get published
>> anyway).
>>
G> At the request of Bill Clegg and George Ferguson
G> I increased the number of figures so that the rule of 19 could always be
G> applied, adding an extra figure for safety in some cases. I assumed that
G> any program reading the CIF file to make tables could then round off as
G> appropriate. So for example if the next IUCr Meeting passes a resolution to
G> implement a 'rule of 23' to improve the precision of structures published in
G> Acta, I would not have to send out new versions of my programs to everyone.
G>
G> The references are to a more or less complete test version of SHELX-96 that
G> I intend to release at the IUCr Meeting in Seattle. I hope to resolve all
G> such problems before then !
The assumption that "any program reading the CIF file to make tables could
then round off as appropriate" is wrong. Elsewhere in your message you
remark "removing extra figures is simply a question of intelligent software",
and I would accept that. But as I never tire of telling people, ciftex is
NOT "intelligent", in that sense. However, I accept your point that the
rounding off should be done by Acta, and I shall look into the best way of
achieving this.
That's all for now - it's Sunday lunchtime, and I'm no longer able to tell
my DDLs from my DTDs.
Best wishes
Brian
*** c96.050796 Sat Jul 27 09:46:50 1996
--- cif_core.dic Sun Jul 28 13:11:03 1996
***************
*** 28,34 ****
data_on_this_dictionary
_dictionary_name cif_core.dic
_dictionary_version 2.0
! _dictionary_update 1996-06-28
_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 1996-07-28
_dictionary_history
;
1991-05-27 Created from CIF Dictionary text. SRH
***************
*** 87,101 ****
1996-06-27 Added _journal_language BMcM
1996-06-28 Added area-detector definitions from mmCIF dictionary:
! _diffrn_measurement_device_details, *_specific and *_type;
! _diffrn_radiation_detector_details, *_specific, *_type;
! _diffrn_radiation_source_details, *_power, *_specific,
! *_target, *_type; reflns_shell category BMcM
Added _refine_ls_d_res_high and *_low and changed wording of
! definitions for R factors to include these. BMcM
Added 'h' and 'f' flags to _refln_observed_status. BMcM
1996-07-05 Some typos fixed and examples modified as suggested by
! P.Strickland and I.D.Brown. BMcM
;
#################
--- 87,141 ----
1996-06-27 Added _journal_language BMcM
1996-06-28 Added area-detector definitions from mmCIF dictionary:
! _diffrn_measurement_device_details, *_specific and *_type;
! _diffrn_radiation_detector_details, *_specific, *_type;
! _diffrn_radiation_source_details, *_power, *_specific,
! *_target, *_type; reflns_shell category BMcM
Added _refine_ls_d_res_high and *_low and changed wording of
! definitions for R factors to include these. BMcM
Added 'h' and 'f' flags to _refln_observed_status. BMcM
1996-07-05 Some typos fixed and examples modified as suggested by
! P.Strickland and I.D.Brown. BMcM
! 1996-07-27 BMcM:
! Added example for _diffrn_orient_refln_[] from G. Madariaga
! U~ij~ changed to U^ij^ a la Nomenclature Commission
! Definition of _diffrn_ambient_environment changed to omit vacuum
! as a possible default environment
! Changed definitions of *_site_symmetry_* items to I.D.Brown's
! suggested wording.
! Compressed various journal indexing categories into one
! Changed upper enumeration values for _refln_symmetry_epsilon
! and _refln_symmetry_multiplicity to 48.
! Added references to deprecated use of B values.
! Modified descriptions of phone, fax number conventions
! _publ_manuscript_incl_ entries reworded for greater
! clarity and given individual data blocks
! Added _list_reference to _symmetry_equiv_pos_id and changed
! _list value to 'both' for *_as_xyz to allow the P1 case
! Added _atom_site_B_equiv_geom for completeness
! Modified definitions of _atom_sites_[Cartn,fract]_tran_vector_
! Added _units stuff to _chemical_formula_weight_* and
! _exptl_crystal_density_ items
! Added *_theta, *_omega to _diffrn_orient_refln_angle_
! Added 'q' to enumeration list for _diffrn_refln_scan_mode
! Reworded definition in _diffrn_scale_group_[]
! Permitted esd for _refln_phase_meas (necessitates splitting
! _refln_phase_ datablock in two)
! Added _type_conditions esd for _reflns_scale_meas
! 1996-07-28 BMcM:
! Added example for refln_scale_[] and second example for
! _refln_[] from Xtal test data set.
! Changed references to category names to CAPITALS.
! Merged CELL and CELL_MEASUREMENT categories.
! Added _units deg to all angle quantities.
! Renamed _citation_journal_coden_CAS as
! _citation_journal_abstract_id_CAS
! Removed _diffrn_measurement_device_details, *_specific,
! *_type, _diffrn_radiation_detector_details, *_specific,
! *_type, _diffrn_radiation_source_power, *_specific,
! *_target, *_type, pending full analysis of requirements
! for describing diffraction apparatus.
! Reworded _exptl_crystal_F_000 definition again
;
#################
***************
*** 185,191 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _atom_site_ category record details about
the atom sites in a crystal structure, such as the positional
coordinates, atomic displacement parameters, magnetic moments
and directions, and so on.
--- 225,231 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the ATOM_SITE category record details about
the atom sites in a crystal structure, such as the positional
coordinates, atomic displacement parameters, magnetic moments
and directions, and so on.
***************
*** 204,210 ****
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_U_'
! _related_function constant
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 244,250 ----
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_U_'
! _related_function conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 212,218 ****
components in angstroms squared which appear in the structure
factor term:
! T = exp{-1/4 sum~i~ [ sum~j~ (B~ij~ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
--- 252,258 ----
components in angstroms squared which appear in the structure
factor term:
! T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
***************
*** 219,224 ****
--- 259,268 ----
The unique elements of the real symmetric matrix are
entered by row.
+
+ The IUCr Commission on Nomenclature recommends against the use
+ of B for reporting atomic displacement parameters. U, being
+ directly proportional to B, is preferred.
;
data_atom_site_aniso_label
***************
*** 273,279 ****
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_B_'
! _related_function constant
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 317,323 ----
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_B_'
! _related_function conversion
_units A^2^
_units_detail 'Angstroms squared'
_definition
***************
*** 281,287 ****
components in angstroms squared which appear in the
structure factor term:
! T = exp{-2pi^2^ sum~i~ [sum~j~ (U~ij~ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
--- 325,331 ----
components in angstroms squared which appear in the
structure factor term:
! T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
***************
*** 308,313 ****
--- 352,383 ----
calculated) are given.
;
+ data_atom_site_B_equiv_geom
+ _name '_atom_site_B_equiv_geom'
+ _category atom_site
+ _type numb
+ _type_conditions esd
+ _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
+ ; Equivalent isotropic atomic displacement parameter, B(equiv),
+ in angstroms squared, calculated as the geometric mean of
+ the anisotropic atomic displacement parameters.
+
+ B(equiv) = (B~i~ B~j~ B~k~)^1/3^
+
+ B~n~ = the principal components of the orthogonalised B^ij^
+
+ The IUCr Commission on Nomenclature recommends against the use
+ of B for reporting atomic displacement parameters. U, being
+ directly proportional to B, is preferred.
+ ;
+
data_atom_site_B_iso_or_equiv
_name '_atom_site_B_iso_or_equiv'
_category atom_site
***************
*** 317,323 ****
_list_reference '_atom_site_label'
_enumeration_range 0.0:
_related_item '_atom_site_U_iso_or_equiv'
! _related_function constant
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 387,393 ----
_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
***************
*** 325,338 ****
temperature factor, B(equiv), in angstroms squared, calculated
from anisotropic temperature factor parameters.
! B(equiv) = (1/3) sum~i~[sum~j~(B~ij~ a*~i~ a*~j~ A~i~.A~j~)]
A = the real-space cell lengths
a* = the reciprocal-space cell lengths
! B~ij~ = 8 pi^2^ U~ij~
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
;
--- 395,412 ----
temperature factor, B(equiv), in angstroms squared, calculated
from anisotropic temperature factor parameters.
! B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ A~i~.A~j~)]
A = the real-space cell lengths
a* = the reciprocal-space cell lengths
! B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
+
+ The IUCr Commission on Nomenclature recommends against the use
+ of B for reporting atomic displacement parameters. U, being
+ directly proportional to B, is preferred.
;
***************
*** 661,667 ****
U(equiv) = (U~i~ U~j~ U~k~)^1/3^
! U~n~ = the principal components of the orthogonalised U~ij~
;
data_atom_site_U_iso_or_equiv
--- 735,741 ----
U(equiv) = (U~i~ U~j~ U~k~)^1/3^
! U~n~ = the principal components of the orthogonalised U^ij^
;
data_atom_site_U_iso_or_equiv
***************
*** 673,679 ****
_list_reference '_atom_site_label'
_enumeration_range 0.0:10.0
_related_item '_atom_site_B_iso_or_equiv'
! _related_function constant
_units A^2^
_units_detail 'Angstroms squared'
_definition
--- 747,753 ----
_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
***************
*** 681,687 ****
atomic displacement parameter, U(equiv), in angstroms squared,
calculated from anisotropic atomic displacement parameters.
! U(equiv) = (1/3) sum~i~[sum~j~(U~ij~ a*~i~ a*~j~ A~i~.A~j~)]
A = the real-space cell lengths
a* = the reciprocal-space cell lengths
--- 755,761 ----
atomic displacement parameter, U(equiv), in angstroms squared,
calculated from anisotropic atomic displacement parameters.
! U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ A~i~.A~j~)]
A = the real-space cell lengths
a* = the reciprocal-space cell lengths
***************
*** 734,740 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _atom_sites_ category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
--- 808,814 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
***************
*** 753,759 ****
_type numb
_definition
; Matrix elements used to transform fractional coordinates in
! the _atom_sites_ category to Cartesian coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_Cartn_tran_vector_.
--- 827,833 ----
_type numb
_definition
; Matrix elements used to transform fractional coordinates in
! the ATOM_SITES category to Cartesian coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_Cartn_tran_vector_.
***************
*** 780,790 ****
_category atom_sites
_type numb
_definition
! ; Matrix elements used to transform fractional coordinates in
! the _atom_sites_ category to Cartesian coordinates. The axial
alignments of this transformation are described in
! _atom_sites_Cartn_transform_axes. The 3 x 1 translation is
! defined in _atom_sites_Cartn_tran_vector_.
x' |11 12 13| x | 1 |
( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 |
z' |31 32 33| z | 3 |
--- 854,864 ----
_category atom_sites
_type numb
_definition
! ; Elements of a 3 x 1 translation vector used in the
! transformation of fractional coordinates in the
! ATOM_SITES category to Cartesian coordinates. The axial
alignments of this transformation are described in
! _atom_sites_Cartn_transform_axes.
x' |11 12 13| x | 1 |
( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 |
z' |31 32 33| z | 3 |
***************
*** 804,810 ****
_type numb
_definition
; Matrix elements used to transform Cartesian coordinates in
! the _atom_sites_ category to fractional coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_fract_tran_vector_.
--- 878,884 ----
_type numb
_definition
; Matrix elements used to transform Cartesian coordinates in
! the ATOM_SITES category to fractional coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_fract_tran_vector_.
***************
*** 820,830 ****
_category atom_sites
_type numb
_definition
! ; Matrix elements used to transform Cartesian coordinates in
! the _atom_sites_ category to orthogonal coordinates. The axial
alignments of this transformation are described in
! _atom_sites_fract_transform_axes. The 3 x 1 translation is
! defined in _atom_sites_fract_tran_vector_.
x' |11 12 13| x | 1 |
( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 |
z' |31 32 33| z | 3 |
--- 894,904 ----
_category atom_sites
_type numb
_definition
! ; Elements of a 3 x 1 translation vector used in the
! transformation of Cartesian coordinates in the
! ATOM_SITES category to fractional coordinates. The axial
alignments of this transformation are described in
! _atom_sites_Cartn_transform_axes.
x' |11 12 13| x | 1 |
( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 |
z' |31 32 33| z | 3 |
***************
*** 884,890 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
--- 958,964 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
***************
*** 1075,1081 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _audit_ category record details about the
creation and subsequent updating of the data block.
;
--- 1149,1155 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
;
***************
*** 1149,1155 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _audit_author_ category record details about
the author(s) of the data block.
;
--- 1223,1229 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
;
***************
*** 1212,1232 ****
Example 1 - Any file conforming to the current CIF core dictionary.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- ;
- loop_
- _audit_conform_dict_name
- _audit_conform_dict_version
- _audit_conform_dict_location
- cif_core.dic 2.0 ftp://ftp.iucr.ac.uk/pub/cifdic.c96
- mif_core.dic 1.0 ftp://ftp.iucr.ac.uk/pub/mifdic.c93
- ;
- ;
- Example 2 - A file conforming to the current CIF core dictionary and the
- molecular information file (MIF) core dictionary.
- ;
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _audit_conform_ category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
;
--- 1286,1293 ----
Example 1 - Any file conforming to the current CIF core dictionary.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
;
***************
*** 1299,1305 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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 data block.
;
--- 1360,1366 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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 data block.
;
***************
*** 1339,1357 ****
loop_
_example '12(34)9477334'
'12()349477334'
- '(12) 34 947 7334'
- '(12)34-947-7334'
_definition
; The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
! Two styles are permitted. The preferred style includes the
! international dialing prefix, area code in parentheses, and
local number with no spaces.
-
- The alternative style includes the international code in
- parentheses, with area and local codes separated by spaces
- or hyphens.
;
data_audit_contact_author_name
--- 1400,1412 ----
loop_
_example '12(34)9477334'
'12()349477334'
_definition
; The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
! The recommended style includes the international dialing
! prefix, the area code in parentheses, followed by the
local number with no spaces.
;
data_audit_contact_author_name
***************
*** 1379,1398 ****
_type char
loop_
_example '12(34)9477330'
! '1234()9477330'
'12(34)9477330x5543'
- '(12) 34 947 7330 ext 5543'
_definition
; The telephone number of the author of the data block to whom
correspondence should be addressed.
! Two styles are permitted. The preferred style includes the
! international dialing prefix, area code in parentheses, local
! number and any extension number prefixed by 'x', with no spaces.
!
! The alternative style includes the international code in
! parentheses, with area and local codes separated by spaces
! or hyphens, and any extension number preceded by 'ext'.
;
#################
--- 1434,1449 ----
_type char
loop_
_example '12(34)9477330'
! '12()349477330'
'12(34)9477330x5543'
_definition
; The telephone number of the author of the data block to whom
correspondence should be addressed.
! The recommended style includes the international dialing
! prefix, the area code in parentheses, followed by the
! local number and any extension number prefixed by 'x',
! with no spaces.
;
#################
***************
*** 1434,1440 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _audit_link_ category record details about the
relationships between data blocks in the current CIF.
;
--- 1485,1491 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
;
***************
*** 1483,1488 ****
--- 1534,1544 ----
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 1759.0(3)
+
+ _cell_measurement_temperature 293
+ _cell_measurement_reflns_used 25
+ _cell_measurement_theta_min 25
+ _cell_measurement_theta_max 31
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
***************
*** 1490,1497 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _cell_ category record details about the
! crystallographic cell parameters.
;
--- 1546,1553 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the CELL category record details about the
! crystallographic cell parameters and their measurement.
;
***************
*** 1505,1510 ****
--- 1561,1568 ----
_type_conditions esd
_enumeration_range 0.0:180.0
_enumeration_default 90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; Unit-cell angles in degrees of the reported structure.
The values of _refln_index_h, *_k, *_l must correspond to the
***************
*** 1546,1614 ****
_diffrn_reflns_transf_matrix_.
;
- data_cell_special_details
- _name '_cell_special_details'
- _category cell
- _type char
- loop_ _example 'pseudo-orthorhombic'
- 'standard setting from 45 deg rotation around c'
- _definition
- ; A description of special aspects of the cell choice, noting
- possible alternative settings.
- ;
-
- data_cell_volume
- _name '_cell_volume'
- _category cell
- _type numb
- _type_conditions esd
- _enumeration_range 0.0:
- _units A^3^
- _units_detail 'cubic Angstroms'
- _definition
- ; Cell volume V in angstroms cubed.
-
- V = a b c [1 - cos^2^(alpha) - cos^2^(beta) - cos^2^(gamma)
- + 2 cos(alpha) cos(beta) cos(gamma) ] ^1/2^
-
- a = _cell_length_a
- b = _cell_length_b
- c = _cell_length_c
- alpha = _cell_angle_alpha
- beta = _cell_angle_beta
- gamma = _cell_angle_gamma
- ;
-
- ########################
- ## _cell_measurement_ ##
- ########################
-
- data_cell_measurement_[]
- _name '_cell_measurement_[]'
- _category category_overview
- _type null
- loop_ _example
- _example_detail
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- ;
- _cell_measurement_temperature 293
- _cell_measurement_reflns_used 25
- _cell_measurement_theta_min 25
- _cell_measurement_theta_max 31
- ;
- ;
- Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
- Acta Cryst. C47, 2276-2277].
- ;
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- _definition
- ; Data items in the _cell_measurement_ category record details
- about the measurement of the crystallographic cell parameters.
- ;
-
data_cell_measurement_pressure
_name '_cell_measurement_pressure'
! _category cell_measurement
_type numb
_type_conditions esd
_enumeration_range 0.0:
--- 1604,1612 ----
_diffrn_reflns_transf_matrix_.
;
data_cell_measurement_pressure
_name '_cell_measurement_pressure'
! _category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
***************
*** 1619,1628 ****
were measured (not the pressure used to synthesize the sample).
;
-
data_cell_measurement_radiation
_name '_cell_measurement_radiation'
! _category cell_measurement
_type char
loop_ _example 'neutron' 'Cu K\a' 'synchrotron'
_definition
--- 1617,1625 ----
were measured (not the pressure used to synthesize the sample).
;
data_cell_measurement_radiation
_name '_cell_measurement_radiation'
! _category cell
_type char
loop_ _example 'neutron' 'Cu K\a' 'synchrotron'
_definition
***************
*** 1632,1638 ****
data_cell_measurement_reflns_used
_name '_cell_measurement_reflns_used'
! _category cell_measurement
_type numb
_definition
; The total number of reflections used to determine the unit cell.
--- 1629,1635 ----
data_cell_measurement_reflns_used
_name '_cell_measurement_reflns_used'
! _category cell
_type numb
_definition
; The total number of reflections used to determine the unit cell.
***************
*** 1642,1648 ****
data_cell_measurement_temperature
_name '_cell_measurement_temperature'
! _category cell_measurement
_type numb
_type_conditions esd
_enumeration_range 0.0:
--- 1639,1645 ----
data_cell_measurement_temperature
_name '_cell_measurement_temperature'
! _category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
***************
*** 1656,1664 ****
data_cell_measurement_theta_
loop_ _name '_cell_measurement_theta_max'
'_cell_measurement_theta_min'
! _category cell_measurement
_type numb
_enumeration_range 0.0:90.0
_definition
; The maximum and minimum theta angles in degrees of reflections
used to measure the unit cell.
--- 1653,1663 ----
data_cell_measurement_theta_
loop_ _name '_cell_measurement_theta_max'
'_cell_measurement_theta_min'
! _category cell
_type numb
_enumeration_range 0.0:90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; The maximum and minimum theta angles in degrees of reflections
used to measure the unit cell.
***************
*** 1666,1672 ****
data_cell_measurement_wavelength
_name '_cell_measurement_wavelength'
! _category cell_measurement
_type numb
_enumeration_range 0.0:
_units A
--- 1665,1671 ----
data_cell_measurement_wavelength
_name '_cell_measurement_wavelength'
! _category cell
_type numb
_enumeration_range 0.0:
_units A
***************
*** 1678,1685 ****
--- 1677,1716 ----
_diffrn_radiation_wavelength.
;
+ data_cell_special_details
+ _name '_cell_special_details'
+ _category cell
+ _type char
+ loop_ _example 'pseudo-orthorhombic'
+ 'standard setting from 45 deg rotation around c'
+ _definition
+ ; A description of special aspects of the cell choice, noting
+ possible alternative settings.
+ ;
+ data_cell_volume
+ _name '_cell_volume'
+ _category cell
+ _type numb
+ _type_conditions esd
+ _enumeration_range 0.0:
+ _units A^3^
+ _units_detail 'cubic Angstroms'
+ _definition
+ ; Cell volume V in angstroms cubed.
+ V = a b c [1 - cos^2^(alpha) - cos^2^(beta) - cos^2^(gamma)
+ + 2 cos(alpha) cos(beta) cos(gamma) ] ^1/2^
+
+ a = _cell_length_a
+ b = _cell_length_b
+ c = _cell_length_c
+ alpha = _cell_angle_alpha
+ beta = _cell_angle_beta
+ gamma = _cell_angle_gamma
+ ;
+
+
##############################
## _cell_measurement_refln_ ##
##############################
***************
*** 1699,1705 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _cell_measurement_refln_ category record
details about the reflections used in determination of the
crystallographic cell parameters.
--- 1730,1736 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used in determination of the
crystallographic cell parameters.
***************
*** 1727,1732 ****
--- 1758,1765 ----
_list yes
_list_reference '_cell_measurement_refln_index_'
_enumeration_range 0.0:90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; Theta angle in degrees for the reflection used for
measurement of the unit cell with the indices
***************
*** 1754,1760 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
--- 1787,1793 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
***************
*** 2221,2226 ****
--- 2254,2261 ----
_category chemical_formula
_type numb
_enumeration_range 1.0:
+ _units Da
+ _units_detail 'daltons'
_definition
; Formula mass in daltons. This mass should correspond to the
formulae given under _chemical_formula_structural, *_iupac,
***************
*** 2234,2239 ****
--- 2269,2276 ----
_category chemical_formula
_type numb
_enumeration_range 1.0:
+ _units Da
+ _units_detail 'daltons'
_definition
; Formula mass in daltons measured by a non-diffraction experiment.
;
***************
*** 2300,2306 ****
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _citation_ category record details about the
literature cited relevant to the contents of the data block.
;
--- 2337,2343 ----
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the CITATION category record details about the
literature cited relevant to the contents of the data block.
;
***************
*** 2433,2440 ****
assigned to the journal cited; relevant for journal articles.
;
! data_citation_journal_coden_CAS
! _name '_citation_journal_coden_CAS'
_category citation
_type char
_list yes
--- 2470,2477 ----
assigned to the journal cited; relevant for journal articles.
;
! data__citation_journal_abstract_id_CAS
! _name '_citation_journal_abstract_id_CAS'
_category citation
_type char
_list yes
***************
*** 2634,2640 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _citation_author_ category record details
about the authors associated with the citations in the
_citation_ list.
;
--- 2671,2677 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
_citation_ list.
;
***************
*** 2708,2714 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _citation_editor_ category record details
about the editor associated with the book or book chapter
citations in the _citation_ list.
;
--- 2745,2751 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the CITATION_EDITOR category record details
about the editor associated with the book or book chapter
citations in the _citation_ list.
;
***************
*** 2786,2792 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _computing_ category record details about the
computer programs used in the crystal structure analysis.
;
--- 2823,2829 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
;
***************
*** 2830,2836 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _database_ category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
--- 2867,2873 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DATABASE category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
***************
*** 2891,2897 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_ category record details about the
intensity measurements.
;
--- 2928,2934 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN category record details about the
intensity measurements.
;
***************
*** 2900,2906 ****
_category diffrn
_type char
_definition
! ; The gas or liquid surrounding the sample, if not air or vacuum.
;
data_diffrn_ambient_pressure
--- 2937,2943 ----
_category diffrn
_type char
_definition
! ; The gas or liquid surrounding the sample, if not air.
;
data_diffrn_ambient_pressure
***************
*** 2987,2993 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_attenuator_ category record details
about the diffraction attenuator scales employed.
;
--- 3024,3030 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
;
***************
*** 2997,3002 ****
--- 3034,3040 ----
_type char
_list yes
_list_mandatory yes
+ _list_link_child '_diffrn_refln_attenuator_code'
_definition
; A code associated with a particular attenuator setting. This code
is referenced by the _diffrn_refln_attenuator_code which is
***************
*** 3036,3059 ****
Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- ;
- _diffrn_measurement_device_type 'three-circle diffractometer'
- _diffrn_measurement_device_specific 'Supper model x'
- _diffrn_measurement_device_details 'none'
- _diffrn_measurement_method '\w scan'
-
- _diffrn_measurement_details
- ; 440 frames, 0.20 \%, 150 s, detector distance 12 cm,
- detector angle 22.5 \%
- ;
- ;
- ;
- Example 2 - based on PDB entry 5HVP and laboratory records for the
- structure corresponding to PDB entry 5HVP
- ;
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_measurement_ category record details
about the device used to orient and/or position the crystal
during intensity measurement and the manner in which the
diffraction intensities were measured.
--- 3074,3081 ----
Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during intensity measurement and the manner in which the
diffraction intensities were measured.
***************
*** 3064,3071 ****
_category diffrn_measurement
_type char
_example
! ; 440 frames, 0.20 \%, 150 s, detector distance 12 cm,
! detector angle 22.5 \%
;
_definition
; A description of special aspects of the intensity measurement.
--- 3086,3093 ----
_category diffrn_measurement
_type char
_example
! ; The results may not be entirely reliable as the measurement was
! made during a heat wave when the air-conditioning had failed.
;
_definition
; A description of special aspects of the intensity measurement.
***************
*** 3081,3125 ****
diffraction intensities.
;
- data_diffrn_measurement_device_details
- _name '_diffrn_measurement_device_details'
- _category diffrn_measurement
- _type char
- _definition
- ; A description of special aspects of the device used to measure
- the diffraction intensities.
- ;
-
- data_diffrn_measurement_device_specific
- _name '_diffrn_measurement_device_specific'
- _category diffrn_measurement
- _type char
- loop_
- _example 'Supper model q'
- 'Huber model r'
- 'Enraf-Nonius model s'
- 'homemade'
- _definition
- ; The particular device used to measure the diffraction
- intensities. In general this will be a manufacturer,
- description, model number or some combination of these.
- ;
-
- data_diffrn_measurement_device_type
- _name '_diffrn_measurement_device_type'
- _category diffrn_measurement
- _type char
- loop_
- _example 'three-circle diffractometer'
- 'four-circle diffractometer'
- '\k-geometry diffractometer'
- 'oscillation camera'
- 'precession camera'
- _definition
- ; The general class of the device used to measure the
- diffraction intensities.
- ;
-
data_diffrn_measurement_method
_name '_diffrn_measurement_method'
_category diffrn_measurement
--- 3103,3108 ----
***************
*** 3150,3155 ****
--- 3133,3140 ----
_diffrn_orient_matrix_UB_31 0.00587
_diffrn_orient_matrix_UB_32 -0.13766
_diffrn_orient_matrix_UB_33 0.02277
+
+ _diffrn_orient_matrix_type 'TEXSAN convention (MSC, 1989)'
;
;
Example 1 - data set n-alkylation_C-4 of Hussain, Fleming, Norman & Chang
***************
*** 3157,3163 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_orient_matrix_ category record details
about the orientation matrix used in data measurement.
;
--- 3142,3148 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in data measurement.
;
***************
*** 3202,3215 ****
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! End of Example 1
;
;
! Example 1 - need example here
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_orient_refln_ category record details
about the reflections that define the orientation matrix used in
measurement of diffraction intensities.
;
--- 3187,3220 ----
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! loop_
! _diffrn_orient_refln_index_h
! _diffrn_orient_refln_index_k
! _diffrn_orient_refln_index_l
! _diffrn_orient_refln_angle_theta
! _diffrn_orient_refln_angle_phi
! _diffrn_orient_refln_angle_omega
! _diffrn_orient_refln_angle_kappa
! -3 2 3 7.35 44.74 2.62 17.53
! -4 1 0 9.26 83.27 8.06 5.79
! 0 0 6 5.85 -43.93 -25.36 86.20
! 2 1 3 7.36 -57.87 6.26 5.42
! 0 0 -6 5.85 -161.59 36.96 -86.79
! -3 1 0 6.74 80.28 5.87 2.60
! 2 0 3 5.86 -76.86 -0.17 21.34
! 0 0 12 11.78 -44.02 -19.51 86.41
! 0 0 -12 11.78 -161.67 42.81 -86.61
! -5 1 0 11.75 86.24 9.16 7.44
! 0 4 6 11.82 -19.82 10.45 4.19
! 5 0 6 14.13 -77.28 10.17 15.34
! 8 0 0 20.79 -77.08 25.30 -13.96
;
;
! Example 1 - typical output listing from Enraf-Nonius CAD-4 diffractometer.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
measurement of diffraction intensities.
;
***************
*** 3217,3228 ****
--- 3222,3237 ----
data_diffrn_orient_refln_angle_
loop_ _name '_diffrn_orient_refln_angle_chi'
'_diffrn_orient_refln_angle_kappa'
+ '_diffrn_orient_refln_angle_omega'
'_diffrn_orient_refln_angle_phi'
'_diffrn_orient_refln_angle_psi'
+ '_diffrn_orient_refln_angle_theta'
_category diffrn_orient_refln
_type numb
_list yes
_list_reference '_diffrn_orient_refln_index_'
+ _units deg
+ _units_detail 'degrees'
_definition
; Diffractometer angles in degrees of a reflection used to define
the orientation matrix. See _diffrn_orient_matrix_UB_ and
***************
*** 3265,3289 ****
Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- ;
- _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 '8 mm 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 1.5418
- ;
- ;
- Example 2 - based on PDB entry 5HVP and laboratory records for the
- structure corresponding to PDB entry 5HVP
- ;
- # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_radiation_ category record details
about the radiation and detector used in measuring diffraction
intensities.
;
--- 3274,3281 ----
Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_RADIATION category record details
about the radiation and detector used in measuring diffraction
intensities.
;
***************
*** 3311,3324 ****
; The detector used to measure the diffraction intensities.
;
- data_diffrn_radiation_detector_details
- _name '_diffrn_radiation_detector_details'
- _category diffrn_radiation
- _type char
- _definition
- ; A description of special aspects of the radiation detector.
- ;
-
data_diffrn_radiation_detector_dtime
_name '_diffrn_radiation_detector_dtime'
_category diffrn_radiation
--- 3303,3308 ----
***************
*** 3330,3362 ****
; The deadtime in microseconds of _diffrn_radiation_detector.
;
- data_diffrn_radiation_detector_specific
- _name '_diffrn_radiation_detector_specific'
- _category diffrn_radiation
- _type char
- loop_
- _example 'Siemens model x'
- 'Kodak XG'
- 'MAR Research model y'
- _definition
- ; The particular radiation detector. In general this will be a
- manufacturer, description, model number or some combination of
- these.
- ;
-
- data_diffrn_radiation_detector_type
- _name '_diffrn_radiation_detector_type'
- _category diffrn_radiation
- _type char
- loop_
- _example 'multiwire'
- 'imaging plate'
- 'CCD'
- 'film'
- _definition
- ; The general class of the radiation detector.
- ;
-
data_diffrn_radiation_filter_edge
_name '_diffrn_radiation_filter_edge'
_category diffrn_radiation
--- 3314,3319 ----
***************
*** 3403,3408 ****
--- 3360,3367 ----
_list both
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:
+ _units deg
+ _units_detail 'degrees'
_definition
; The angle in degrees of the perpendicular polarisation component
to the diffraction plane. See _diffrn_radiation_polarisn_ratio.
***************
*** 3460,3515 ****
; A description of special aspects of the source of radiation.
;
- data_diffrn_radiation_source_power
- _name '_diffrn_radiation_source_power'
- _category diffrn_radiation
- _type char
- loop_
- _example '50 kV, 35 mA'
- '8 kW'
- '12 GeV'
- _definition
- ; The power of the radiation source.
- ;
-
- data_diffrn_radiation_source_specific
- _name '_diffrn_radiation_source_specific'
- _category diffrn_radiation
- _type char
- loop_
- _example 'Rigaku RU200'
- 'Philips fine-focus Mo'
- 'NSLS beamline X8C'
- _definition
- ; 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.
- ;
-
- data_diffrn_radiation_source_target
- _name '_diffrn_radiation_source_target'
- _category diffrn_radiation
- _type char
- loop_
- _example '8mm x 0.4 mm fine-focus'
- 'broad focus'
- _definition
- ; The nature of the cathode target of the radiation source.
- ;
-
- data_diffrn_radiation_source_type
- _name '_diffrn_radiation_source_type'
- _category diffrn_radiation
- _type char
- loop_
- _example 'sealed tube'
- 'rotating anode'
- 'synchrotron'
- _definition
- ; The general class of the source of radiation.
- ;
-
data_diffrn_radiation_type
_name '_diffrn_radiation_type'
_category diffrn_radiation
--- 3419,3424 ----
***************
*** 3544,3550 ****
loop_ _example x1 x2 neut
_definition
; The code identifying each value of _diffrn_radiation_wavelength.
! Items in 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.
--- 3453,3459 ----
loop_ _example x1 x2 neut
_definition
; The code identifying each value of _diffrn_radiation_wavelength.
! Items in 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.
***************
*** 3617,3623 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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
--- 3526,3532 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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
***************
*** 3639,3644 ****
--- 3548,3555 ----
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
+ _units deg
+ _units_detail 'degrees'
_definition
; The diffractometer angles in degrees of a reflection. These
correspond to the specified orientation matrix and the original
***************
*** 3651,3656 ****
--- 3562,3568 ----
_type char
_list yes
_list_reference '_diffrn_refln_index_'
+ _list_link_parent '_diffrn_attenuator_code'
_definition
; The code identifying the attenuator setting for this reflection.
This code must match one of the _diffrn_attenuator_code values.
***************
*** 3680,3685 ****
--- 3592,3598 ----
_type char
_list yes
_list_reference '_diffrn_refln_index_'
+ _list_link_parent '_exptl_crystal_id'
_definition
; Code identifying each crystal if multiple crystals are used. Is
used to link with _exptl_crystal_id in the _exptl_crystal_ list.
***************
*** 3693,3698 ****
--- 3606,3613 ----
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; Total slit apertures in degrees in the diffraction plane
(*_horiz) and perpendicular to the diffraction plane (*_vert).
***************
*** 3763,3768 ****
--- 3678,3684 ----
loop_ _enumeration
_enumeration_detail om 'omega scan'
ot 'omega/2theta scan'
+ q 'Q-scans (arbitrary reciprocal directions)'
_definition
; The code identifying the mode of scanning with a diffractometer.
See _diffrn_refln_scan_width and _diffrn_refln_scan_mode_backgd.
***************
*** 3814,3819 ****
--- 3730,3737 ----
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; The scan width in degrees of the scan mode defined by the code
_diffrn_refln_scan_mode.
***************
*** 3906,3912 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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
--- 3824,3830 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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
***************
*** 3979,3984 ****
--- 3897,3904 ----
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
+ _units deg
+ _units_detail 'degrees'
_definition
; Theta angle limits in degrees for the measured intensities.
;
***************
*** 4023,4030 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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 multi-crystal
--- 3943,3951 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_SCALE_GROUP category record details
! of the scaling factors applied to place all intensities in
! the reflection lists on a common scale.
Scaling groups might, for instance, correspond to each film
in a multi-film data set, or each crystal in a multi-crystal
***************
*** 4081,4087 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _diffrn_standard_refln_ category record details
about the reflections treated as standards during the measurement
of diffraction intensities.
--- 4002,4008 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of diffraction intensities.
***************
*** 4139,4145 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
--- 4060,4066 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
***************
*** 4155,4162 ****
_definition
; The percentage decrease in the mean of the intensities
for the set of standard reflections at the start of the
! measurement process and at the finish. This value is intended
! as a measure of the overall decay in crystal quality
during the diffraction measurement process.
;
--- 4076,4083 ----
_definition
; The percentage decrease in the mean of the intensities
for the set of standard reflections at the start of the
! measurement process and at the finish. This value usually
! affords a measure of the overall decay in crystal quality
during the diffraction measurement process.
;
***************
*** 4214,4222 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
data_exptl_absorpt_coefficient_mu
--- 4135,4143 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the EXPTL category record details about the
! the experimental work prior to the intensity measurement, and
! about the absorption correction technique employed.
;
data_exptl_absorpt_coefficient_mu
***************
*** 4323,4329 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
--- 4244,4250 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
***************
*** 4346,4351 ****
--- 4267,4274 ----
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
+ _units Mgm^-3^
+ _units_detail 'megagrams per cubic metre'
_definition
; Density values calculated from crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
***************
*** 4355,4363 ****
--- 4278,4289 ----
_name '_exptl_crystal_density_meas'
_category exptl_crystal
_type numb
+ _type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
+ _units Mgm^-3^
+ _units_detail 'megagrams per cubic metre'
_definition
; Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
***************
*** 4368,4376 ****
--- 4294,4305 ----
_name '_exptl_crystal_density_meas_temp'
_category exptl_crystal
_type numb
+ _type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
+ _units K
+ _units_detail 'kelvins'
_definition
; Temperature in kelvins at which _exptl_crystal_density_meas
was determined.
***************
*** 4412,4419 ****
_definition
; The effective number of electrons in the crystal unit cell
contributing to F(000). It may contain dispersion contributions,
! and is calculated as the sum of the real parts of the scattering
! factors at theta = 0.
;
data_exptl_crystal_id
--- 4341,4352 ----
_definition
; The effective number of electrons in the crystal unit cell
contributing to F(000). It may contain dispersion contributions,
! and is calculated as
!
! F(000) = ( sum (f~r~^2^ + f~i~^2^) )^1/2^
!
! f~r~ = real part of the scattering factors at theta = 0
! f~i~ = imaginary part of the scattering factors at theta = 0
;
data_exptl_crystal_id
***************
*** 4422,4427 ****
--- 4355,4361 ----
_type char
_list yes
_list_mandatory yes
+ _list_link_child '_diffrn_refln_crystal_id'
_definition
; Code identifying each crystal if multiple crystals are used. It
is used to link with _diffrn_refln_crystal_id in intensity
***************
*** 4493,4499 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _exptl_crystal_face_ category record details
of the crystal faces.
;
--- 4427,4433 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
;
***************
*** 4506,4511 ****
--- 4440,4447 ----
_type numb
_list yes
_list_reference '_exptl_crystal_face_index_'
+ _units deg
+ _units_detail 'degrees'
_definition
; The diffractometer angle settings in degrees for a specific
crystal face associated with _exptl_crystal_face_perp_dist.
***************
*** 4627,4633 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _geom_angle_ category record details about the
bond angles, as calculated from the contents of the _atom_,
_cell_, and _symmetry_ data.
;
--- 4563,4569 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the GEOM_ANGLE category record details about the
bond angles, as calculated from the contents of the _atom_,
_cell_, and _symmetry_ data.
;
***************
*** 4639,4644 ****
--- 4575,4582 ----
_type_conditions esd
_list yes
_list_reference '_geom_angle_atom_site_label_'
+ _units deg
+ _units_detail 'degrees'
_definition
; Angle in degrees defined by the three sites
_geom_angle_atom_site_label_1, *_2 and *_3. Site at *_2
***************
*** 4692,4707 ****
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'mmm'.
! These numbers are combined to form the code 'n mmm' or n_mmm.
! 'n' is the sequence number of the symmetry elements as listed in
! _symmetry_equiv_pos_as_xyz. 'mmm' are the concatenated cell
! translations along x, y, z with respect to the base number 555.
! The symmetry transformation is applied to the coordinates given
! by _atom_site_fract_x, *_y, *_z identified by _atom_site_label.
! If there are no cell translations the translation number may be
! omitted. If no symmetry operations or translations are applicable
! then a single period '.' may be used.
;
#################
--- 4630,4653 ----
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'klm'.
! These numbers are combined to form the code 'n klm' or n_klm.
! The character string n_klm is composed as follows:
!
! 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
! the atom used in calculating the angle. These translations
! (x,y,z) are related to (k,l,m) by the relations
! k = 5 + x
! l = 5 + y
! m = 5 + z
! By adding 5 to the translations, the use of negative numbers
! is avoided.
;
#################
***************
*** 4739,4745 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _geom_bond_ category record details about
bonds, as calculated from the contents of the _atom_, _cell_,
and _symmetry_ data.
;
--- 4685,4691 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the GEOM_BOND category record details about
bonds, as calculated from the contents of the _atom_, _cell_,
and _symmetry_ data.
;
***************
*** 4801,4817 ****
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry equivalent
! position number 'n' and the cell translation number 'mmm'.
! These numbers are combined to form the code 'n mmm' or n_mmm.
! 'n' is the sequence number of the symmetry elements as listed in
! _symmetry_equiv_pos_as_xyz. 'mmm' are the concatenated cell
! translations along x, y, z with respect to the base number 555.
! The symmetry transformation is applied to the coordinates given
! by _atom_site_fract_x, *_y, *_z identified by _atom_site_label.
! If there are no cell translations the translation number may be
! omitted. If no symmetry operations or translations are applicable
! then a single period '.' may be used.
;
####################
--- 4747,4771 ----
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'klm'.
! These numbers are combined to form the code 'n klm' or n_klm.
! The character string n_klm is composed as follows:
!
! 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
! the atom used in calculating the bond. These translations
! (x,y,z) are related to (k,l,m) by the relations
! k = 5 + x
! l = 5 + y
! m = 5 + z
! By adding 5 to the translations, the use of negative numbers
! is avoided.
;
####################
***************
*** 4842,4848 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _geom_contact_ category record details about
interatomic contacts, as calculated from the contents of the
_atom_, _cell_, and _symmetry_ data.
;
--- 4796,4802 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the GEOM_CONTACT category record details about
interatomic contacts, as calculated from the contents of the
_atom_, _cell_, and _symmetry_ data.
;
***************
*** 4904,4919 ****
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'mmm'.
! These numbers are combined to form the code 'n mmm' or n_mmm.
! 'n' is the sequence number of the symmetry elements as listed in
! _symmetry_equiv_pos_as_xyz. 'mmm' are the concatenated cell
! translations along x, y, z with respect to the base number 555.
! The symmetry transformation is applied to the coordinates given
! by _atom_site_fract_x, *_y, *_z identified by _atom_site_label.
! If there are no cell translations the translation number may be
! omitted. If no symmetry operations or translations are applicable
! then a single period '.' may be used.
;
##################
--- 4858,4881 ----
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'klm'.
! These numbers are combined to form the code 'n klm' or n_klm.
! The character string n_klm is composed as follows:
!
! 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
! the atom used in calculating the contact. These translations
! (x,y,z) are related to (k,l,m) by the relations
! k = 5 + x
! l = 5 + y
! m = 5 + z
! By adding 5 to the translations, the use of negative numbers
! is avoided.
;
##################
***************
*** 4949,4955 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _geom_hbond_ category record details about
hydrogen bonds, as calculated from the contents of the _atom_,
_cell_, and _symmetry_ data.
;
--- 4911,4917 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the GEOM_HBOND category record details about
hydrogen bonds, as calculated from the contents of the _atom_,
_cell_, and _symmetry_ data.
;
***************
*** 4962,4967 ****
--- 4924,4931 ----
_type_conditions esd
_list yes
_list_reference '_geom_hbond_atom_site_label_'
+ _units deg
+ _units_detail 'degrees'
_definition
; Angle in degrees defined by the three sites
_geom_hbond_atom_site_label_D, *_H and *_A. Site at *_D
***************
*** 5033,5049 ****
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry equivalent
! position number 'n' and the cell translation number 'mmm'.
! These numbers are combined to form the code 'n mmm' or n_mmm.
! 'n' is the sequence number of the symmetry elements as listed in
! _symmetry_equiv_pos_as_xyz. 'mmm' are the concatenated cell
! translations along x, y, z with respect to the base number 555.
! The symmetry transformation is applied to the coordinates given
! by _atom_site_fract_x, *_y, *_z identified by _atom_site_label.
! If there are no cell translations the translation number may be
! omitted. If no symmetry operations or translations are applicable
! then a single period '.' may be used.
;
####################
--- 4997,5021 ----
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'klm'.
! These numbers are combined to form the code 'n klm' or n_klm.
! The character string n_klm is composed as follows:
!
! 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
! the atom used in calculating the hydrogen bond. These
! translations (x,y,z) are related to (k,l,m) by the relations
! k = 5 + x
! l = 5 + y
! m = 5 + z
! By adding 5 to the translations, the use of negative numbers
! is avoided.
;
####################
***************
*** 5082,5088 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _geom_torsion_ category record details about
interatomic torsion angles, as calculated from the contents of
the _atom_, _cell_, and _symmetry_ data.
;
--- 5054,5060 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the GEOM_TORSION category record details about
interatomic torsion angles, as calculated from the contents of
the _atom_, _cell_, and _symmetry_ data.
;
***************
*** 5094,5099 ****
--- 5066,5073 ----
_type_conditions esd
_list yes
_list_reference '_geom_torsion_atom_site_label_'
+ _units deg
+ _units_detail 'degrees'
_definition
; The torsion angle in degrees bounded by the four atom sites
identified by the _geom_torsion_atom_site_label_ codes. These
***************
*** 5158,5174 ****
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry equivalent
! position number 'n' and the cell translation number 'mmm'.
! These numbers are combined to form the code 'n mmm' or n_mmm.
! 'n' is the sequence number of the symmetry elements as listed in
! _symmetry_equiv_pos_as_xyz. 'mmm' are the concatenated cell
! translations along x, y, z with respect to the base number 555.
! The symmetry transformation is applied to the coordinates given
! by _atom_site_fract_x, *_y, *_z identified by _atom_site_label.
! If there are no cell translations the translation number may be
! omitted. If no symmetry operations or translations are applicable
! then a single period '.' may be used.
;
###############
--- 5132,5156 ----
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
! ; The symmetry code of each atom site as the symmetry-equivalent
! position number 'n' and the cell translation number 'klm'.
! These numbers are combined to form the code 'n klm' or n_klm.
! The character string n_klm is composed as follows:
!
! 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
! the atom used in calculating the angle. These translations
! (x,y,z) are related to (k,l,m) by the relations
! k = 5 + x
! l = 5 + y
! m = 5 + z
! By adding 5 to the translations, the use of negative numbers
! is avoided.
;
###############
***************
*** 5205,5211 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _journal_ category record details about the
book keeping entries used by the journal staff when processing
a CIF submitted for publication.
--- 5187,5193 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the JOURNAL category record details about the
book keeping entries used by the journal staff when processing
a CIF submitted for publication.
***************
*** 5257,5299 ****
; Data items specified by the journal staff.
;
! data_journal_index_author
! _name '_journal_index_author'
! _category journal_index_author
! _type char
! _definition
! ; Indexing terms supplied by journals staff for the author index.
! ;
! data_journal_index_formula_inorganic
! _name '_journal_index_formula_inorganic'
! _category journal_index_formula_inorganic
! _type char
! _definition
! ; Indexing terms supplied by journals staff for the inorganic
! formula index.
;
!
! data_journal_index_formula_organic
! _name '_journal_index_formula_organic'
! _category journal_index_formula_organic
! _type char
_definition
! ; Indexing terms supplied by journals staff for the organic
! formula index.
;
! data_journal_index_subject_
! loop_ _name '_journal_index_subject_head'
! '_journal_index_subject_term'
! _category journal_index_subject
_type char
_definition
! ; Indexing headwords and terms supplied by journals staff
! for the subject index.
;
-
############
## _publ_ ##
############
--- 5239,5290 ----
; Data items specified by the journal staff.
;
! #####################
! ## _journal_index_ ##
! #####################
! data_journal_index_[]
! _name '_journal_index_[]'
! _category category_overview
! _type null
! loop_ _example
! _example_detail
! # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
! loop_
! _journal_index_type
! _journal_index_term
! _journal_index_subterm
! O C16H19NO4 .
! S alkaloids (-)-norcocaine
! S (-)-norcocaine .
! S
! ; [2R,3S-(2\b,3\b)]-methyl
! 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate
! ; .
! ;
! ;
! Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [(1994).
! Acta Cryst. C50, 2067-2069].
! ;
! # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the JOURNAL_INDEX category are used to list
! terms employed in generating the journal indexes.
!
! Normally the creator of a CIF will not specify these data items.
;
! data_journal_index_
! loop_ _name '_journal_index_subterm'
! '_journal_index_term'
! '_journal_index_type'
! _category journal_index
_type char
_definition
! ; Indexing terms supplied by journals staff.
;
############
## _publ_ ##
############
***************
*** 5342,5349 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _publ_ category are used when submitting a
! manuscript for publication.
;
--- 5333,5347 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the PUBL category are used when submitting a
! manuscript for publication. They refer either to the paper as
! whole, or to specific named elements within a paper (such as
! the title and abstract, or the Comment and Experimental
! sections of Acta Crystallographica Section C). The data items
! in the PUBL_BODY category should be used for the textual
! content of other submissions. Typically, each journal will
! supply a list of the specific items it requires in its Notes
! for Authors.
;
***************
*** 5357,5369 ****
'_publ_contact_author_address' replace
'_publ_contact_author_name' replace
_example
! ; Professor Dr J.U. Blogs
! Department of Structural Chemistry
! RRDD Institute of Technology
! Building #6-M57
! Highho Street
! Citytown 64664
! COUNTRYHERE
;
_definition
; The name and address of the author submitting the manuscript and
--- 5355,5366 ----
'_publ_contact_author_address' replace
'_publ_contact_author_name' replace
_example
! ; Professor George Ferguson
! Department of Chemistry and Biochemistry
! University of Guelph
! Ontario
! Canada
! N1G 2W1
;
_definition
; The name and address of the author submitting the manuscript and
***************
*** 5377,5388 ****
_category publ
_type char
_example
! ; Department of Structural Chemistry
! RRDD Institute of Technology
! Building #6-M57
! Highho Street
! Citytown 64664
! COUNTRYHERE
;
_definition
; The address of the author submitting the manuscript and
--- 5374,5384 ----
_category publ
_type char
_example
! ; Department of Chemistry and Biochemistry
! University of Guelph
! Ontario
! Canada
! N1G 2W1
;
_definition
; The address of the author submitting the manuscript and
***************
*** 5394,5400 ****
_name '_publ_contact_author_name'
_category publ
_type char
! _example 'Professor Dr J.U. Blogs'
_definition
; The name of the author submitting the manuscript and
data block. This is the person contacted by the journal
--- 5390,5396 ----
_name '_publ_contact_author_name'
_category publ
_type char
! _example 'Professor George Ferguson'
_definition
; The name of the author submitting the manuscript and
data block. This is the person contacted by the journal
***************
*** 5418,5436 ****
loop_
_example '12(34)9477334'
'12()349477334'
- '(12) 34 947 7334'
- '(12)34-947-7334'
_definition
; Facsimile telephone number of the author submitting the
manuscript and data block.
! Two styles are permitted. The preferred style includes the
! international dialing prefix, area code in parentheses, and
! local number with no spaces.
!
! The alternative style includes the international code in
! parentheses, with area and local codes separated by spaces
! or hyphens.
;
data_publ_contact_author_phone
--- 5414,5428 ----
loop_
_example '12(34)9477334'
'12()349477334'
_definition
; Facsimile telephone number of the author submitting the
manuscript and data block.
! The recommended style includes the international dialing
! prefix, the area code in parentheses, followed by the
! local number with no spaces. The earlier convention of including
! the international dialing prefixes in parentheses is no longer
! recommended.
;
data_publ_contact_author_phone
***************
*** 5441,5458 ****
_example '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
- '(12) 34 947 7330 ext 5543'
_definition
; Telephone number of the author submitting the manuscript and
data block.
! Two styles are permitted. The preferred style includes the
! international dialing prefix, area code in parentheses, local
! number and any extension number prefixed by 'x', with no spaces.
!
! The alternative style includes the international code in
! parentheses, with area and local codes separated by spaces
! or hyphens, and any extension number preceded by 'ext'.
;
data_publ_contact_letter
--- 5433,5448 ----
_example '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
_definition
; Telephone number of the author submitting the manuscript and
data block.
! The recommended style includes the international dialing
! prefix, the area code in parentheses, followed by the
! local number and any extension number prefixed by 'x',
! with no spaces. The earlier convention of including
! the international dialing prefixes in parentheses is no longer
! recommended.
;
data_publ_contact_letter
***************
*** 5568,5574 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _publ_author_ category record details of
the authors of a manuscript submitted for publication.
;
--- 5558,5564 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
;
***************
*** 5689,5699 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _publ_body_ category permit labelling of
different text sections within the body of a submitted paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
! (such as in Acta Crystallographica Section C).
;
data_publ_body_contents
--- 5679,5691 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the PUBL_BODY category permit labelling of
different text sections within the body of a submitted paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
! (such as in Acta Crystallographica Section C). Typically,
! each journal will supply a list of the specific items it
! requires in its Notes for Authors.
;
data_publ_body_contents
***************
*** 5801,5836 ****
cosmetic headings in comments.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
! data_publ_manuscript_incl_extra_
! loop_ _name '_publ_manuscript_incl_extra_item'
! '_publ_manuscript_incl_extra_info'
! '_publ_manuscript_incl_extra_defn'
_category publ_manuscript_incl
_type char
_list yes
! _example
! ; '_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
;
_definition
! ; These data items are used to specify the need to include specific
! data into a manuscript which is not normally requested by the
! journal. *_item specifies the data name; *_info provides the
! reasons for the inclusion; and *_defn flags whether this is a
! standard CIF definition or not (flags are 'yes' or 'no'). The
! example shows how these three items are looped. Note that *_item
! names MUST be enclosed in single quotes.
;
##############
## _refine_ ##
##############
--- 5793,5867 ----
cosmetic headings in comments.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ;
+ loop_
+ _publ_manuscript_incl_extra_item
+ _publ_manuscript_incl_extra_info
+ _publ_manuscript_incl_extra_defn
+ '_atom_site_symmetry_multiplicity' 'to emphasise special sites' yes
+ '_chemical_compound_source' 'rare material, unusual source' yes
+ '_reflns_d_resolution_high' 'limited data is a problem here' yes
+ '_crystal_magnetic_permeability' 'unusual value for this material' no
+ ;
+ ;
+ Example 2 - hypothetical example including both standard CIF data items
+ and a non_CIF quantity which the author wishes to list.
+ ;
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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. Although these fields are
! primarily intended to identify CIF data items that the author
! wishes to include in a published paper, they can also be used
! to identify data names created so that non-CIF items can be
! included in the publication. Note that *_item names MUST be
! enclosed in single quotes.
;
! data_publ_manuscript_incl_extra_defn
! _name '_publ_manuscript_incl_extra_defn'
_category publ_manuscript_incl
_type char
_list yes
! _list_reference '_publ_manuscript_incl_extra_item'
! loop_ _enumeration
! _enumeration_detail
! no 'not a standard CIF data name'
! yes 'a standard CIF data name'
! _enumeration_default yes
! _definition
! ; Flags whether the corresponding data item marked for inclusion
! in a journal request list is a standard CIF definition or not
! (flags are 'yes' or 'no').
;
+
+ data_publ_manuscript_incl_extra_info
+ _name '_publ_manuscript_incl_extra_info'
+ _category publ_manuscript_incl
+ _type char
+ _list yes
+ _list_reference '_publ_manuscript_incl_extra_item'
_definition
! ; A short note indicating the reason why the author wishes the
! corresponding data item marked for inclusion in the journal
! request list to be published.
;
+ data_publ_manuscript_incl_extra_item
+ _name '_publ_manuscript_incl_extra_item'
+ _category publ_manuscript_incl
+ _type char
+ _list yes
+ _list_mandatory yes
+ _definition
+ ; Specifies the inclusion of specific data into a manuscript
+ which is not normally requested by the journal. The values
+ of this item are the extra data names (which MUST be enclosed
+ in single quotes) that will be added to the journal request list.
+ ;
+
##############
## _refine_ ##
##############
***************
*** 5883,5889 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _refine_ category record details about the
structure refinement parameters.
;
--- 5914,5920 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the REFINE category record details about the
structure refinement parameters.
;
***************
*** 6402,6409 ****
[(1993). Acta Cryst. C49, 1352-1354].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _refln_ category record details about the
reflections used to determine the _atom_site_ data items.
The _refln_ data items refer to individual reflections and must
--- 6433,6470 ----
[(1993). Acta Cryst. C49, 1352-1354].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ;
+ loop_
+ _refln_index_h
+ _refln_index_k
+ _refln_index_l
+ _refln_F_meas
+ _refln_F_calc
+ _refln_F_sigma
+ _refln_observed_status
+ _refln_scale_group_code
+ 0 0 6 34.935 36.034 3.143 o 1
+ 0 0 12 42.599 40.855 2.131 o 1
+ 0 1 0 42.500 42.507 4.719 o 1
+ 0 1 1 59.172 57.976 4.719 o 1
+ 0 1 2 89.694 94.741 4.325 o 1
+ 0 1 3 51.743 52.241 3.850 o 1
+ 0 1 4 9.294 10.318 2.346 o 1
+ 0 1 5 41.160 39.951 3.313 o 1
+ 0 1 6 6.755 7.102 .895 < 1
+ 0 1 7 30.693 31.171 2.668 o 1
+ 0 1 8 12.324 12.085 2.391 o 1
+ 0 1 9 15.348 15.122 2.239 o 1
+ 0 1 10 17.622 19.605 1.997 o 1
+ ;
+ ;
+ Example 2 - based on standard test data set p6122 of the Xtal distribution
+ [Hall, King & Stewart (1995). Xtal3.4 User's Manual. Univ.
+ Western Australia]
+ ;
+ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the REFLN category record details about the
reflections used to determine the _atom_site_ data items.
The _refln_ data items refer to individual reflections and must
***************
*** 6491,6498 ****
_list_mandatory yes
_definition
; Miller indices 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.
;
data_refln_intensity_
--- 6552,6559 ----
_list_mandatory yes
_definition
; Miller indices 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.
;
data_refln_intensity_
***************
*** 6549,6565 ****
respect to inclusion in refinement and calculation of R-factors.
;
! data_refln_phase_
! loop_ _name '_refln_phase_calc'
! '_refln_phase_meas'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
! ; The calculated and measured structure-factor phase in degrees.
;
data_refln_refinement_status
_name '_refln_refinement_status'
_category refln
--- 6610,6640 ----
respect to inclusion in refinement and calculation of R-factors.
;
! data_refln_phase_calc
! _name '_refln_phase_calc'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
+ _units deg
+ _units_detail 'degrees'
_definition
! ; The calculated structure-factor phase in degrees.
;
+ data_refln_phase_meas
+ _name '_refln_phase_meas'
+ _category refln
+ _type numb
+ _type_conditions esd
+ _list yes
+ _list_reference '_refln_index_'
+ _units deg
+ _units_detail 'degrees'
+ _definition
+ ; The measured structure-factor phase in degrees.
+ ;
+
data_refln_refinement_status
_name '_refln_refinement_status'
_category refln
***************
*** 6608,6614 ****
_type numb
_list yes
_list_reference '_refln_index_'
! _enumeration_range 1:32
_definition
; The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
--- 6683,6689 ----
_type numb
_list yes
_list_reference '_refln_index_'
! _enumeration_range 1:48
_definition
; The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
***************
*** 6621,6627 ****
_type numb
_list yes
_list_reference '_refln_index_'
! _enumeration_range 1:24
_definition
; The number of symmetry-equivalent reflections. The equivalent
reflections have the same structure-factor value because of the
--- 6696,6702 ----
_type numb
_list yes
_list_reference '_refln_index_'
! _enumeration_range 1:48
_definition
; The number of symmetry-equivalent reflections. The equivalent
reflections have the same structure-factor value because of the
***************
*** 6685,6691 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _reflns_ category record details about the
reflections used to determine the _atom_site_ data items.
The _refln_ data items refer to individual reflections and must
--- 6760,6766 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the REFLNS category record details about the
reflections used to determine the _atom_site_ data items.
The _refln_ data items refer to individual reflections and must
***************
*** 6769,6780 ****
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
;
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
--- 6844,6863 ----
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
+ loop_
+ _reflns_scale_group_code
+ _reflns_scale_meas_F
+ 1 .895447
+
;
;
+ Example 2 - based on standard test data set p6122 of the Xtal distribution
+ [Hall, King & Stewart (1995). Xtal3.4 User's Manual. Univ.
+ Western Australia]
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; 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.
;
***************
*** 6798,6803 ****
--- 6881,6887 ----
'_reflns_scale_meas_intensity'
_category reflns_scale
_type numb
+ _type_conditions esd
_enumeration_range 0.0:
_list yes
_list_reference '_reflns_scale_group_code'
***************
*** 6838,6844 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _reflns_shell_ category record details about
the reflections used to determine the _atom_site_ data items,
as broken down by shells of resolution.
;
--- 6922,6928 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the REFLNS_SHELL category record details about
the reflections used to determine the _atom_site_ data items,
as broken down by shells of resolution.
;
***************
*** 7066,7072 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _symmetry_ category record details about the
space-group symmetry.
;
--- 7150,7156 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the SYMMETRY category record details about the
space-group symmetry.
;
***************
*** 7153,7159 ****
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the _symmetry_equiv_ category list the
symmetry equivalent positions for the space group.
;
--- 7237,7243 ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
! ; Data items in the SYMMETRY_EQUIV category list the
symmetry equivalent positions for the space group.
;
***************
*** 7162,7172 ****
_category symmetry_equiv
_type numb
_list yes
_definition
; A code identifying each entry in the _symmetry_equiv_pos_as_xyz
list. It should be the sequence number of the entry in that
list, and should be identified with the code 'n' in
! _geom_*_symmetry_ codes of the form 'n_mmm'.
;
data_symmetry_equiv_pos_as_xyz
--- 7246,7257 ----
_category symmetry_equiv
_type numb
_list yes
+ _list_reference '_symmetry_equiv_pos_as_xyz'
_definition
; A code identifying each entry in the _symmetry_equiv_pos_as_xyz
list. It should be the sequence number of the entry in that
list, and should be identified with the code 'n' in
! _geom_*_symmetry_ codes of the form 'n_klm'.
;
data_symmetry_equiv_pos_as_xyz
***************
*** 7173,7179 ****
_name '_symmetry_equiv_pos_as_xyz'
_category symmetry_equiv
_type char
! _list yes
_example -y+x,-y,1/3+z
_definition
; Symmetry equivalent position in the 'xyz' representation. Except
--- 7258,7264 ----
_name '_symmetry_equiv_pos_as_xyz'
_category symmetry_equiv
_type char
! _list both
_example -y+x,-y,1/3+z
_definition
; Symmetry equivalent position in the 'xyz' representation. Except
***************
*** 7183,7189 ****
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
-
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
--- 7268,7273 ----
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