##############################################################################
# #
# CIF CORE DEFINITIONS #
# -------------------- #
# #
# This dictionary contains the names and definitions of the Core data items #
# recognised by the International Union of Crystallography for the exchange #
# of data between laboratories and submissions to journals and databases. #
# #
# The STAR/DDL dictionary is available as the file "ddl_core.dic" #
# located at URL ftp://ftp.iucr.org/pub/ddldic.c95 #
# #
# Copyright 2004 International Union of Crystallography #
##############################################################################
data_on_this_dictionary
_dictionary_name cif_core.dic
_dictionary_version 2.3.1
_dictionary_update 2005-06-27
_dictionary_history
;
1991-05-27 Created from CIF Dictionary text. SRH
1991-05-30 Validated with CYCLOPS & CIF ms. SRH
1991-06-03 Adjustments to some definitions. SRH
1991-06-06 Adjustments a la B. McMahon. SRH
1991-06-18 Additions & some redefinitions. SRH
1991-07-04 Corrected 90:0 in *_detect_slit_. SRH
1991-09-20 Additions & some redefinitions. SRH
1991-09-20 Final published version. IUCr
1991-11-12 Add _diffrn_ambient_environment. SRH
1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH
1993-02-23 Apply global_ and 'unknown' -> '?' SRH
1993-03-05 Changes resulting from MM dictionary. SRH
1993-05-20 Changes arising from new DDL commands. SRH
1993-08-05 Additional finetuning pre-Beijing. SRH
1993-12-22 Introductory sections added to categories. BMcM
1993-12-22 Additional categories from mm work: audit_author,
citation, atom_sites_fract_tran_matrix. BMcM
1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM
1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM
1994-03-01 Add 'atom_site_aniso_ratio'. BMcM
1994-04-15 Comments from IDB on draft version for circulation. BMcM
1994-04-15 Added _publ_section_exptl_solution. BMcM
1994-07-14 Added B. H. Toby's suggested _diffrn_radiation_xray_symbol
and _diffrn_radiation_xray_target. BMcM
1994-08-05 Revised definition for _diffrn_reflns_number (S.R. Hall). BMcM
1994-08-05 Added _atom_type_scat_length_neutron (B.H. Toby). BMcM
1994-10-13 Reworded _diffrn_standards_ a la S.R. Hall. BMcM
1994-10-13 Added _diffrn_radiation_probe for non-X-ray experiments. BMcM
1995-01-17 Rewording of definition of _chemical_melting_point. BMcM
1995-02-24 Changed text references to e.s.d to 'standard uncertainty'. BMcM
1995-07-08 Added _chemical_formula_iupac. BMcM
1995-07-09 Finally added _symmetry_equiv_pos_id. BMcM
1995-07-09 _units_extension, _units_conversion and _units_description
superseded by _units and _units_detail. Suffixed datanames
retained as separate entries. BMcM
1995-10-23 Added _refine_ls_R_Fsqd_factor and _refine_ls_R_I_factor BMcM
1996-03-25 Correlated with mmCIF release 0.8 BMcM
1996-05-16 Added some extra datanames for use by Acta:
_publ_section_synopsis, _publ_section_title_footnote,
_publ_author_footnote, _journal_paper_category, and various
_journal_index_ categories BMcM
1996-05-20 Added geom_hbond category BMcM
1996-06-10 Datanames with suffixes to indicate units moved to a new
compatibility dictionary cif_compat.dic BMcM
1996-06-10 Embarrassing _units_ stuff removed from geom_hbond BMcM
1996-06-10 _list_mandatory and _list_reference added to _publ_author_
datanames (where _list was given as "both") BMcM
1996-06-10 Added audit_conform category BMcM
1996-06-11 Added audit_link category BMcM
1996-06-11 Reworded _exptl_crystal_F_000 definition BMcM
1996-06-11 Added _atom_site_U_equiv_geom BMcM
1996-06-11 Added publ_body category BMcM
1996-06-27 Added examples for most of the remaining category overviews
BMcM
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
1996-08-03 Reworded _refine_ls_number_reflns definition a la S.R.Hall BMcM
1996-09-10 BMcM:
Clarified _diffrn_attenuator_scale definition with help from SRH
In _refln_symmetry_multiplicity, changed 'structure-factor
value' to 'structure-factor magnitudes'
Slight modification to _diffrn_reflns_number to exclude all
systematic absences, not just those due to centring
Removed footnote markers from example of
_publ_section_title_footnote
Added new example to SYMMETRY_EQUIV category to explain the
use of _symmetry_equiv_pos_id
Reworking of DIFFRN_RADIATION and DIFFRN_MEASUREMENT
categories and introduction of DIFFRN_DETECTOR and
DIFFRN_SOURCE a la I.D.Brown
1996-09-11 Corrected category assignment for _diffrn_standards_ items BMcM
1996-09-12 BMcM:
Added _cell_id and _cell_measurement_refln_id
Changed the term "id" to "identifier" in definitions
Renamed _citation_journal_abstract_id_CAS as
_citation_abstract_id_CAS
Added _audit_block_code and changed definition of
_audit_link_block_code to refer to it
1996-09-18 BMcM:
Fine tuning of IDB's new DIFFRN categories: in DIFFRN_DETECTOR
changed *_type to *_device and added *_device_type. Moved
_diffrn_radiation_detector back to DIFFRN_RADIATION category
with expanded definition. Reworded definitions of
_diffrn_measurement_device and *_device_type. In
DIFFRN_RADIATION changed enumeration range for
*_polarisn_norm to -180:180 and added 'as viewed from the
specimen' to the definition; also added 'Cu K-L~2,3~' to
examples for *_type. Reworded definitions for
_diffrn_refln_index and _diffrn_source_target, and changed
_type of _diffrn_source_power to "numb".
Introduced _diffrn_detector_dtime in the DIFFRN_DETECTOR
category and restored _diffrn_radiation_detector_dtime to
DIFFRN_RADIATION
1996-09-25 BMcM:
Reworded definitions of _atom_site_disorder_assembly and *_group
1996-10-02 BMcM:
Changed _symmetry_equiv_pos_id to _symmetry_equiv_pos_site_id
in recognition of the technical meaning of 'position' in
International Tables
Addition of the names of the relevant units to definitions of
_atom_type_scat_length_neutron, _exptl_crystal_size_,
_geom_hbond_distance_, _refine_ls_d_res_high and *_low,
_reflns_shell_d_res_high and *_low; and cosmetic expansion
of units listed in the definitions for _diffrn_source_current,
*_power and *_voltage
Addition of '_related_function conversion' to
_atom_site_B_equiv_geom and *_U_equiv_geom and
_atom_site_B_iso_or_equiv and *_U_iso_or_equiv
Examples for CELL_MEASUREMENT_REFLN and DIFFRN_REFLN from
Gotzon Madariaga
Renamed _atom_site_U_equiv_geom as _atom_site_U_equiv_geom_mean
and likewise for *_B_* to increase the consistency of
abbreviations, as suggested by I.D. Brown
Added disorder example to the ATOM_SITE category description
1996-10-15 BMcM:
Modified description of example for DIFFRN_REFLN
Changed _enumeration_range of _atom_site_attached_hydrogens
from 0:4 to 0:8 (cf CSD entry with refcode DUTMAG01) (PRE)
Added '_enumeration_default cif' to _publ_body_format
Changed underscores to spaces in the example for the Hall
spacegroup symbol in data_symmetry_[]
Deleted extraneous '_' in data_(_)citation_abstract_id_CAS
1996-10-27 BMcM: Changed psiscan to psi-scan at request of SRH
1996-11-05 BMcM:
Changed _citation_book_coden_ISBN to _citation_book_id_ISBN,
_citation_journal_coden_ASTM to _citation_journal_id_ASTM,
_citation_journal_coden_CSD to _citation_journal_id_CSD,
_citation_journal_coden_ISSN to _citation_journal_id_ISSN,
and _citation_Medline_AN to _citation_database_id_Medline.
Also modified description of CODEN in _citation_journal_id_ASTM
and _database_journal_ASTM (suggested by PMDF)
The phrase 'diffraction data' modified to 'intensities' in
several places, some other cosmetic commas and enforcement
of consistent lower-case units names (PMDF)
Clarification of the definition for
_diffrn_radiation_polarisn_norm (PMDF)
Added 'constr' to _refine_ls_hydrogen_treatment (SRH)
Corrected misassignment of category of
_diffrn_radiation_detector_dtime (H.J.Bernstein)
1996-11-06 BMcM:
Added "_list yes" to items in the REFLNS_SHELL category (IDB)
Added "measured" to definition of _reflns_shell_number_unique_all
Changed enumeration range for _diffrn_standards_decay_% to
":100" and added statement about negative values (PMDF/SRH)
1996-11-08 BMcM:
_diffrn_radiation_detector, _diffrn_radiation_detector_dtime and
_diffrn_radiation_source removed (these will be transferred to
cif_compat.dic for compatibility with files conforming to the
original dictionary)
_diffrn_radiation_wavelength_* items moved to new category
1996-11-12 BMcM:
Deleted _cell_id and _cell_measurement_refln_id, and
clarified the intent of the CELL category in _cell_[] (PMDF)
Some small rewordings of various _diffrn_* items due to
B.H.Toby
1996-11-14 BMcM:
Imposed consistency on the nomenclature of diffraction device
data names: _diffrn_detector_device_type -> *_detector_type,
_diffrn_measurement_device_details -> *_measurement_details,
*_measurement_device_type -> *_measurement_type; introduction
of _diffrn_source_device and parallel definitions. Existing
*_measurement_details example moved to *_special_details (PMDF)
1996-11-21 BMcM:
Reintroduced _diffrn_measurement_device_details, further tidying
of data names thus: _diffrn_measurement_type -> *_device_type;
_diffrn_detector_device and _diffrn_source_device both drop
"_device" (PMDF)
Added _journal_data_validation_number and
_publ_requested_category to enable handling of CIF-access
submissions by Acta Cryst. C
1996-11-23 A few typos fixed. BMcM
1996-11-24 BMcM:
Added 'gaussian', 'multi-scan' and 'numerical' to enumeration
list for _exptl_absorpt_correction_type (SRH)
Added 'mixed' to enumeration list for
_refine_ls_hydrogen_treatment (SRH)
1996-11-25 A few typos fixed (BMcM)
1996-11-27 BMcM:
Removed looped _related_item from _publ_contact_author and
reintroduced _diffrn_radiation_detector, *_dtime and
_diffrn_radiation_source (see 1996-11-08) with
"_related_function replace" as a preparation for
using this mechanism further in version 2.1.
1996-11-27 Release version 2.0. IUCr
1997-01-20 BMcM:
Some small changes thanks to PMDF. Double space after period
at end of sentence changed to single space throughout;
_citation_database_id_Medline _diffrn_detector_type moved
to correct alphabetic sequence; space introduced between
sentences in definition of _citation_journal_id_CSD; some
other minor grammatical changes
1997-10-30 BMcM: (changes to align with Acta C Notes for Authors)
Obsoleted *_obs_* entries in REFLNS and REFINE_LS categories
and replaced with *_gt_*; obsoleted _refine_ls_shift/esd_
by _refine_ls_shift/su_; obsoleted
_atom_site_thermal_displace_type by *_adp_type
1997-11-05 BMcM: (changes to align with Acta C Notes for Authors)
Added _diffrn_detector_area_resol_mean,
_diffrn_measured_fraction_theta_max and *_full,
_diffrn_reflns_theta_full
1997-11-05 BMcM: Added _reflns_number_Friedel; changed various *_obs
items in examples to *_gt equivalents and likewise for
other obsoleted items
1997-11-24 BMcM: Slightly changed wording of _reflns_number_Friedel and
_reflns_threshold_expression at suggestion of I.D.Brown.
Modified definition of _refine_ls_abs_structure_Flack and
changed the text of the example in category REFINE at
the request of H.D.Flack.
1997-12-08 BMcM: Removed the phrase "(enantiomorph or polarity)" from
_refine_ls_abs_structure_Flack and *_Rogers because
"absolute structure" is a phrase uniquely defined (H.D.Flack)
1997-12-08 BMcM: Several instances of \s changed to u
1997-12-08 BMcM: Modified definitions of _reflns_number_total and
*_Friedel (after H.D.Flack) to clarify the distinction between
crystal-class and Laue-symmetry independent reflection sets
1997-12-08 BMcM: Added _chemical_absolute_configuration and
_chemical_optical_rotation (H.D.Flack)
1998-08-04 BMcM: Moved _diffrn_pressure_history and _diffrn_thermal_history
from draft msCIF dictionary to core as
_exptl_crystal_pressure_history and
_exptl_crystal_thermal_history (G. Madariaga/I.D.Brown)
Moved _diffrn_symmetry_description and REFINE_LS_CLASS
from draft msCIF dictionary to core (G. Madariaga/I.D.Brown)
1998-08-04 BMcM: Minor rewordings of _refine_ls_R_Fsqd_factor,
_refine_ls_R_I_factor, various definitions referring to
F_calc in electrons, and _reflns_shell_number_unique_*
(I.D.Brown)
1998-08-04 BMcM: added _reflns_Friedel_coverage (H.D.Flack/S.R.Hall)
1998-08-04 BMcM: changed formula for F(000) (from
F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ to
F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ ) (H.D.Flack)
1998-08-04 BMcM: added 'syn' and 'unk' as enumerations to
_chemical_absolute_configuration (H.D.Flack/A.Linden)
1998-09-02 BMcM: added _exptl_crystal_size_length and modified slightly
the definition of _exptl_crystal_size_ (W.Clegg/I.D.Brown)
Added _diffrn_attenuator_material (I.D.Brown)
Added sentence explaining the physical meaning of the
_enumeration_range to _refine_ls_abs_structure_Flack
(H.D.Flack)
Some rewording in _chemical_absolute_configuration implying
that for absolute configuration determination the measurement
and reporting of the optical rotation in solution are
considered mandatory. (H.D.Flack)
Some rewording in _reflns_number_total and *_gt to clarify
the inclusion of Friedel reflections; addition of
_reflns_Friedel_coverage; deletion of _reflns_number_Friedel
(H.D.Flack/S.R.Hall)
Further minor rewording to _reflns_shell_number_unique_all,
*_gt, *_obs (H.D.Flack)
1998-09-10 BMcM: transferred _diffrn_reflns_number_of_classes and the
categories DIFFRN_REFLNS_CLASS, REFLNS_CLASS and
REFLNS_SHELL_CLASS from the draft msCIF dictionary; added
_diffrn_refln_class_code and _refln_class_code to link
individual reflections to their related categories.
1998-12-08 BMcM: implemented H.D. Flack's reworking of DIFFRN_REFLNS_CLASS,
REFLNS_CLASS, REFLNS_SHELL_CLASS and REFINE_LS_CLASS, deleting
the latter two; removed _diffrn_reflns_number_of_classes.
1998-12-15 BMcM: completed the above reworking; fixed embarrassing typo for
_related_function
1999-01-16 BMcM: coreDMG review of version 2.1beta5. Numerous small changes
from I.D.Brown, the most significant being:
_atom_site_occupancy definition clarifies how to impose an
experimental uncertainty on the _enumeration_range;
_atom_site_U_iso_or_equiv enumeration range set to infinity;
_atom_type_analytical_mass_% enumeration range set as 0:100;
expanded definitions of _diffrn_radiation_probe and *_type to
clarify the distinction between these two items;
added reference to _exptl_crystal_size to the definition of
_exptl_crystal_description, and modified the definition of
_exptl_crystal_face_diffr_ ;
new data item _refln_d_spacing;
clarified the role of _reflns_special_details in specifying
whether Friedel pairs have been averaged;
Numerous small changes from H.D.Flack, most significantly:
removed enumeration range from _diffrn_refln_counts_ because
*_net can go negative;
fixed various typos in equations for wR and S;
removed reference to Friedel reflections from
_refln_symmetry_multiplicity
1999-01-24 BMcM: further revision to wording of _refln_symmetry_multiplicity
following discussions by HDF and IDB
Numerous small changes from G.Madariaga, most significantly:
a instead of A for real-space cell lengths
(_atom_site_B_iso_or_equiv and _atom_site_U_iso_or_equiv);
_related_function alternate for _atom_site_Cartn_ & _fract_;
"or scattering lengths" added to _atom_type_scat_source;
deleted incorrect _list_reference in DIFFRN_RADIATION;
added rtf to enumeration in _publ_body_format;
added enumeration range to _refine_ls_abs_structure_Rogers
1999-02-04 BMcM: fixed some long lines
1999-02-06 BMcM: data names using sigma as an indicator of experimental
standard uncertainty replaced by equivalents using the
preferred 'u' notation (HDF):
_diffrn_refln_intensity_sigma
_diffrn_reflns_av_sigmaI/netI
_diffrn_reflns_class_av_sgI/I
_diffrn_standards_scale_sigma
_reflns_shell_meanI_over_sigI_all
_reflns_shell_meanI_over_sigI_gt
(_reflns_shell_meanI_over_sigI_obs already replaced by *_gt)
addition of '_related function alternate' to new data
items corresponding to old items with
'_related_function replace' (SRH)
Example for _citation_journal_id_CSD changed to 0070 to
reflect current practice at PDB (F.C.Bernstein)
Added _atom_type_scat_dispersion_source (GM)
1999-03-24 Some minor cosmetic modifications (BMcM)
1999-03-24 Release version 2.1. IUCr
2001-01-09 BMcM: simplified entry for _chemical_absolute_configuration
(H.D.Flack)
Added _geom_bond_valence and the new categories
VALENCE_PARAM and VALENCE_REF (I.D.Brown)
2001-01-11 BMcM: Categories EI, EO, EM added to _publ_requested_category
2001-01-11 Release version 2.2. IUCr
2003-09-28 BMcM: incorporated changes approved by COMCIFS following
discussions of the core Dictionary Management Group:
_atom_site_fract_ nonsense enumeration default value removed
_atom_site_refinement_flags deprecated in favour of new
*_flags_posn, *_adp and *_occupancy items
_atom_sites_special_details added
_cell_reciprocal_angle_ and *_length_ added
'_type_conditions esd' added to _chemical_melting_point
_chemical_melting_point_gt and *_lt added
Added several new items describing chemical properties to
the CHEMICAL category: _chemical_properties_biological and
*_physical, _chemical_temperature_decomposition_* and
*_sublimation_*, at the request of CCDC
_citation_database_id_CSD added at request of CCDC
Several additional tags storing deposition numbers of
database entries and record revision history at
request of CCDC: _database_code_depnum_ccdc_fiz,
*_journal, *_archive and _database_CSD_history
Added _diffrn_ambient_pressure_gt,lt and *_temperature_gt,lt
Added _diffrn_source_take-off_angle
Added _diffrn_standards_decay_%_lt
_diffrn_reflns_measured_fraction_resolution_full and *_max
introduced as replacements for
_diffrn_measured_fraction_theta_full and *_max, moved
to a more appropriate category and defined in terms
of resolution rather than angle which depends on the
radiation used.
Likewise for _diffrn_reflns_resolution_full and *_max as
replacements for _diffrn_reflns_theta_full and *_max
More specific parsable tags for crystal colour introduced as
_exptl_crystal_colour_primary, *_modifier and *_lustre
Added _exptl_crystal_density_meas_gt,lt and *_meas_temp_gt,lt
Added _exptl_crystal_recrystallization_method
Added _publ_contact_author_id_iucr and _publ_author_id_iucr
to allow unique author identification by IUCr database
reference identifier
More datanames for recording imprecise quantities:
_refine_ls_shift/su_max_lt and _refine_ls_shift/su_mean_lt
Added the categories SPACE_GROUP and SPACE_GROUP_SYMOP
as imports from the symmetry dictionary cif_sym.dic
Added _related_function 'replace' to a number of items in
the old SYMMETRY category pointing to the preferred
items from the new SPACE_GROUP category
2003-08-19 BMcM: formal approval for COMCIFS for the additions and
contingent changes discussed on the coreDMG discussion
list from June 2002
2003-09-29 BMcM: second round of changes from coreDMG discussions:
Added _enumeration_range to new _chemical_temperature_* items;
Expanded definition of _space_group_symop_operation_xyz to
make explicit the need for inclusion of centring
translations (HDF/IDB)
Removed _diffrn_reflns_measured_fraction_resolution_full and
*_max for reconsideration following suggestion by
Curt Haltiwanger that terms are needed that do not
refer to resolution or theta
Likewise removed _diffrn_standards_decay_%_lt for further
consideration, and added _type_conditions esd to
_diffrn_standards_decay_% as a measurable quantity
(CH/HDF)
Modified _example_detail for _space_group_symop_operation_xyz
to use a full and unambiguous wording in accordance
with International Tables A (CH/IDB/HDF)
2003-09-29 Removed "_type_conditions esd" from the remaining *_gt and
*_lt items at the suggestion of Gotzon Madariaga:
since these are ceiling/floor values a measurable
uncertainty is pointless (BMcM)
2003-10-01 Fixed some typos following checking by IDB (BMcM)
2003-10-03 BMcM: Final editorial pass. Added _related_function alternate
to _exptl_crystal_colour. Also added this flag to the
new items which replace existing ones:
_atom_site_refinement_flags_* and the _space_group_ items
2003-10-04 Release version 2.3. IUCr
2004-06-06 BMcM: minor editorial changes for International Tables Volume G.
Text of _atom_sites_*_tran_* definitions changed to
ATOM_SITE from STOM_SITES.
Some realignment of examples to fit column width.
2004-09-11 BMcM: corrected related item error in
_atom_site_refinement_flags_posn, *_adp and *_occupancy
2004-11-26 NJA: updated reference to IT Vol A from 1987 to 2002
2004-12-22 NJA: minor corrections to hyphenation, spelling and punctuation
atom_site definition: ', and so on' removed
_atom_site_aniso_B_: 1/4 in formula replaced by (1/4)
_atom_site_aniso_label: '...atom coordinate list' changed
to '...atom in the atom coordinate list'
_atom_site_B_iso_or_equiv: 'anisotropic temperature factor
parameters' changed to 'anisotropic displacement
components'
_atom_site_label: 'Each label may have...' changed to
'Different labels may have...'
_atom_site_type_symbol: '...atom specie(s)...' changed to
'atom species (singular or plural)...'
_atom_type_scat_Cromer_Mann_: reference to Volume C
updated to 2004
_atom_type_symbol: 'atom specie(s)' changed to
'atom species (singular or plural)'
_audit_conform_dict_location: 'where the conformant
dictionary resides' changed to 'for the dictionary
to which the current data block conforms'
_audit_conform_dict_version: 'conformant dictionary'
changed to 'dictionary to which the current data
block conforms'
2004-12-23 NJA: minor corrections to hyphenation, spelling and punctuation
_audit_contact_author_fax,_audit_contact_author_phone:
edited slightly
_cell_angle_: 'in degrees of the reported structure'
changed to 'of the reported structure in degrees'
_cell_measurement_pressure: 'pressure used to synthesize
the sample' changed to 'pressure at which the sample
was synthesized'
_cell_measurement_theta_: 'angles in degrees of reflections
used to measure the unit cell' changed to 'angles
of reflections used to measure the unit cell in degrees'
_cell_reciprocal_angle_: 'angles in degrees defining
the reciprocal cell' changed to 'angles defining
the reciprocal cell in degrees'
_chemical_[]: 'compounds' changed to 'compound'
_chemical_optical_rotation: 'c is the value of CONC in g'
changed to 'c is the value of CONC as defined above'.
_chemical_properties_physical, _biological: 'free
description' changed to 'free-text description'
_chemical_conn_atom_display_: 'if absent...staff.' deleted
_citation_[]: 'literature cited relevant' changed to
'literature cited as being relevant'
_citation_*: 'book chapters' changed to 'books or
book chapters'
_citation_country: 'both journal articles and' deleted
_citation_database_id_CSD: 'containing' changed to
'that contains'
_citation_language: 'citation appears' changed to
'cited article is written'
_diffrn_crystal_treatment: 'intensity measurement' changed
to 'the intensity measurements'
_diffrn_special_details: 'diffraction measurement' changed
to 'intensity-measurement'
_diffrn_attenuator_scale: 'This scale must be multiplied
by the measured intensity to convert it...' changed
to 'The measured intensity must be multiplied by
this scale to convert it...'
_diffrn_orient_matrix_[]: 'used in data measurement'
changed to 'used in the measurement of the
diffraction intensities'
_diffrn_orient_refln_angle_: 'in degrees of a reflection...
matrix' changed to 'of a reflection...matrix in degrees'
_diffrn_radiation_probe,_diffrn_radiation_type:
definitions reworded slightly
_diffrn_refln_angle_: 'in degrees of a reflection' changed
to 'of a reflection in degrees'
_diffrn_refln_elapsed_time: 'diffraction measurement'
changed to 'the diffraction experiment'
_diffrn_refln_scale_group_code: 'applying' changed to
'applicable'
_diffrn_refln_scan_mode: 'with a diffractometer' changed to
'for measurements using a diffractometer'
_diffrn_refln_scan_rate: 'to measure the intensity in
degrees per minute' changed to 'in degrees per minute
to measure the intensity'
_diffrn_refln_standard_code: 'identifying' changed to
'indicating'; 'intensity' changed to 'reflection'
_diffrn_reflns_class_d_res_high,_low: defintions rephrased.
_diffrn_source_details: 'used' deleted.
_diffrn_source_target: 'for generation of' changed to
'to generate'
_diffrn_standards_decay_%: 'at the start of the measurement
process and at the finish' changed to 'from the start of
the measurement process to the end'
_diffrn_standards_number: 'used in the diffraction
measurements' changed to 'used during the measurement of
the diffraction intensities'
_exptl_absorpt_correction_type: 'no more detailed
information is' changed to 'more detailed information
is not'.
_exptl_crystal_[]: 'and so on' deleted
_exptl_crystal_face_perp_dist: 'millimetres of the face'
changed to 'millimetres from the face'
_geom_[], _geom_angle_[], _geom_bond_[], _geom_contact_[],
_geom_hbond_[], _geom_torsion_[]: 'contents of the' deleted
_geom_contact_[], _geom_torsion_[]: year for reference for
example 1 corrected from 1991 to 1992
_geom_hbond_angle_DHA: 'Site at *_D' changed to 'Site at *_H'
_publ_contact_author_fax: definition rephrased slightly
_publ_requested_category: Cif-access codes marked as '(no
longer in use)'
2005-01-05 NJA: minor corrections to hyphenation, spelling and punctuation
_refine_ls_*: 'least squares' changed to 'least-squares
refinement'
_refine_ls_restrained_S_all: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_restrained_S_gt: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_restrained_S_obs: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_shift/esd_*: 'divided by' changed to 'to'
_refine_ls_shift/su_*: 'divided by' changed to 'to'
_refine_ls_class_d_res_*: edited slightly
_refine_ls_d_res_*: edited slightly
_refln_intensity_*: edited slightly
_refln_symmetry_multiplicity: reference to Volume A updated
to (2002), Chapter 10.1
_reflns_d_resolution_*: edited slightly
_reflns_class_d_res_*: edited slightly
_reflns_shell_d_res_*: edited slightly
_space_group_name_Hall: erratum added to reference to Hall
(1981); reference to Volume B updated to 2001.
_space_group_name_H-M_alt: reference to Volume A updated
to (2002)
_symmetry_Int_Tables_number: reference to Volume A updated
to (2002)
_symmetry_space_group_name_Hall: erratum added to reference
to Hall (1981)
_symmetry_space_group_name_H-M: reference to Volume A
updated to (2002)
_symmetry_equiv_pos_as_xyz: reference to Volume A updated
to (2002)
2005-01-11 NJA: more minor corrections to hyphenation, spelling and
punctuation
2005-01-21 NJA: _reflns_shell_Rmerge_I_obs: related item changed from
_reflns_shell_Rmerge_I_obs to _reflns_shell_Rmerge_I_gt
2005-06-21 NJA: corrections to proofs of Intl Tables G Chapter 4.1 included.
New data name _publ_author_email added.
2005-06-27 BMcM: Removed _list_mandatory yes from _atom_site_aniso_label
in response to cif-developers list discussion
;
###############
## ATOM_SITE ##
###############
data_atom_site_[]
_name '_atom_site_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_calc_attached_atom
O1 .4154(4) .5699(1) .3026(0) .060(1) Uani ? ?
C2 .5630(5) .5087(2) .3246(1) .060(2) Uani ? ?
C3 .5350(5) .4920(2) .3997(1) .048(1) Uani ? ?
N4 .3570(3) .5558(1) .4167(0) .039(1) Uani ? ?
C5 .3000(5) .6122(2) .3581(1) .045(1) Uani ? ?
O21 .6958(5) .4738(2) .2874(1) .090(2) Uani ? ?
C31 .4869(6) .3929(2) .4143(2) .059(2) Uani ? ?
# - - - - data truncated for brevity - - - -
H321C .04(1) .318(3) .320(2) .14000 Uiso ? ?
H322A .25(1) .272(4) .475(3) .19000 Uiso ? ?
H322B .34976 .22118 .40954 .19000 Uiso calc C322
H322C .08(1) .234(4) .397(3) .19000 Uiso ? ?
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_aniso_label
_atom_site_aniso_B_11
_atom_site_aniso_B_22
_atom_site_aniso_B_33
_atom_site_aniso_B_12
_atom_site_aniso_B_13
_atom_site_aniso_B_23
_atom_site_aniso_type_symbol
O1 .071(1) .076(1) .0342(9) .008(1) .0051(9) -.0030(9) O
C2 .060(2) .072(2) .047(1) .002(2) .013(1) -.009(1) C
C3 .038(1) .060(2) .044(1) .007(1) .001(1) -.005(1) C
N4 .037(1) .048(1) .0325(9) .0025(9) .0011(9) -.0011(9) N
C5 .043(1) .060(1) .032(1) .001(1) -.001(1) .001(1) C
# - - - - data truncated for brevity - - - -
O21 .094(2) .109(2) .068(1) .023(2) .038(1) -.010(1) O
C51 .048(2) .059(2) .049(1) .002(1) -.000(1) .007(1) C
C511 .048(2) .071(2) .097(3) -.008(2) -.003(2) .010(2) C
C512 .078(2) .083(2) .075(2) .009(2) -.005(2) .033(2) C
C513 .074(2) .055(2) .075(2) .004(2) .001(2) -.010(2) C
# - - - - data truncated for brevity - - - -
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
_atom_site_chemical_conn_number
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
S1 1 0.74799(9) -0.12482(11) 0.27574(9) 0.0742(3)
S2 2 1.08535(10) 0.16131(9) 0.34061(9) 0.0741(3)
N1 3 1.0650(2) -0.1390(2) 0.2918(2) 0.0500(5)
C1 4 0.9619(3) -0.0522(3) 0.3009(2) 0.0509(6)
# - - - - data truncated for brevity - - - -
;
;
Example 3 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label # *_assembly 'M' is a disordered methyl
_atom_site_occupancy # with configurations 'A' and 'B':
_atom_site_disorder_assembly #
_atom_site_disorder_group # H11B H11A H13B
# . | .
C1 1 . . # . | .
H11A .5 M A # . | .
H12A .5 M A # C1 --------C2---
H13A .5 M A # / . \
H11B .5 M B # / . \
H12B .5 M B # / . \
H13B .5 M B # H12A H12B H13A
;
;
Example 4 - hypothetical example to illustrate the description of a
disordered methyl group.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_SITE category record details about
the atom sites in a crystal structure, such as the positional
coordinates, atomic displacement parameters, and magnetic moments
and directions.
;
data_atom_site_adp_type
_name '_atom_site_adp_type'
_category atom_site
_type char
_related_item '_atom_site_thermal_displace_type'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_definition
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
data_atom_site_aniso_B_
loop_ _name '_atom_site_aniso_B_11'
'_atom_site_aniso_B_12'
'_atom_site_aniso_B_13'
'_atom_site_aniso_B_22'
'_atom_site_aniso_B_23'
'_atom_site_aniso_B_33'
_category atom_site
_type numb
_type_conditions esd
_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
; These are the standard anisotropic atomic displacement
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
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
_name '_atom_site_aniso_label'
_category atom_site
_type char
_list yes
_list_link_parent '_atom_site_label'
_definition
; Anisotropic atomic displacement parameters are usually looped in
a separate list. If this is the case, this code must match the
_atom_site_label of the associated atom in the atom coordinate
list and conform with the same rules described in
_atom_site_label.
;
data_atom_site_aniso_ratio
_name '_atom_site_aniso_ratio'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_aniso_label'
_enumeration_range 1.0:
_definition
; Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
data_atom_site_aniso_type_symbol
_name '_atom_site_aniso_type_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_aniso_label'
_list_link_parent '_atom_site_type_symbol'
_definition
; This _atom_type_symbol code links the anisotropic atom
parameters to the atom-type data associated with this site and
must match one of the _atom_type_symbol codes in this list.
;
data_atom_site_aniso_U_
loop_ _name '_atom_site_aniso_U_11'
'_atom_site_aniso_U_12'
'_atom_site_aniso_U_13'
'_atom_site_aniso_U_22'
'_atom_site_aniso_U_23'
'_atom_site_aniso_U_33'
_category atom_site
_type numb
_type_conditions esd
_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
; These are the standard anisotropic atomic displacement
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
The unique elements of the real symmetric matrix are
entered by row.
;
data_atom_site_attached_hydrogens
_name '_atom_site_attached_hydrogens'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0:8
_enumeration_default 0
loop_ _example
_example_detail 2 'water oxygen'
1 'hydroxyl oxygen'
4 'ammonium nitrogen'
_definition
; The number of hydrogen atoms attached to the atom at this site
excluding any hydrogen atoms for which coordinates (measured or
calculated) are given.
;
data_atom_site_B_equiv_geom_mean
_name '_atom_site_B_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_B_iso_or_equiv' alternate
'_atom_site_U_equiv_geom_mean' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; 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 orthogonalized 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
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_B_equiv_geom_mean' alternate
'_atom_site_U_iso_or_equiv' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B(equiv), in angstroms squared,
calculated from anisotropic displacement components.
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.
;
data_atom_site_calc_attached_atom
_name '_atom_site_calc_attached_atom'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_enumeration_default '.'
_definition
; The _atom_site_label of the atom site to which the 'geometry-
calculated' atom site is attached.
;
data_atom_site_calc_flag
_name '_atom_site_calc_flag'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail d 'determined from diffraction measurements'
calc 'calculated from molecular geometry'
c 'abbreviation for "calc"'
dum 'dummy site with meaningless coordinates'
_enumeration_default d
_definition
; A standard code to signal whether the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy coordinates.
The abbreviation 'c' may be used in place of 'calc'.
;
data_atom_site_Cartn_
loop_ _name '_atom_site_Cartn_x'
'_atom_site_Cartn_y'
'_atom_site_Cartn_z'
_category atom_site
_type numb
_type_conditions esd
_related_item '_atom_site_fract_'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
_units A
_units_detail 'angstroms'
_definition
; The atom-site coordinates in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform_axes description.
;
data_atom_site_chemical_conn_number
_name '_atom_site_chemical_conn_number'
_category atom_site
_type numb
_list yes
_list_link_parent '_chemical_conn_atom_number'
_list_reference '_atom_site_label'
_enumeration_range 1:
_definition
; This number links an atom site to the chemical connectivity list.
It must match a number specified by _chemical_conn_atom_number.
;
data_atom_site_constraints
_name '_atom_site_constraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_enumeration_default '.'
_example 'pop=1.0-pop(Zn3)'
_definition
; A description of the constraints applied to parameters at this
site during refinement. See also _atom_site_refinement_flags
and _refine_ls_number_constraints.
;
data_atom_site_description
_name '_atom_site_description'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_example 'Ag/Si disordered'
_definition
; A description of special aspects of this site. See also
_atom_site_refinement_flags.
;
data_atom_site_disorder_assembly
_name '_atom_site_disorder_assembly'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _example
_example_detail A 'disordered methyl assembly with groups 1 and 2'
B 'disordered sites related by a mirror'
S 'disordered sites independent of symmetry'
_definition
; A code which identifies a cluster of atoms that show long-range
positional disorder but are locally ordered. Within each such
cluster of atoms, _atom_site_disorder_group is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
;
data_atom_site_disorder_group
_name '_atom_site_disorder_group'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _example
_example_detail 1 'unique disordered site in group 1'
2 'unique disordered site in group 2'
-1 'symmetry-independent disordered site'
_definition
; A code which identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the hydrogen
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. "-1") is used to
indicate sites disordered about a special position.
;
data_atom_site_fract_
loop_ _name '_atom_site_fract_x'
'_atom_site_fract_y'
'_atom_site_fract_z'
_category atom_site
_type numb
_type_conditions esd
_related_item '_atom_site_Cartn_'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
_definition
; Atom-site coordinates as fractions of the _cell_length_ values.
;
data_atom_site_label
_name '_atom_site_label'
_category atom_site
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_atom_site_aniso_label'
'_geom_angle_atom_site_label_1'
'_geom_angle_atom_site_label_2'
'_geom_angle_atom_site_label_3'
'_geom_bond_atom_site_label_1'
'_geom_bond_atom_site_label_2'
'_geom_contact_atom_site_label_1'
'_geom_contact_atom_site_label_2'
'_geom_hbond_atom_site_label_D'
'_geom_hbond_atom_site_label_H'
'_geom_hbond_atom_site_label_A'
'_geom_torsion_atom_site_label_1'
'_geom_torsion_atom_site_label_2'
'_geom_torsion_atom_site_label_3'
'_geom_torsion_atom_site_label_4'
loop_ _example C12 Ca3g28 Fe3+17 H*251
boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0
_definition
; The _atom_site_label is a unique identifier for a particular site
in the crystal. This code is made up of a sequence of up to seven
components, _atom_site_label_component_0 to *_6, which may be
specified as separate data items. Component 0 usually matches one
of the specified _atom_type_symbol codes. This is not mandatory
if an _atom_site_type_symbol item is included in the atom-site
list. The _atom_site_type_symbol always takes precedence over
an _atom_site_label in the identification of the atom type. The
label components 1 to 6 are optional, and normally only
components 0 and 1 are used. Note that components 0 and 1 are
concatenated, while all other components, if specified, are
separated by an underscore. Underscores are
only used if higher-order components exist. If an intermediate
component is not used, it may be omitted provided the underscore
separators are inserted. For example, the label 'C233__ggg' is
acceptable and represents the components C, 233, '' and ggg.
Different labels may have a different number of components.
;
data_atom_site_label_component_
loop_ _name '_atom_site_label_component_0'
'_atom_site_label_component_1'
'_atom_site_label_component_2'
'_atom_site_label_component_3'
'_atom_site_label_component_4'
'_atom_site_label_component_5'
'_atom_site_label_component_6'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_definition
; Component 0 is normally a code which matches identically with
one of the _atom_type_symbol codes. If this is the case, then the
rules governing the _atom_type_symbol code apply. If, however,
the data item _atom_site_type_symbol is also specified in the
atom-site list, component 0 need not match this symbol or adhere
to any of the _atom_type_symbol rules.
Component 1 is referred to as the "atom number". When component 0
is the atom-type code, it is used to number the sites with the
same atom type. This component code must start with at least one
digit which is not followed by a + or - sign (to distinguish it
from the component 0 rules).
Components 2 to 6 contain the identifier, residue, sequence,
asymmetry identifier and alternate codes, respectively. These
codes may be composed of any characters except an underscore.
;
data_atom_site_occupancy
_name '_atom_site_occupancy'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:1.0
_enumeration_default 1.0
_definition
; The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site. The
value must lie in the 99.97% Gaussian confidence interval
-3u =< x =< 1 + 3u. The _enumeration_range of 0.0:1.0 is thus
correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
;
data_atom_site_refinement_flags
_name '_atom_site_refinement_flags'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_
_related_item
_related_function
'_atom_site_refinement_flags_posn' replace
'_atom_site_refinement_flags_adp' replace
'_atom_site_refinement_flags_occupancy' replace
loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
S 'special-position constraint on site'
G 'rigid-group refinement of site'
R 'riding-atom site attached to non-riding atom'
D 'distance or angle restraint on site'
T 'thermal displacement constraints'
U 'Uiso or Uij restraint (rigid bond)'
P 'partial occupancy constraint'
_definition
; A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site. This
item should not be used. It has been replaced by
_atom_site_refinement_flags_posn, *_adp and *_occupancy. It is
retained in this dictionary only to provide compatibility with
legacy CIFs.
;
data_atom_site_refinement_flags_adp
_name '_atom_site_refinement_flags_adp'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail
. 'no constraints on atomic displacement parameters'
T 'special-position constraints on atomic displacement parameters'
U 'Uiso or Uij restraint (rigid bond)'
TU 'both constraints applied'
_definition
; A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
;
data_atom_site_refinement_flags_occupancy
_name '_atom_site_refinement_flags_occupancy'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail . 'no constraints on site-occupancy parameters'
P 'site-occupancy constraint'
_definition
; A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
;
data_atom_site_refinement_flags_posn
_name '_atom_site_refinement_flags_posn'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail
. 'no constraints on positional coordinates'
D 'distance or angle restraint on positional coordinates'
G 'rigid-group refinement of positional coordinates'
R 'riding-atom site attached to non-riding atom'
S 'special-position constraint on positional coordinates'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
_definition
; A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
;
data_atom_site_restraints
_name '_atom_site_restraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_example 'restrained to planar ring'
_definition
; A description of restraints applied to specific parameters at
this site during refinement. See also _atom_site_refinement_flags
and _refine_ls_number_restraints.
;
data_atom_site_symmetry_multiplicity
_name '_atom_site_symmetry_multiplicity'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_enumeration_range 1:192
_definition
; The multiplicity of a site due to the space-group symmetry as
given in International Tables for Crystallography Vol. A (2002).
;
data_atom_site_thermal_displace_type
_name '_atom_site_thermal_displace_type'
_category atom_site
_type char
_related_item '_atom_site_adp_type'
_related_function replace
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_definition
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
data_atom_site_type_symbol
_name '_atom_site_type_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_list_link_parent '_atom_type_symbol'
_list_link_child '_atom_site_aniso_type_symbol'
loop_ _example Cu Cu2+ dummy Fe3+Ni2+
S- H* H(SDS)
_definition
; A code to identify the atom species (singular or plural)
occupying this site.
This code must match a corresponding _atom_type_symbol. The
specification of this code is optional if component 0 of the
_atom_site_label is used for this purpose. See _atom_type_symbol.
;
data_atom_site_U_equiv_geom_mean
_name '_atom_site_U_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_U_iso_or_equiv' alternate
'_atom_site_B_equiv_geom_mean' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Equivalent isotropic atomic displacement parameter, U(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U(equiv) = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalized U^ij^
;
data_atom_site_U_iso_or_equiv
_name '_atom_site_U_iso_or_equiv'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_U_equiv_geom_mean' alternate
'_atom_site_B_iso_or_equiv' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Isotropic atomic displacement parameter, or equivalent isotropic
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
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
;
data_atom_site_Wyckoff_symbol
_name '_atom_site_Wyckoff_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_definition
; The Wyckoff symbol (letter) as listed in the space-group tables
of International Tables for Crystallography Vol. A (2002).
;
################
## ATOM_SITES ##
################
data_atom_sites_[]
_name '_atom_sites_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_atom_sites_Cartn_transform_axes
'c along z, astar along x, b along y'
_atom_sites_Cartn_tran_matrix_11 58.39
_atom_sites_Cartn_tran_matrix_12 0.00
_atom_sites_Cartn_tran_matrix_13 0.00
_atom_sites_Cartn_tran_matrix_21 0.00
_atom_sites_Cartn_tran_matrix_22 86.70
_atom_sites_Cartn_tran_matrix_23 0.00
_atom_sites_Cartn_tran_matrix_31 0.00
_atom_sites_Cartn_tran_matrix_32 0.00
_atom_sites_Cartn_tran_matrix_33 46.27
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
data_atom_sites_Cartn_tran_matrix_
loop_ _name '_atom_sites_Cartn_tran_matrix_11'
'_atom_sites_Cartn_tran_matrix_12'
'_atom_sites_Cartn_tran_matrix_13'
'_atom_sites_Cartn_tran_matrix_21'
'_atom_sites_Cartn_tran_matrix_22'
'_atom_sites_Cartn_tran_matrix_23'
'_atom_sites_Cartn_tran_matrix_31'
'_atom_sites_Cartn_tran_matrix_32'
'_atom_sites_Cartn_tran_matrix_33'
_category atom_sites
_type numb
_definition
; Matrix elements used to transform fractional coordinates in
the ATOM_SITE 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 |
;
data_atom_sites_Cartn_transform_axes
_name '_atom_sites_Cartn_transform_axes'
_category atom_sites
_type char
_example 'a parallel to x; b in the plane of y and z'
_definition
; A description of the relative alignment of the crystal cell
axes to the Cartesian orthogonal axes as applied in the
transformation matrix _atom_sites_Cartn_tran_matrix_.
;
data_atom_sites_Cartn_tran_vector_
loop_ _name '_atom_sites_Cartn_tran_vector_1'
'_atom_sites_Cartn_tran_vector_2'
'_atom_sites_Cartn_tran_vector_3'
_category atom_sites
_type numb
_definition
; Elements of a 3 x 1 translation vector used in the
transformation of fractional coordinates in the
ATOM_SITE 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 |
;
data_atom_sites_fract_tran_matrix_
loop_ _name '_atom_sites_fract_tran_matrix_11'
'_atom_sites_fract_tran_matrix_12'
'_atom_sites_fract_tran_matrix_13'
'_atom_sites_fract_tran_matrix_21'
'_atom_sites_fract_tran_matrix_22'
'_atom_sites_fract_tran_matrix_23'
'_atom_sites_fract_tran_matrix_31'
'_atom_sites_fract_tran_matrix_32'
'_atom_sites_fract_tran_matrix_33'
_category atom_sites
_type numb
_definition
; Matrix elements used to transform Cartesian coordinates in
the ATOM_SITE 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_.
x' |11 12 13| x | 1 |
( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 |
z' |31 32 33| z | 3 |
;
data_atom_sites_fract_tran_vector_
loop_ _name '_atom_sites_fract_tran_vector_1'
'_atom_sites_fract_tran_vector_2'
'_atom_sites_fract_tran_vector_3'
_category atom_sites
_type numb
_definition
; Elements of a 3 x 1 translation vector used in the
transformation of Cartesian coordinates in the
ATOM_SITE 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 |
;
data_atom_sites_solution_
loop_ _name '_atom_sites_solution_primary'
'_atom_sites_solution_secondary'
'_atom_sites_solution_hydrogens'
_category atom_sites
_type char
loop_ _enumeration
_enumeration_detail difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
_definition
; Codes which identify the methods used to locate the initial
atom sites. The *_primary code identifies how the first
atom sites were determined; the *_secondary code identifies
how the remaining non-hydrogen sites were located; and the
*_hydrogens code identifies how the hydrogen sites were located.
;
data_atom_sites_special_details
_name '_atom_sites_special_details'
_category atom_sites
_type char
_definition
; Additional information about the atomic coordinates not coded
elsewhere in the CIF.
;
###############
## ATOM_TYPE ##
###############
data_atom_type_[]
_name '_atom_type_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_type_symbol
_atom_type_oxidation_number
_atom_type_number_in_cell
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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.
;
data_atom_type_analytical_mass_%
_name '_atom_type_analytical_mass_%'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0.0:100.0
_definition
; Mass percentage of this atom type derived from chemical analysis.
;
data_atom_type_description
_name '_atom_type_description'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
loop_ _example deuterium 0.34Fe+0.66Ni
_definition
; A description of the atom(s) designated by this atom type. In
most cases, this will be the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
;
data_atom_type_number_in_cell
_name '_atom_type_number_in_cell'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0:
_definition
; Total number of atoms of this atom type in the unit cell.
;
data_atom_type_oxidation_number
_name '_atom_type_oxidation_number'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range -8:8
_enumeration_default 0
_definition
; Formal oxidation state of this atom type in the structure.
;
data_atom_type_radius_
loop_ _name '_atom_type_radius_bond'
'_atom_type_radius_contact'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0.0:5.0
_units A
_units_detail 'angstroms'
_definition
; The effective intra- and intermolecular bonding radii in
angstroms of this atom type.
;
data_atom_type_scat_Cromer_Mann_
loop_ _name '_atom_type_scat_Cromer_Mann_a1'
'_atom_type_scat_Cromer_Mann_a2'
'_atom_type_scat_Cromer_Mann_a3'
'_atom_type_scat_Cromer_Mann_a4'
'_atom_type_scat_Cromer_Mann_b1'
'_atom_type_scat_Cromer_Mann_b2'
'_atom_type_scat_Cromer_Mann_b3'
'_atom_type_scat_Cromer_Mann_b4'
'_atom_type_scat_Cromer_Mann_c'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_definition
; The Cromer-Mann scattering-factor coefficients used to calculate
the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5
;
data_atom_type_scat_dispersion_
loop_ _name '_atom_type_scat_dispersion_imag'
'_atom_type_scat_dispersion_real'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_default 0.0
_definition
; The imaginary and real components of the anomalous-dispersion
scattering factor, f'' and f', in electrons for this atom type
and the radiation given in _diffrn_radiation_wavelength.
;
data_atom_type_scat_dispersion_source
_name '_atom_type_scat_dispersion_source'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_example 'International Tables Vol. IV Table 2.3.1'
_definition
; Reference to source of real and imaginary dispersion
corrections for scattering factors used for this atom type.
;
data_atom_type_scat_length_neutron
_name '_atom_type_scat_length_neutron'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_default 0.0
_units fm
_units_detail 'femtometres'
_definition
; The bound coherent scattering length in femtometres for the
atom type at the isotopic composition used for the diffraction
experiment.
;
data_atom_type_scat_source
_name '_atom_type_scat_source'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_example 'International Tables Vol. IV Table 2.4.6B'
_definition
; Reference to source of scattering factors or scattering lengths
used for this atom type.
;
data_atom_type_scat_versus_stol_list
_name '_atom_type_scat_versus_stol_list'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_definition
; A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly
recommended.
;
data_atom_type_symbol
_name '_atom_type_symbol'
_category atom_type
_type char
_list yes
_list_mandatory yes
_list_link_child '_atom_site_type_symbol'
loop_ _example C Cu2+ H(SDS) dummy FeNi
_definition
; The code used to identify the atom species (singular or plural)
representing this atom type. Normally this code is the element
symbol. The code may be composed of any character except an
underscore with the additional proviso that digits designate an
oxidation state and must be followed by a + or - character.
;
###########
## AUDIT ##
###########
data_audit_[]
_name '_audit_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_audit_block_code TOZ_1991-03-20
_audit_creation_date 1991-03-20
_audit_creation_method from_xtal_archive_file_using_CIFIO
_audit_update_record
; 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.
;
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
;
data_audit_block_code
_name '_audit_block_code'
_category audit
_type char
_example TOZ_1991-03-20
_definition
; A code intended to identify uniquely the current data block.
;
data_audit_creation_date
_name '_audit_creation_date'
_category audit
_type char
_example 1990-07-12
_definition
; The date that the data block was created. The date format
is yyyy-mm-dd.
;
data_audit_creation_method
_name '_audit_creation_method'
_category audit
_type char
_example 'spawned by the program QBEE'
_definition
; A description of how data were entered into the data block.
;
data_audit_update_record
_name '_audit_update_record'
_category audit
_type char
_example '1990-07-15 Updated by the Co-editor'
_definition
; A record of any changes to the data block. The update format
is a date (yyyy-mm-dd) followed by a description of the
changes. The latest update entry is added to the bottom of
this record.
;
##################
## AUDIT_AUTHOR ##
##################
data_audit_author_[]
_name '_audit_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_author_name
_audit_author_address
'Fitzgerald, Paula M. D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
'Van Middlesworth, J. F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
;
data_audit_author_address
_name '_audit_author_address'
_category audit_author
_type char
_list yes
_list_reference '_audit_author_name'
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The address of an author of this data block. If there are
multiple authors, _audit_author_address is looped with
_audit_author_name.
;
data_audit_author_name
_name '_audit_author_name'
_category audit_author
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of an author of this data block. If there are multiple
authors, _audit_author_name is looped with _audit_author_address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
###################
## AUDIT_CONFORM ##
###################
data_audit_conform_[]
_name '_audit_conform_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_audit_conform_dict_name cif_core.dic
_audit_conform_dict_version 2.3.1
_audit_conform_dict_location
ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic
;
;
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.
;
data_audit_conform_dict_location
_name '_audit_conform_dict_location'
_category audit_conform
_type char
_list both
_list_reference '_audit_conform_dict_name'
_definition
; A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
;
data_audit_conform_dict_name
_name '_audit_conform_dict_name'
_category audit_conform
_type char
_list both
_list_mandatory yes
_definition
; The string identifying the highest-level dictionary defining
data names used in this file.
;
data_audit_conform_dict_version
_name '_audit_conform_dict_version'
_category audit_conform
_type char
_list both
_list_reference '_audit_conform_dict_name'
_definition
; The version number of the dictionary to which the
current data block conforms.
;
##########################
## AUDIT_CONTACT_AUTHOR ##
##########################
data_audit_contact_author_[]
_name '_audit_contact_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_contact_author_name
_audit_contact_author_address
_audit_contact_author_email
_audit_contact_author_fax
_audit_contact_author_phone
'Fitzgerald, Paula M. D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
'paula_fitzgerald@merck.com'
'1(908)5945510'
'1(908)5945510'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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.
;
data_audit_contact_author_address
_name '_audit_contact_author_address'
_category audit_contact_author
_type char
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The mailing address of the author of the data block to whom
correspondence should be addressed.
;
data_audit_contact_author_email
_name '_audit_contact_author_email'
_category audit_contact_author
_type char
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; The electronic mail address of the author of the data block
to whom correspondence should be addressed, in a form
recognizable to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
;
data_audit_contact_author_fax
_name '_audit_contact_author_fax'
_category audit_contact_author
_type char
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 starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces.
;
data_audit_contact_author_name
_name '_audit_contact_author_name'
_category audit_contact_author
_type char
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of the author of the data block to whom correspondence
should be addressed.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_audit_contact_author_phone
_name '_audit_contact_author_phone'
_category audit_contact_author
_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 starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces.
;
################
## AUDIT_LINK ##
################
data_audit_link_[]
_name '_audit_link_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link_block_code
_audit_link_block_description
. 'discursive text of paper with two structures'
morA_(1) 'structure 1 of 2'
morA_(2) 'structure 2 of 2'
;
;
Example 1 - multiple structure paper, as illustrated
in A Guide to CIF for Authors (1995). IUCr: Chester.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link_block_code
_audit_link_block_description
. 'publication details'
KSE_COM 'experimental data common to ref./mod. structures'
KSE_REF 'reference structure'
KSE_MOD 'modulated structure'
;
;
Example 2 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
;
data_audit_link_block_code
_name '_audit_link_block_code'
_category audit_link
_type char
_list yes
_list_mandatory yes
_definition
; The value of _audit_block_code associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
;
data_audit_link_block_description
_name '_audit_link_block_description'
_category audit_link
_type char
_list yes
_list_reference '_audit_link_block_code'
_definition
; A textual description of the relationship of the referenced
data block to the current one.
;
##########
## CELL ##
##########
data_cell_[]
_name '_cell_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_cell_length_a 5.959(1)
_cell_length_b 14.956(1)
_cell_length_c 19.737(3)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 1759.0(3)
_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
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CELL category record details about the
crystallographic cell parameters and their measurement.
;
data_cell_angle_
loop_ _name '_cell_angle_alpha'
'_cell_angle_beta'
'_cell_angle_gamma'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:180.0
_enumeration_default 90.0
_units deg
_units_detail 'degrees'
_definition
; Unit-cell angles of the reported structure in degrees.
The values of _refln_index_h, *_k, *_l must correspond to the
cell defined by these values and _cell_length_a, *_b and *_c.
The values of _diffrn_refln_index_h, *_k, *_l may not correspond
to these values if a cell transformation took place following
the measurement of the diffraction intensities. See also
_diffrn_reflns_transf_matrix_.
;
data_cell_formula_units_Z
_name '_cell_formula_units_Z'
_category cell
_type numb
_enumeration_range 1:
_definition
; The number of the formula units in the unit cell as specified
by _chemical_formula_structural, _chemical_formula_moiety or
_chemical_formula_sum.
;
data_cell_length_
loop_ _name '_cell_length_a'
'_cell_length_b'
'_cell_length_c'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Unit-cell lengths in angstroms corresponding to the structure
reported. The values of _refln_index_h, *_k, *_l must
correspond to the cell defined by these values and _cell_angle_
values. The values of _diffrn_refln_index_h, *_k, *_l may not
correspond to these values if a cell transformation took place
following the measurement of the diffraction intensities. See
also _diffrn_reflns_transf_matrix_.
;
data_cell_measurement_pressure
_name '_cell_measurement_pressure'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure at which the sample was
synthesized).
;
data_cell_measurement_radiation
_name '_cell_measurement_radiation'
_category cell
_type char
loop_ _example 'neutron' 'Cu K\a' 'synchrotron'
_definition
; Description of the radiation used to measure the unit-cell data.
See also _cell_measurement_wavelength.
;
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.
These reflections may be specified as _cell_measurement_refln_
data items.
;
data_cell_measurement_temperature
_name '_cell_measurement_temperature'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The temperature in kelvins at which the unit-cell parameters
were measured (not the temperature of synthesis).
;
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 of reflections
used to measure the unit cell in degrees.
;
data_cell_measurement_wavelength
_name '_cell_measurement_wavelength'
_category cell
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The wavelength in angstroms of the radiation used to measure
the unit cell. If this is not specified, the wavelength is
assumed to be the same as that given in
_diffrn_radiation_wavelength.
;
data_cell_reciprocal_angle_
loop_ _name '_cell_reciprocal_angle_alpha'
'_cell_reciprocal_angle_beta'
'_cell_reciprocal_angle_gamma'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:180.0
_enumeration_default 90.0
_units deg
_units_detail 'degrees'
_definition
; The angles defining the reciprocal cell in degrees. These
are related to those in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
data_cell_reciprocal_length_
loop_ _name '_cell_reciprocal_length_a'
'_cell_reciprocal_length_b'
'_cell_reciprocal_length_c'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The reciprocal-cell lengths in inverse angstroms. These are
related to the real cell by:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
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 ##
############################
data_cell_measurement_refln_[]
_name '_cell_measurement_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_cell_measurement_refln_index_h
_cell_measurement_refln_index_k
_cell_measurement_refln_index_l
_cell_measurement_refln_theta
-2 4 1 8.67
0 3 2 9.45
3 0 2 9.46
-3 4 1 8.93
-2 1 -2 7.53
10 0 0 23.77
0 10 0 23.78
-5 4 1 11.14
# - - - - data truncated for brevity - - - -
;
;
Example 1 - extracted from the CAD-4 listing for Rb~2~S~2~O~6~ at room
temperature (unpublished).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used in the determination of the
crystallographic cell parameters.
The _cell_measurement_refln_ data items would in general be used
only for diffractometer measurements.
;
data_cell_measurement_refln_index_
loop_ _name '_cell_measurement_refln_index_h'
'_cell_measurement_refln_index_k'
'_cell_measurement_refln_index_l'
_category cell_measurement_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of a reflection used for measurement of
the unit cell.
;
data_cell_measurement_refln_theta
_name '_cell_measurement_refln_theta'
_category cell_measurement_refln
_type numb
_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
_cell_measurement_refln_index_.
;
##############
## CHEMICAL ##
##############
data_chemical_[]
_name '_chemical_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_name_systematic
trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)
;
;
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CHEMICAL category record details about the
composition and chemical properties of the compound. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
;
data_chemical_absolute_configuration
_name '_chemical_absolute_configuration'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail rm
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration
;
ad
; absolute configuration established by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
rmad
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration and confirmed by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
syn
; absolute configuration has not been
established by anomalous-dispersion
effects in diffraction measurements on
the crystal. The enantiomer has been
assigned by reference to an unchanging
chiral centre in the synthetic
procedure
;
unk
; absolute configuration is unknown,
there being no firm chemical evidence
for its assignment to hand and it
having not been established by
anomalous-dispersion effects in
diffraction measurements on the
crystal. An arbitrary choice of
enantiomer has been made
;
. 'inapplicable'
_definition
; Necessary conditions for the assignment of
_chemical_absolute_configuration are given by H. D. Flack and
G. Bernardinelli (1999, 2000).
Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
;
data_chemical_compound_source
_name '_chemical_compound_source'
_category chemical
_type char
loop_ _example 'From Norilsk (USSR)'
'Extracted from the bark of Cinchona Naturalis'
_definition
; Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
;
data_chemical_melting_point
_name '_chemical_melting_point'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The temperature in kelvins at which the crystalline solid changes
to a liquid.
;
data_chemical_melting_point_
loop_ _name '_chemical_melting_point_gt'
'_chemical_melting_point_lt'
_category chemical
_type numb
_related_item '_chemical_melting_point'
_related_function alternate
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; A temperature in kelvins below which (*_lt) or above
which (*_gt) the melting point (the temperature at which the
crystalline solid changes to a liquid) lies. These items allow a
range of temperatures to be given.
_chemical_melting_point should always be used in preference
to these items whenever possible.
;
data_chemical_name_common
_name '_chemical_name_common'
_category chemical
_type char
_example '1-bromoestradiol'
_definition
; Trivial name by which the compound is commonly known.
;
data_chemical_name_mineral
_name '_chemical_name_mineral'
_category chemical
_type char
_example chalcopyrite
_definition
; Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
_chemical_compound_source.
;
data_chemical_name_structure_type
_name '_chemical_name_structure_type'
_category chemical
_type char
loop_ _example perovskite sphalerite A15
_definition
; Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
;
data_chemical_name_systematic
_name '_chemical_name_systematic'
_category chemical
_type char
_example '1-bromoestra-1,3,5(10)-triene-3,17\b-diol'
_definition
; IUPAC or Chemical Abstracts full name of the compound.
;
data_chemical_optical_rotation
_name '_chemical_optical_rotation'
_category chemical
_type char
_example '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)'
_definition
; The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where:
TEMP is the temperature of the measurement in degrees
Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g per 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC as defined above, and
SOLV is the chemical formula of the solvent.
;
data_chemical_properties_biological
_name '_chemical_properties_biological'
_category chemical
_type char
loop_ _example
; diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
;
; antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
;
; weakly potent lipoxygenase nonredox inhibitor
;
; no influenza A virus sialidase inhibitory and
plaque reduction activities
;
; low toxicity against Drosophila melanogaster
;
_definition
; A free-text description of the biological properties of the
material.
;
data_chemical_properties_physical
_name '_chemical_properties_physical'
_category chemical
_type char
loop_ _example air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
'ferromagnetic at low temperature'
'paramagnetic and thermochromic'
_definition
; A free-text description of the physical properties of the
material.
;
data_chemical_temperature_decomposition
_name '_chemical_temperature_decomposition'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_example 350
_definition
; The temperature in kelvins at which the solid decomposes.
;
data_chemical_temperature_decomposition_
loop_ _name '_chemical_temperature_decomposition_gt'
'_chemical_temperature_decomposition_lt'
_category chemical
_type numb
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_chemical_temperature_decomposition'
_related_function alternate
_example 350
_definition
; A temperature in kelvins below which (*_lt) or above which
(*_gt) the solid is known to decompose. These items allow
a range of temperatures to be given.
_chemical_temperature_decomposition should always be used in
preference to these items whenever possible.
;
data_chemical_temperature_sublimation
_name '_chemical_temperature_sublimation'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_example 350
_definition
; The temperature in kelvins at which the solid sublimes.
;
data_chemical_temperature_sublimation_
loop_ _name '_chemical_temperature_sublimation_gt'
'_chemical_temperature_sublimation_lt'
_category chemical
_type numb
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_chemical_temperature_sublimation'
_related_function alternate
_example 350
_definition
; A temperature in kelvins below which (*_lt) or above which
(*_gt) the solid is known to sublime. These items allow a
range of temperatures to be given.
_chemical_temperature_sublimation should always be used in
preference to these items whenever possible.
;
########################
## CHEMICAL_CONN_ATOM ##
########################
data_chemical_conn_atom_[]
_name '_chemical_conn_atom_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_chemical_conn_atom_number
_chemical_conn_atom_type_symbol
_chemical_conn_atom_display_x
_chemical_conn_atom_display_y
_chemical_conn_atom_NCA
_chemical_conn_atom_NH
1 S .39 .81 1 0
2 S .39 .96 2 0
3 N .14 .88 3 0
4 C .33 .88 3 0
5 C .11 .96 2 2
6 C .03 .96 2 2
7 C .03 .80 2 2
8 C .11 .80 2 2
9 S .54 .81 1 0
10 S .54 .96 2 0
11 N .80 .88 3 0
12 C .60 .88 3 0
13 C .84 .96 2 2
14 C .91 .96 2 2
15 C .91 .80 2 2
16 C .84 .80 2 2
;
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a 2D
chemical diagram to be reconstructed for use in a publication or
in a database search for structural and substructural
relationships.
The _chemical_conn_atom_ data items provide information about
the chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide,
they must also contain symmetry-generated atoms, so that the
_chemical_conn_atom_ and _chemical_conn_bond_ data items will
always describe a complete chemical entity.
;
data_chemical_conn_atom_charge
_name '_chemical_conn_atom_charge'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range -6:6
_enumeration_default 0
loop_ _example
_example_detail 1 'for an ammonium nitrogen'
-1 'for a chloride ion'
_definition
; The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
data_chemical_conn_atom_display_
loop_ _name '_chemical_conn_atom_display_x'
'_chemical_conn_atom_display_y'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0.0:1.0
_definition
; The 2D Cartesian coordinates (x,y) of the position of this atom
in a recognizable chemical diagram. The coordinate origin is at
the lower left corner, the x axis is horizontal and the y axis is
vertical. The coordinates must lie in the range 0.0 to 1.0. These
coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
;
data_chemical_conn_atom_NCA
_name '_chemical_conn_atom_NCA'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0:
_definition
; The number of connected atoms excluding terminal hydrogen atoms.
;
data_chemical_conn_atom_NH
_name '_chemical_conn_atom_NH'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0:
_definition
; The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the _atom_site_ list. This number will be the same as
_atom_site_attached_hydrogens only if none of the hydrogen
atoms appear in the _atom_site_ list.
;
data_chemical_conn_atom_number
_name '_chemical_conn_atom_number'
_category chemical_conn_atom
_type numb
_list yes
loop_ _list_link_child '_atom_site_chemical_conn_number'
'_chemical_conn_bond_atom_1'
'_chemical_conn_bond_atom_2'
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 1:
_definition
; The chemical sequence number to be associated with this atom.
;
data_chemical_conn_atom_type_symbol
_name '_chemical_conn_atom_type_symbol'
_category chemical_conn_atom
_type char
_list yes
_list_mandatory yes
_definition
; A code identifying the atom type. This code must match an
_atom_type_symbol code in the _atom_type_ list or be a
recognizable element symbol.
;
########################
## CHEMICAL_CONN_BOND ##
########################
data_chemical_conn_bond_[]
_name '_chemical_conn_bond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_chemical_conn_bond_atom_1
_chemical_conn_bond_atom_2
_chemical_conn_bond_type
4 1 doub 4 3 sing
4 2 sing 5 3 sing
6 5 sing 7 6 sing
8 7 sing 8 3 sing
10 2 sing 12 9 doub
12 11 sing 12 10 sing
13 11 sing 14 13 sing
15 14 sing 16 15 sing
16 11 sing 17 5 sing
18 5 sing 19 6 sing
20 6 sing 21 7 sing
22 7 sing 23 8 sing
24 8 sing 25 13 sing
26 13 sing 27 14 sing
28 14 sing 29 15 sing
30 15 sing 31 16 sing
32 16 sing
;
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a 2D
chemical diagram to be reconstructed for use in a publication
or in a database search for structural and substructural
relationships.
The _chemical_conn_bond_ data items specify the connections
between the atoms in the _chemical_conn_atom_ list and the nature
of the chemical bond between these atoms.
;
data_chemical_conn_bond_atom_
loop_ _name '_chemical_conn_bond_atom_1'
'_chemical_conn_bond_atom_2'
_category chemical_conn_bond
_type numb
_list yes
_list_link_parent '_chemical_conn_atom_number'
_enumeration_range 1:
_definition
; Atom numbers which must match with chemical sequence numbers
specified as _chemical_conn_atom_number values. These link the
bond connection to the chemical numbering and atom sites.
;
data_chemical_conn_bond_type
_name '_chemical_conn_bond_type'
_category chemical_conn_bond
_type char
_list yes
_list_reference '_chemical_conn_bond_atom_'
loop_ _enumeration
_enumeration_detail sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
_enumeration_default sing
_definition
; The chemical bond type associated with the connection between
the two sites _chemical_conn_bond_atom_1 and *_2.
;
######################
## CHEMICAL_FORMULA ##
######################
data_chemical_formula_[]
_name '_chemical_formula_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_formula_moiety 'C18 H25 N O3'
_chemical_formula_sum 'C18 H25 N O3'
_chemical_formula_weight 303.40
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_formula_iupac '[Mo (C O)4 (C18 H33 P)2]'
_chemical_formula_moiety 'C40 H66 Mo O4 P2'
_chemical_formula_structural '((C O)4 (P (C6 H11)3)2)Mo'
_chemical_formula_sum 'C40 H66 Mo O4 P2'
_chemical_formula_weight 768.81
;
;
Example 2 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; _chemical_formula_ items specify the composition and chemical
properties of the compound. The formula data items must agree
with those that specify the density, unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula_analytical, *_structural and *_sum. For the
data item *_moiety, the formula construction is broken up into
residues or moieties, i.e. groups of atoms that form a molecular
unit or molecular ion. The rules given below apply within each
moiety but different requirements apply to the way that moieties
are connected (see _chemical_formula_moiety).
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A
count of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of (element
symbol + count).
(4) Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parenthesis.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. (An exception to this rule
exists for *_moiety formulae where pre- and post-multipliers
are permitted for molecular units.)
(5) Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
_chemical_formula_structural, the order of the elements within
any group or moiety depends on whether carbon is present or
not. If carbon is present, the order should be: C, then H,
then the other elements in alphabetical order of their
symbol. If carbon is not present, the elements are listed
purely in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula_moiety and _chemical_formula_sum.
;
data_chemical_formula_analytical
_name '_chemical_formula_analytical'
_category chemical_formula
_type char
_example 'Fe2.45(2) Ni1.60(3) S4'
_definition
; Formula determined by standard chemical analysis including trace
elements. See the _chemical_formula_[] category description for
rules for writing chemical formulae. Parentheses are used only
for standard uncertainties (e.s.d.'s).
;
data_chemical_formula_iupac
_name '_chemical_formula_iupac'
_category chemical_formula
_type char
_example '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H'
_definition
; Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other _chemical_formula_ entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other _chemical_formula_ data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
;
data_chemical_formula_moiety
_name '_chemical_formula_moiety'
_category chemical_formula
_type char
loop_ _example 'C7 H4 Cl Hg N O3 S'
'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5(H2 O1)'
"(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)"
_definition
; Formula with each discrete bonded residue or ion shown as a
separate moiety. See the _chemical_formula_[] category
description for rules for writing chemical formulae. In addition
to the general formulae requirements, the following rules apply:
(1) Moieties are separated by commas ','.
(2) The order of elements within a moiety follows general rule
(5) in the _chemical_formula_[] category description.
(3) Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
(4) Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
;
data_chemical_formula_structural
_name '_chemical_formula_structural'
_category chemical_formula
_type char
loop_ _example 'Ca ((Cl O3)2 O)2 (H2 O)6'
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
_definition
; See the _chemical_formula_[] category description for the rules
for writing chemical formulae for inorganics, organometallics,
metal complexes etc., in which bonded groups are preserved
as discrete entities within parentheses, with post-multipliers
as required. The order of the elements should give as much
information as possible about the chemical structure.
Parentheses may be used and nested as required. This formula
should correspond to the structure as actually reported,
i.e. trace elements not included in atom-type and atom-site
lists should not be included in this formula (see also
_chemical_formula_analytical).
;
data_chemical_formula_sum
_name '_chemical_formula_sum'
_category chemical_formula
_type char
loop_ _example 'C18 H19 N7 O8 S'
_definition
; See the _chemical_formula_[] category description for the rules
for writing chemical formulae in which all discrete bonded
residues and ions are summed over the constituent elements,
following the ordering given in general rule (5) in the
_chemical_formula_[] category description. Parentheses are not
normally used.
;
data_chemical_formula_weight
_name '_chemical_formula_weight'
_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,
*_moiety or *_sum and, together with the Z value and cell
parameters, should yield the density given as
_exptl_crystal_density_diffrn.
;
data_chemical_formula_weight_meas
_name '_chemical_formula_weight_meas'
_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.
;
##############
## CITATION ##
##############
data_citation_[]
_name '_citation_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_id
_citation_coordinate_linkage
_citation_title
_citation_country
_citation_page_first
_citation_page_last
_citation_year
_citation_journal_abbrev
_citation_journal_volume
_citation_journal_issue
_citation_journal_id_ASTM
_citation_journal_id_ISSN
_citation_book_title
_citation_book_publisher
_citation_book_id_ISBN
_citation_special_details
primary yes
; Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and
acetyl-pepstatin at 2.0-Angstroms resolution.
;
US 14209 14219 1990 'J. Biol. Chem.' 265 .
HBCHA3 0021-9258 . . .
; The publication that directly relates to this coordinate
set.
;
2 no
; Three-dimensional structure of aspartyl-protease from
human immunodeficiency virus HIV-1.
;
UK 615 619 1989 'Nature' 337 .
NATUAS 0028-0836 . . .
; Determination of the structure of the unliganded enzyme.
;
3 no
; Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.
;
US 1919 1921 1989 'J. Biol. Chem.' 264 .
HBCHA3 0021-9258 . . .
; Crystallization of the unliganded enzyme.
;
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CITATION category record details about the
literature cited as being relevant to the contents of the data
block.
;
data_citation_abstract
_name '_citation_abstract'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
;
data_citation_abstract_id_CAS
_name '_citation_abstract_id_CAS'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The Chemical Abstracts Service (CAS) abstract identifier;
relevant for journal articles.
;
data_citation_book_id_ISBN
_name '_citation_book_id_ISBN'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for books or book chapters.
;
data_citation_book_publisher
_name '_citation_book_publisher'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'John Wiley'
_definition
; The name of the publisher of the citation; relevant
for books or book chapters.
;
data_citation_book_publisher_city
_name '_citation_book_publisher_city'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'New York'
_definition
; The location of the publisher of the citation; relevant
for books or book chapters.
;
data_citation_book_title
_name '_citation_book_title'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The title of the book in which the citation appeared; relevant
for books or book chapters.
;
data_citation_coordinate_linkage
_name '_citation_coordinate_linkage'
_category citation
_type char
_list yes
_list_reference '_citation_id'
loop_ _enumeration
_enumeration_detail no 'citation unrelated to current coordinates'
n 'abbreviation for "no"'
yes 'citation related to current coordinates'
y 'abbreviation for "yes"'
_definition
; _citation_coordinate_linkage states whether or not this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to creation of the data block, the value of this data item
would be 'no'.
;
data_citation_country
_name '_citation_country'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The country of publication; relevant for books and book
chapters.
;
data_citation_database_id_CSD
_name '_citation_database_id_CSD'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example LEKKUH
_definition
; Identifier ('refcode') of the database record in the Cambridge
Structural Database that contains details of the cited structure.
;
data_citation_database_id_Medline
_name '_citation_database_id_Medline'
_category citation
_type numb
_list yes
_list_reference '_citation_id'
_enumeration_range 1:
_example 89064067
_definition
; Accession number used by Medline to categorize a specific
bibliographic entry.
;
data_citation_id
_name '_citation_id'
_category citation
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_citation_author_citation_id'
'_citation_editor_citation_id'
loop_ _example primary 1 2 3
_definition
; The value of _citation_id must uniquely identify a record in the
_citation_ list.
The _citation_id 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
data_citation_journal_abbrev
_name '_citation_journal_abbrev'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'J. Mol. Biol.'
_definition
; Abbreviated name of the journal cited as given in the Chemical
Abstracts Service Source Index.
;
data_citation_journal_id_ASTM
_name '_citation_journal_id_ASTM'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The American Society for Testing and Materials (ASTM) code
assigned to the journal cited (also referred to as the CODEN
designator of the Chemical Abstracts Service); relevant for
journal articles.
;
data_citation_journal_id_CSD
_name '_citation_journal_id_CSD'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example '0070'
_definition
; The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
;
data_citation_journal_id_ISSN
_name '_citation_journal_id_ISSN'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
;
data_citation_journal_full
_name '_citation_journal_full'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'Journal of Molecular Biology'
_definition
; Full name of the journal cited; relevant for journal articles.
;
data_citation_journal_issue
_name '_citation_journal_issue'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 2
_definition
; Issue number of the journal cited; relevant for journal
articles.
;
data_citation_journal_volume
_name '_citation_journal_volume'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 174
_definition
; Volume number of the journal cited; relevant for journal
articles.
;
data_citation_language
_name '_citation_language'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example German
_definition
; Language in which the cited article is written.
;
data_citation_page_
loop_ _name '_citation_page_first'
'_citation_page_last'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The first and last pages of the citation; relevant for
journal articles, books and book chapters.
;
data_citation_special_details
_name '_citation_special_details'
_category citation
_type char
_list yes
_list_reference '_citation_id'
loop_ _example
; citation relates to this precise coordinate set
;
; citation relates to earlier low-resolution structure
;
; citation relates to further refinement of structure
reported in citation 2
;
_definition
; A description of special aspects of the relationship
of the contents of the data block to the literature item cited.
;
data_citation_title
_name '_citation_title'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example
; Structure of diferric duck ovotransferrin at 2.35 \%A
resolution.
;
_definition
; The title of the citation; relevant for journal articles, books
and book chapters.
;
data_citation_year
_name '_citation_year'
_category citation
_type numb
_list yes
_list_reference '_citation_id'
_example 1984
_definition
; The year of the citation; relevant for journal articles, books
and book chapters.
;
#####################
## CITATION_AUTHOR ##
#####################
data_citation_author_[]
_name '_citation_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_author_citation_id
_citation_author_name
primary 'Fitzgerald, P.M.D.'
primary 'McKeever, B.M.'
primary 'Van Middlesworth, J.F.'
primary 'Springer, J.P.'
primary 'Heimbach, J.C.'
primary 'Leu, C.-T.'
primary 'Herber, W.K.'
primary 'Dixon, R.A.F.'
primary 'Darke, P.L.'
2 'Navia, M.A.'
2 'Fitzgerald, P.M.D.'
2 'McKeever, B.M.'
2 'Leu, C.-T.'
2 'Heimbach, J.C.'
2 'Herber, W.K.'
2 'Sigal, I.S.'
2 'Darke, P.L.'
2 'Springer, J.P.'
3 'McKeever, B.M.'
3 'Navia, M.A.'
3 'Fitzgerald, P.M.D.'
3 'Springer, J.P.'
3 'Leu, C.-T.'
3 'Heimbach, J.C.'
3 'Herber, W.K.'
3 'Sigal, I.S.'
3 'Darke, P.L.'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
_citation_ list.
;
data_citation_author_citation_id
_name '_citation_author_citation_id'
_category citation_author
_type char
_list yes
_list_mandatory yes
_list_link_parent '_citation_id'
_definition
; The value of _citation_author_citation_id must match an
identifier specified by _citation_id in the _citation_ list.
;
data_citation_author_name
_name '_citation_author_name'
_category citation_author
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; Name of an author of the citation; relevant for journal
articles, books and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_citation_author_ordinal
_name '_citation_author_ordinal'
_category citation_author
_type char
_list yes
_definition
; This data name defines the order of the author's name in the
list of authors of a citation.
;
#####################
## CITATION_EDITOR ##
#####################
data_citation_editor_[]
_name '_citation_editor_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_editor_citation_id
_citation_editor_name
5 'McKeever, B.M.'
5 'Navia, M.A.'
5 'Fitzgerald, P.M.D.'
5 'Springer, J.P.'
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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.
;
data_citation_editor_citation_id
_name '_citation_editor_citation_id'
_category citation_editor
_type char
_list yes
_list_mandatory yes
_list_link_parent '_citation_id'
_definition
; The value of _citation_editor_citation_id must match an
identifier specified by _citation_id in the _citation_ list.
;
data_citation_editor_name
_name '_citation_editor_name'
_category citation_editor
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; Name of an editor of the citation; relevant for books and
book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_citation_editor_ordinal
_name '_citation_editor_ordinal'
_category citation_editor
_type char
_list yes
_definition
; This data name defines the order of the editor's name in the
list of editors of a citation.
;
###############
## COMPUTING ##
###############
data_computing_[]
_name '_computing_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_computing_data_collection 'CAD-4 (Enraf-Nonius, 1989)'
_computing_cell_refinement 'CAD-4 (Enraf-Nonius, 1989)'
_computing_data_reduction 'CFEO (Solans, 1978)'
_computing_structure_solution 'SHELXS86 (Sheldrick, 1990)'
_computing_structure_refinement 'SHELXL93 (Sheldrick, 1993)'
_computing_molecular_graphics 'ORTEPII (Johnson, 1976)'
_computing_publication_material 'PARST (Nardelli, 1983)'
;
;
Example 1 - Rodr\'iguez-Romero, Ruiz-P\'erez & Solans
[Acta Cryst. (1996), C52, 1415-1417].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
;
data_computing_
loop_ _name '_computing_cell_refinement'
'_computing_data_collection'
'_computing_data_reduction'
'_computing_molecular_graphics'
'_computing_publication_material'
'_computing_structure_refinement'
'_computing_structure_solution'
_category computing
_type char
loop_ _example 'CAD-4 (Enraf-Nonius, 1989)'
'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)'
'FRODO (Jones, 1986), ORTEP (Johnson, 1965)'
'CRYSTALS (Watkin, 1988)'
'SHELX85 (Sheldrick, 1985)'
_definition
; Software used in the processing of the data. Give the program
or package name and a brief reference.
;
##############
## DATABASE ##
##############
data_database_[]
_name '_database_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_database_code_CSD 'VOBYUG'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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
only appear in a CIF if they originate from that source.
;
data_database_code_
loop_ _name '_database_code_CAS'
'_database_code_CSD'
'_database_code_ICSD'
'_database_code_MDF'
'_database_code_NBS'
'_database_code_PDB'
'_database_code_PDF'
_category database
_type char
_definition
; The codes are assigned by databases: Chemical Abstracts;
Cambridge Structural Database (organic and metal-organic
compounds); Inorganic Crystal Structure Database; Metals
Data File (metal structures); NBS (NIST) Crystal Data
Database (lattice parameters); Protein Data Bank; and the
Powder Diffraction File (JCPDS/ICDD).
;
data_database_code_depnum_ccdc_fiz
_name '_database_code_depnum_ccdc_fiz'
_category database
_type char
_definition
; Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
;
data_database_code_depnum_ccdc_journal
_name '_database_code_depnum_ccdc_journal'
_category database
_type char
_definition
; Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
;
data_database_code_depnum_ccdc_archive
_name '_database_code_depnum_ccdc_archive'
_category database
_type char
_definition
; Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
;
data_database_CSD_history
_name '_database_CSD_history'
_category database
_type char
_definition
; A history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
;
data_database_journal_
loop_ _name '_database_journal_ASTM'
'_database_journal_CSD'
_category database
_type char
_definition
; The ASTM CODEN designator for a journal as given in the
Chemical Source List maintained by the Chemical Abstracts
Service, and the journal code used in the Cambridge Structural
Database.
;
############
## DIFFRN ##
############
data_diffrn_[]
_name '_diffrn_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_special_details
; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate
1.2\% min^-1^. Background counts for 5 s on each side
every scan.
;
_diffrn_ambient_temperature 293
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN category record details about the
intensity measurements.
;
data_diffrn_ambient_environment
_name '_diffrn_ambient_environment'
_category diffrn
_type char
loop_ _example He vacuum 'mother liquor'
_definition
; The gas or liquid surrounding the sample, if not air.
;
data_diffrn_ambient_pressure
_name '_diffrn_ambient_pressure'
_category diffrn
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The mean hydrostatic pressure in kilopascals at which the
intensities were measured.
;
data_diffrn_ambient_pressure_
loop_ _name '_diffrn_ambient_pressure_gt'
'_diffrn_ambient_pressure_lt'
_category diffrn
_type numb
_related_item '_diffrn_ambient_pressure'
_related_function alternate
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The mean hydrostatic pressure in kilopascals above which (*_gt)
or below which (*_lt) the intensities were measured. These
items allow for a pressure range to be given.
_diffrn_ambient_pressure should always be used in
preference to these items whenever possible.
;
data_diffrn_ambient_temperature
_name '_diffrn_ambient_temperature'
_category diffrn
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The mean temperature in kelvins at which the intensities
were measured.
;
data_diffrn_ambient_temperature_
loop_ _name '_diffrn_ambient_temperature_gt'
'_diffrn_ambient_temperature_lt'
_category diffrn
_type numb
_related_item '_diffrn_ambient_temperature'
_related_function alternate
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The mean temperature in kelvins above which (*_gt) or below
which (*_lt) the intensities were measured. These items allow
a range of temperatures to be given.
_diffrn_ambient_temperature should always be used in preference
to these items whenever possible.
;
data_diffrn_crystal_treatment
_name '_diffrn_crystal_treatment'
_category diffrn
_type char
loop_ _example 'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
_definition
; Remarks about how the crystal was treated prior to the intensity
measurements. Particularly relevant when intensities were
measured at low temperature.
;
data_diffrn_measured_fraction_theta_full
_name '_diffrn_measured_fraction_theta_full'
_category diffrn
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_full.
;
data_diffrn_measured_fraction_theta_max
_name '_diffrn_measured_fraction_theta_max'
_category diffrn
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_max.
;
data_diffrn_special_details
_name '_diffrn_special_details'
_category diffrn
_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
; Special details of the intensity-measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
;
data_diffrn_symmetry_description
_name '_diffrn_symmetry_description'
_category diffrn
_type char
_definition
; Observed diffraction point symmetry, systematic absences and
possible space group(s) or superspace group(s) compatible with
these.
;
#######################
## DIFFRN_ATTENUATOR ##
#######################
data_diffrn_attenuator_[]
_name '_diffrn_attenuator_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_attenuator_code
_diffrn_attenuator_scale
0 1.00
1 16.97
2 33.89
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
;
data_diffrn_attenuator_code
_name '_diffrn_attenuator_code'
_category diffrn_attenuator
_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
stored with the intensities. See _diffrn_attenuator_scale.
;
data_diffrn_attenuator_material
_name '_diffrn_attenuator_material'
_category diffrn_attenuator
_type char
_list yes
_list_reference '_diffrn_attenuator_code'
_definition
; Material from which the attenuator is made.
;
data_diffrn_attenuator_scale
_name '_diffrn_attenuator_scale'
_category diffrn_attenuator
_type numb
_list yes
_list_reference '_diffrn_attenuator_code'
_enumeration_range 1.0:
_definition
; The scale factor applied when an intensity measurement is
reduced by an attenuator identified by _diffrn_attenuator_code.
The measured intensity must be multiplied by this scale to
convert it to the same scale as unattenuated intensities.
;
#####################
## DIFFRN_DETECTOR ##
#####################
data_diffrn_detector_[]
_name '_diffrn_detector_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_detector 'multiwire'
_diffrn_detector_type 'Siemens'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
data_diffrn_detector
_name '_diffrn_detector'
_category diffrn_detector
_type char
_related_item '_diffrn_radiation_detector'
_related_function alternate
loop_
_example 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
_definition
; The general class of the radiation detector.
;
data_diffrn_detector_area_resol_mean
_name '_diffrn_detector_area_resol_mean'
_category diffrn_detector
_type numb
_enumeration_range 0.0:
_units mm^-1^
_units_detail 'pixels per millimetre'
_definition
; The resolution of an area detector, in pixels/mm.
;
data_diffrn_detector_details
_name '_diffrn_detector_details'
_category diffrn_detector
_type char
_definition
; A description of special aspects of the radiation detector.
;
data_diffrn_detector_dtime
_name '_diffrn_detector_dtime'
_category diffrn_detector
_related_item '_diffrn_radiation_detector_dtime'
_related_function alternate
_type numb
_enumeration_range 0.0:
_definition
; The deadtime in microseconds of the detector used to measure
the diffraction intensities.
;
data_diffrn_detector_type
_name '_diffrn_detector_type'
_category diffrn_detector
_type char
_definition
; The make, model or name of the detector device used.
;
data_diffrn_radiation_detector
_name '_diffrn_radiation_detector'
_category diffrn_detector
_type char
_related_item '_diffrn_detector'
_related_function replace
_definition
; The detector used to measure the diffraction intensities.
;
data_diffrn_radiation_detector_dtime
_name '_diffrn_radiation_detector_dtime'
_category diffrn_detector
_type numb
_enumeration_range 0.0:
_related_item '_diffrn_detector_dtime'
_related_function replace
_definition
; The deadtime in microseconds of the detector used to measure
the diffraction intensities.
;
########################
## DIFFRN_MEASUREMENT ##
########################
data_diffrn_measurement_[]
_name '_diffrn_measurement_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_measurement_device_type
'Philips PW1100/20 diffractometer'
_diffrn_measurement_method \q/2\q
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_MEASUREMENT category refer to the
mounting of the sample and to the goniometer on which it is
mounted.
;
data_diffrn_measurement_details
_name '_diffrn_measurement_details'
_category diffrn_measurement
_type char
_example '440 frames of 0.25\%'
_definition
; A description of special aspects of the intensity measurement.
;
data_diffrn_measurement_device
_name '_diffrn_measurement_device'
_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 goniometer or device used to support
and orient the specimen.
;
data_diffrn_measurement_device_details
_name '_diffrn_measurement_device_details'
_category diffrn_measurement
_type char
_example
; commercial goniometer modified locally to
allow for 90\% \t arc
;
_definition
; A description of special aspects of the device used to measure
the diffraction intensities.
;
data_diffrn_measurement_device_type
_name '_diffrn_measurement_device_type'
_category diffrn_measurement
_type char
_definition
; The make, model or name of the measurement device
(goniometer) used.
;
data_diffrn_measurement_method
_name '_diffrn_measurement_method'
_category diffrn_measurement
_type char
_example 'profile data from \q/2\q scans'
_definition
; Method used to measure the intensities.
;
data_diffrn_measurement_specimen_support
_name '_diffrn_measurement_specimen_support'
_category diffrn_measurement
_type char
loop_ _example 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
_definition
; The physical device used to support the crystal during data
collection.
;
##########################
## DIFFRN_ORIENT_MATRIX ##
##########################
data_diffrn_orient_matrix_[]
_name '_diffrn_orient_matrix_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_orient_matrix_UB_11 -0.04170
_diffrn_orient_matrix_UB_12 -0.01429
_diffrn_orient_matrix_UB_13 -0.02226
_diffrn_orient_matrix_UB_21 -0.00380
_diffrn_orient_matrix_UB_22 -0.05578
_diffrn_orient_matrix_UB_23 -0.05048
_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
[Acta Cryst. (1996), C52, 1010-1012].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction intensities.
;
data_diffrn_orient_matrix_type
_name '_diffrn_orient_matrix_type'
_category diffrn_orient_matrix
_type char
_definition
; A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
;
data_diffrn_orient_matrix_UB_
loop_ _name '_diffrn_orient_matrix_UB_11'
'_diffrn_orient_matrix_UB_12'
'_diffrn_orient_matrix_UB_13'
'_diffrn_orient_matrix_UB_21'
'_diffrn_orient_matrix_UB_22'
'_diffrn_orient_matrix_UB_23'
'_diffrn_orient_matrix_UB_31'
'_diffrn_orient_matrix_UB_32'
'_diffrn_orient_matrix_UB_33'
_category diffrn_orient_matrix
_type numb
_definition
; The elements of the diffractometer orientation matrix. These
define the dimensions of the reciprocal cell and its orientation
to the local diffractometer axes. See _diffrn_orient_matrix_type.
;
#########################
## DIFFRN_ORIENT_REFLN ##
#########################
data_diffrn_orient_refln_[]
_name '_diffrn_orient_refln_[]'
_category category_overview
_type null
loop_ _example
_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 an 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
the measurement of the diffraction intensities.
;
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 of a reflection used to define
the orientation matrix in degrees. See
_diffrn_orient_matrix_UB_ and
_diffrn_orient_refln_index_h, *_k and *_l.
;
data_diffrn_orient_refln_index_
loop_ _name '_diffrn_orient_refln_index_h'
'_diffrn_orient_refln_index_k'
'_diffrn_orient_refln_index_l'
_category diffrn_orient_refln
_type numb
_list yes
_list_mandatory yes
_definition
; The indices of a reflection used to define the orientation
matrix. See _diffrn_orient_matrix_.
;
######################
## DIFFRN_RADIATION ##
######################
data_diffrn_radiation_[]
_name '_diffrn_radiation_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_radiation_type 'Cu K\a'
_diffrn_radiation_monochromator 'graphite'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_RADIATION category describe the
radiation used in measuring the diffraction intensities, its
collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data items
in the DIFFRN_DETECTOR category.
;
data_diffrn_radiation_collimation
_name '_diffrn_radiation_collimation'
_category diffrn_radiation
_type char
loop_ _example '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
_definition
; The collimation or focusing applied to the radiation.
;
data_diffrn_radiation_filter_edge
_name '_diffrn_radiation_filter_edge'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Absorption edge in angstroms of the radiation filter used.
;
data_diffrn_radiation_inhomogeneity
_name '_diffrn_radiation_inhomogeneity'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_definition
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
data_diffrn_radiation_monochromator
_name '_diffrn_radiation_monochromator'
_category diffrn_radiation
_type char
loop_ _example 'Zr filter' 'Ge 220' 'none'
'equatorial mounted graphite'
_definition
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used, the material and the indices of the
Bragg reflection are specified.
;
data_diffrn_radiation_polarisn_norm
_name '_diffrn_radiation_polarisn_norm'
_category diffrn_radiation
_type numb
_enumeration_range -180.0:180.0
_units deg
_units_detail 'degrees'
_definition
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
data_diffrn_radiation_polarisn_ratio
_name '_diffrn_radiation_polarisn_ratio'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_definition
; Polarization ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarized to the
parallel polarized components of the radiation. The perpendicular
component forms an angle of _diffrn_radiation_polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the plane
containing the incident and reflected beams).
;
data_diffrn_radiation_probe
_name '_diffrn_radiation_probe'
_category diffrn_radiation
_type char
loop_ _enumeration x-ray
neutron
electron
gamma
_definition
; The nature of the radiation used (i.e. the name of the
subatomic particle or the region of the electromagnetic
spectrum). It is strongly recommended that this information
be given, so that the probe radiation can be simply determined.
;
data_diffrn_radiation_type
_name '_diffrn_radiation_type'
_category diffrn_radiation
_type char
loop_ _example 'Cu K\a' 'Cu K\a~1~'
'Cu K-L~2,3~' white-beam
_definition
; The type of the radiation. This is used to give a more
detailed description than _diffrn_radiation_probe and is
typically a description of the X-ray wavelength in Siegbahn
notation.
;
data_diffrn_radiation_xray_symbol
_name '_diffrn_radiation_xray_symbol'
_category diffrn_radiation
_type char
loop_ _enumeration
_enumeration_detail
K-L~3~ 'K\a~1~ in older Siegbahn notation'
K-L~2~ 'K\a~2~ in older Siegbahn notation'
K-M~3~ 'K\b~1~ in older Siegbahn notation'
K-L~2,3~ 'use where K-L~3~ and K-L~2~ are not resolved'
_definition
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
###################################
### DIFFRN_RADIATION_WAVELENGTH ###
###################################
data_diffrn_radiation_wavelength_[]
_name '_diffrn_radiation_wavelength_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_radiation_wavelength 1.5418
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_RADIATION_WAVELENGTH category describe
the wavelength of the radiation used in measuring the diffraction
intensities. Items may be looped to identify and assign weights
to distinct wavelength components from a polychromatic beam.
;
data_diffrn_radiation_wavelength
_name '_diffrn_radiation_wavelength'
_category diffrn_radiation_wavelength
_type numb
_list both
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The radiation wavelength in angstroms.
;
data_diffrn_radiation_wavelength_id
_name '_diffrn_radiation_wavelength_id'
_category diffrn_radiation_wavelength
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_wavelength_id'
loop_ _example x1 x2 neut
_definition
; An arbitrary 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.
;
data_diffrn_radiation_wavelength_wt
_name '_diffrn_radiation_wavelength_wt'
_category diffrn_radiation_wavelength
_type numb
_list yes
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:1.0
_enumeration_default 1.0
_definition
; The relative weight of a wavelength identified by the code
_diffrn_radiation_wavelength_id in the list of wavelengths.
;
##################
## DIFFRN_REFLN ##
##################
data_diffrn_refln_[]
_name '_diffrn_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_refln_index_h
_diffrn_refln_index_k
_diffrn_refln_index_l
_diffrn_refln_angle_chi
_diffrn_refln_scan_rate
_diffrn_refln_counts_bg_1
_diffrn_refln_counts_total
_diffrn_refln_counts_bg_2
_diffrn_refln_angle_theta
_diffrn_refln_angle_phi
_diffrn_refln_angle_omega
_diffrn_refln_angle_kappa
_diffrn_refln_scan_width
_diffrn_refln_elapsed_time
0 0 -16 0. 4.12 28 127 36 33.157 -75.846 16.404 50.170 1.516 19.43
0 0 -15 0. 4.12 38 143 28 30.847 -75.846 14.094 50.170 1.516 19.82
0 0 -14 0. 1.03 142 742 130 28.592 -75.846 11.839 50.170 1.516 21.32
0 0 -13 0. 4.12 26 120 37 26.384 -75.846 9.631 50.170 1.450 21.68
0 0 -12 0. 0.97 129 618 153 24.218 -75.846 7.464 50.170 1.450 23.20
0 0 -11 0. 4.12 33 107 38 22.087 -75.846 5.334 50.170 1.384 23.55
0 0 -10 0. 4.12 37 146 33 19.989 -75.846 3.235 50.170 1.384 23.90
0 0 -9 0. 4.12 50 179 49 17.918 -75.846 1.164 50.170 1.384 24.25
# - - - - data truncated for brevity - - - -
3 4 -4 0. 1.03 69 459 73 30.726 -53.744 46.543 -47.552 1.516 2082.58
3 4 -5 0. 1.03 91 465 75 31.407 -54.811 45.519 -42.705 1.516 2084.07
3 14 -6 0. 1.03 84 560 79 32.228 -55.841 44.745 -38.092 1.516 2085.57
# - - - - data truncated for brevity - - - -
;
;
Example 1 - extracted from the CAD-4 listing for Tl~2~Cd~2~(SO~4~)~3~ at
85 K (unpublished).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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
measurements and must be included in looped lists.
(The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLNS data items
are not looped.)
;
data_diffrn_refln_angle_
loop_ _name '_diffrn_refln_angle_chi'
'_diffrn_refln_angle_kappa'
'_diffrn_refln_angle_omega'
'_diffrn_refln_angle_phi'
'_diffrn_refln_angle_psi'
'_diffrn_refln_angle_theta'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_units deg
_units_detail 'degrees'
_definition
; The diffractometer angles of a reflection in degrees. These
correspond to the specified orientation matrix and the original
measured cell before any subsequent cell transformations.
;
data_diffrn_refln_attenuator_code
_name '_diffrn_refln_attenuator_code'
_category diffrn_refln
_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.
;
data_diffrn_refln_class_code
_name '_diffrn_refln_class_code'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
_list_link_parent '_diffrn_reflns_class_code'
_definition
; The code identifying the class to which this reflection has
been assigned. This code must match a value of
_diffrn_reflns_class_code. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be defined by the
number m=sum|m~i~|, where the m~i~ are the integer coefficients
that, in addition to h,k,l, index the corresponding diffraction
vector in the basis defined for the reciprocal lattice.
;
data_diffrn_refln_counts_
loop_ _name '_diffrn_refln_counts_bg_1'
'_diffrn_refln_counts_bg_2'
'_diffrn_refln_counts_net'
'_diffrn_refln_counts_peak'
'_diffrn_refln_counts_total'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_definition
; The diffractometer counts for the measurements: background
before the peak, background after the peak, net counts after
background removed, counts for peak scan or position, and the
total counts (background plus peak).
;
data_diffrn_refln_crystal_id
_name '_diffrn_refln_crystal_id'
_category diffrn_refln
_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.
;
data_diffrn_refln_detect_slit_
loop_ _name '_diffrn_refln_detect_slit_horiz'
'_diffrn_refln_detect_slit_vert'
_category diffrn_refln
_type numb
_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).
;
data_diffrn_refln_elapsed_time
_name '_diffrn_refln_elapsed_time'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units min
_units_detail 'minutes'
_definition
; Elapsed time in minutes from the start of the diffraction
experiment to the measurement of this intensity.
;
data_diffrn_refln_index_
loop_ _name '_diffrn_refln_index_h'
'_diffrn_refln_index_k'
'_diffrn_refln_index_l'
_category diffrn_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of a measured reflection. These need not match
the _refln_index_h, *_k, *_l values if a transformation of the
original measured cell has taken place. Details of the cell
transformation are given in _diffrn_reflns_reduction_process.
See also _diffrn_reflns_transf_matrix_.
;
data_diffrn_refln_intensity_net
_name '_diffrn_refln_intensity_net'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Net intensity calculated from the diffraction counts after
the attenuator and standard scales have been applied.
;
data_diffrn_refln_intensity_sigma
_name '_diffrn_refln_intensity_sigma'
_category diffrn_refln
_type numb
_related_item '_diffrn_refln_intensity_u'
_related_function replace
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Standard uncertainty (e.s.d.) of the net intensity calculated
from the diffraction counts after the attenuator and standard
scales have been applied.
;
data_diffrn_refln_intensity_u
_name '_diffrn_refln_intensity_u'
_category diffrn_refln
_type numb
_related_item '_diffrn_refln_intensity_sigma'
_related_function alternate
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Standard uncertainty of the net intensity calculated from
the diffraction counts after the attenuator and standard
scales have been applied.
;
data_diffrn_refln_scale_group_code
_name '_diffrn_refln_scale_group_code'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_scale_group_code'
_list_reference '_diffrn_refln_index_'
_definition
; The code identifying the scale applicable to this reflection.
This code must match with a specified _diffrn_scale_group_code
value.
;
data_diffrn_refln_scan_mode
_name '_diffrn_refln_scan_mode'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
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 for measurements
using a diffractometer. See _diffrn_refln_scan_width and
_diffrn_refln_scan_mode_backgd.
;
data_diffrn_refln_scan_mode_backgd
_name '_diffrn_refln_scan_mode_backgd'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
loop_ _enumeration
_enumeration_detail st 'stationary counter background'
mo 'moving counter background'
_definition
; The code identifying the mode of scanning a reflection to measure
the background intensity.
;
data_diffrn_refln_scan_rate
_name '_diffrn_refln_scan_rate'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units deg/min
_units_detail 'degrees per minute'
_definition
; The rate of scanning a reflection in
degrees per minute to measure the intensity.
;
data_diffrn_refln_scan_time_backgd
_name '_diffrn_refln_scan_time_backgd'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units sec
_units_detail 'seconds'
_definition
; The time spent measuring each background in seconds.
;
data_diffrn_refln_scan_width
_name '_diffrn_refln_scan_width'
_category diffrn_refln
_type numb
_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.
;
data_diffrn_refln_sint/lambda
_name '_diffrn_refln_sint/lambda'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The (sin theta)/lambda value in reciprocal angstroms for
this reflection.
;
data_diffrn_refln_standard_code
_name '_diffrn_refln_standard_code'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_standard_refln_code'
_list_reference '_diffrn_refln_index_'
loop_ _example 1 2 3 s1 s2 s3 A B C
_definition
; A code indicating that this reflection was measured as a
standard reflection. The value must be '.' or match one of
the _diffrn_standard_refln_code values.
;
data_diffrn_refln_wavelength
_name '_diffrn_refln_wavelength'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The mean wavelength in angstroms of the radiation used to measure
the intensity of this reflection. This is an important parameter
for reflections measured using energy-dispersive detectors or the
Laue method.
;
data_diffrn_refln_wavelength_id
_name '_diffrn_refln_wavelength_id'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_radiation_wavelength_id'
_list_reference '_diffrn_refln_index_'
loop_ _example x1 x2 neut
_definition
; Code identifying the wavelength in the _diffrn_radiation_ list.
;
###################
## DIFFRN_REFLNS ##
###################
data_diffrn_reflns_[]
_name '_diffrn_reflns_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_reflns_number 1592
_diffrn_reflns_av_R_equivalents 0
_diffrn_reflns_av_unetI/netI .027
_diffrn_reflns_limit_h_min 0
_diffrn_reflns_limit_h_max 6
_diffrn_reflns_limit_k_min -17
_diffrn_reflns_limit_k_max 0
_diffrn_reflns_limit_l_min 0
_diffrn_reflns_limit_l_max 22
_diffrn_reflns_theta_min 3.71
_diffrn_reflns_theta_max 61.97
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLNS data items
are not looped.
(The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.)
;
data_diffrn_reflns_av_R_equivalents
_name '_diffrn_reflns_av_R_equivalents'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_definition
; The residual [sum av|del(I)| / sum |av(I)|] for
symmetry-equivalent reflections used to calculate the
average intensity av(I). The av|del(I)| term is the
average absolute difference between av(I) and the
individual symmetry-equivalent intensities.
;
data_diffrn_reflns_av_sigmaI/netI
_name '_diffrn_reflns_av_sigmaI/netI'
_category diffrn_reflns
_type numb
_related_item '_diffrn_reflns_av_unetI/netI'
_related_function replace
_enumeration_range 0.0:
_definition
; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
;
data_diffrn_reflns_av_unetI/netI
_name '_diffrn_reflns_av_unetI/netI'
_category diffrn_reflns
_type numb
_related_item '_diffrn_reflns_av_sigmaI/netI'
_related_function alternate
_enumeration_range 0.0:
_definition
; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
;
data_diffrn_reflns_limit_
loop_ _name '_diffrn_reflns_limit_h_max'
'_diffrn_reflns_limit_h_min'
'_diffrn_reflns_limit_k_max'
'_diffrn_reflns_limit_k_min'
'_diffrn_reflns_limit_l_max'
'_diffrn_reflns_limit_l_min'
_category diffrn_reflns
_type numb
_definition
; The limits on the Miller indices of the intensities specified
by _diffrn_refln_index_h, *_k, *_l.
;
data_diffrn_reflns_number
_name '_diffrn_reflns_number'
_category diffrn_reflns
_type numb
_enumeration_range 0:
_definition
; The total number of measured intensities, excluding
reflections that are classed as systematically absent arising
from translational symmetry in the crystal unit cell.
;
data_diffrn_reflns_reduction_process
_name '_diffrn_reflns_reduction_process'
_category diffrn_reflns
_type char
_example 'data averaged using Fisher test'
_definition
; A description of the process used to reduce the intensities
into structure-factor magnitudes.
;
data_diffrn_reflns_resolution_full
_name '_diffrn_reflns_resolution_full'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_related_item '_diffrn_reflns_theta_full'
_related_function alternate
_definition
; The resolution in reciprocal angstroms at which the measured
reflection count is close to complete.
;
data_diffrn_reflns_resolution_max
_name '_diffrn_reflns_resolution_max'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_related_item '_diffrn_reflns_theta_max'
_related_function alternate
_definition
; Maximum resolution in reciprocal angstroms of the measured
diffraction pattern.
;
data_diffrn_reflns_theta_full
_name '_diffrn_reflns_theta_full'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; The theta angle (in degrees) at which the measured reflection
count is close to complete. The fraction of unique reflections
measured out to this angle is given by
_diffrn_measured_fraction_theta_full.
;
data_diffrn_reflns_theta_max
_name '_diffrn_reflns_theta_max'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Maximum theta angle in degrees for the measured intensities.
;
data_diffrn_reflns_theta_min
_name '_diffrn_reflns_theta_min'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Minimum theta angle in degrees for the measured intensities.
;
data_diffrn_reflns_transf_matrix_
loop_ _name '_diffrn_reflns_transf_matrix_11'
'_diffrn_reflns_transf_matrix_12'
'_diffrn_reflns_transf_matrix_13'
'_diffrn_reflns_transf_matrix_21'
'_diffrn_reflns_transf_matrix_22'
'_diffrn_reflns_transf_matrix_23'
'_diffrn_reflns_transf_matrix_31'
'_diffrn_reflns_transf_matrix_32'
'_diffrn_reflns_transf_matrix_33'
_category diffrn_reflns
_type numb
_definition
; Elements of the matrix used to transform the diffraction
reflection indices _diffrn_refln_index_h, *_k, *_l into the
_refln_index_h, *_k, *_l indices.
|11 12 13|
(h k l) diffraction |21 22 23| = (h' k' l')
|31 32 33|
;
#########################
## DIFFRN_REFLNS_CLASS ##
#########################
data_diffrn_reflns_class_[]
_name '_diffrn_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_reflns_class_number
_diffrn_reflns_class_d_res_high
_diffrn_reflns_class_d_res_low
_diffrn_reflns_class_av_R_eq
_diffrn_reflns_class_code
_diffrn_reflns_class_description
1580 0.551 6.136 0.015 'Main'
'm=0; main reflections'
1045 0.551 6.136 0.010
'Sat1' 'm=1; first-order satellites'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
;
data_diffrn_reflns_class_av_R_eq
_name '_diffrn_reflns_class_av_R_eq'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual
[sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
used to calculate the average intensity av(I). The av|del(I)|
term is the average absolute difference between av(I) and the
individual intensities.
;
data_diffrn_reflns_class_av_sgI/I
_name '_diffrn_reflns_class_av_sgI/I'
_category diffrn_reflns_class
_type numb
_related_item '_diffrn_reflns_class_av_uI/I'
_related_function replace
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
data_diffrn_reflns_class_av_uI/I
_name '_diffrn_reflns_class_av_uI/I'
_category diffrn_reflns_class
_type numb
_related_item '_diffrn_reflns_class_av_sgI/I'
_related_function alternate
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
data_diffrn_reflns_class_code
_name '_diffrn_reflns_class_code'
_category diffrn_reflns_class
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class.
;
data_diffrn_reflns_class_description
_name '_diffrn_reflns_class_description'
_category diffrn_reflns_class
_type char
_list yes
_list_reference '_diffrn_reflns_class_code'
loop_ _example 'm=1 first order satellites'
'H0L0 common projection reflections'
_definition
; Description of each reflection class.
;
data_diffrn_reflns_class_d_res_high
_name '_diffrn_reflns_class_d_res_high'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; The smallest value in angstroms of the interplanar
spacings of the reflections in each reflection class.
This is called the highest resolution for this reflection class.
;
data_diffrn_reflns_class_d_res_low
_name '_diffrn_reflns_class_d_res_low'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; The highest value in angstroms of the interplanar
spacings of the reflections in each reflection class.
This is called the lowest resolution for this reflection class.
;
data_diffrn_reflns_class_number
_name '_diffrn_reflns_class_number'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0:
_definition
; The total number of measured intensities for each reflection
class, excluding the systematic absences arising from
centring translations.
;
########################
## DIFFRN_SCALE_GROUP ##
########################
data_diffrn_scale_group_[]
_name '_diffrn_scale_group_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_scale_group_code
_diffrn_scale_group_I_net
1 .86473
2 1.0654
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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
data set.
;
data_diffrn_scale_group_code
_name '_diffrn_scale_group_code'
_category diffrn_scale_group
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_scale_group_code'
loop_ _example 1 2 3 s1 A B c1 c2 c3
_definition
; The code identifying a specific measurement group (e.g. for
multi-film or multi-crystal data). The code must match a
_diffrn_refln_scale_group_code in the reflection list.
;
data_diffrn_scale_group_I_net
_name '_diffrn_scale_group_I_net'
_category diffrn_scale_group
_type numb
_list yes
_list_reference '_diffrn_scale_group_code'
_enumeration_range 0.0:
_definition
; The scale for a specific measurement group which is to be
multiplied with the net intensity to place all intensities
in the _diffrn_refln_ or _refln_ list on a common scale.
;
###################
## DIFFRN_SOURCE ##
###################
data_diffrn_source_[]
_name '_diffrn_source_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_source 'rotating anode X-ray tube'
_diffrn_source_type 'Rigaku RU-200'
_diffrn_source_power 50
_diffrn_source_current 180
_diffrn_source_size '8 mm x 0.4 mm broad focus'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
;
data_diffrn_radiation_source
_name '_diffrn_radiation_source'
_category diffrn_source
_type char
_related_item '_diffrn_source'
_related_function replace
_definition
; The source of radiation.
;
data_diffrn_source
_name '_diffrn_source'
_category diffrn_source
_type char
_related_item '_diffrn_radiation_source'
_related_function alternate
loop_
_example 'sealed X-ray tube'
'nuclear reactor'
'spallation source'
'electron microscope'
'rotating-anode X-ray tube'
'synchrotron'
_definition
; The general class of the source of radiation.
;
data_diffrn_source_current
_name '_diffrn_source_current'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units mA
_units_detail 'milliamperes'
_definition
; The current in milliamperes at which the radiation source was
operated.
;
data_diffrn_source_details
_name '_diffrn_source_details'
_category diffrn_source
_type char
_definition
; A description of special aspects of the source.
;
data_diffrn_source_power
_name '_diffrn_source_power'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units kW
_units_detail 'kilowatts'
_definition
; The power in kilowatts at which the radiation source was
operated.
;
data_diffrn_source_size
_name '_diffrn_source_size'
_category diffrn_source
_type char
loop_
_example '8mm x 0.4 mm fine-focus'
'broad focus'
_definition
; The dimensions of the source as viewed from the sample.
;
data_diffrn_source_take-off_angle
_name '_diffrn_source_take-off_angle'
_category diffrn_source
_type numb
_enumeration_range 0:90
_units degrees
_example 1.53
_definition
; The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
;
data_diffrn_source_target
_name '_diffrn_source_target'
_category diffrn_source
_type char
loop_ _enumeration
H He Li Be B C N O F Ne Na Mg Al Si P S Cl
Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge
As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag
Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm
Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir
Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U
Np Pu Am Cm Bk Cf Es Fm Md No Lr
_definition
; The chemical element symbol for the X-ray target
(usually the anode) used to generate X-rays.
This can also be used for spallation sources.
;
data_diffrn_source_type
_name '_diffrn_source_type'
_category diffrn_source
_type char
loop_
_example 'NSLS beamline X8C'
'Rigaku RU200'
_definition
; The make, model or name of the source of radiation.
;
data_diffrn_source_voltage
_name '_diffrn_source_voltage'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units kV
_units_detail 'kilovolts'
_definition
; The voltage in kilovolts at which the radiation source was
operated.
;
###########################
## DIFFRN_STANDARD_REFLN ##
###########################
data_diffrn_standard_refln_[]
_name '_diffrn_standard_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_standard_refln_index_h
_diffrn_standard_refln_index_k
_diffrn_standard_refln_index_l
3 2 4 1 9 1 3 0 10
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of the diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
;
data_diffrn_standard_refln_code
_name '_diffrn_standard_refln_code'
_category diffrn_standard_refln
_type char
_list yes
_list_link_child '_diffrn_refln_standard_code'
_list_reference '_diffrn_standard_refln_index_'
loop_ _example 1 2 3 s1 A B
_definition
; The code identifying a reflection measured as a standard
reflection with the indices _diffrn_standard_refln_index_.
This is the same code as the _diffrn_refln_standard_code in
the _diffrn_refln_ list.
;
data_diffrn_standard_refln_index_
loop_ _name '_diffrn_standard_refln_index_h'
'_diffrn_standard_refln_index_k'
'_diffrn_standard_refln_index_l'
_category diffrn_standard_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of standard reflections used in the diffraction
measurement process.
;
######################
## DIFFRN_STANDARDS ##
######################
data_diffrn_standards_[]
_name '_diffrn_standards_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_standards_number 3
_diffrn_standards_interval_time 120
_diffrn_standards_decay_% 0
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
;
data_diffrn_standards_decay_%
_name '_diffrn_standards_decay_%'
_category diffrn_standards
_type numb
_type_conditions esd
_enumeration_range :100
_definition
; The percentage decrease in the mean of the intensities
for the set of standard reflections from the start of the
measurement process to the end. This value usually
affords a measure of the overall decay in crystal quality
during the diffraction measurement process. Negative values
are used in exceptional instances where the final intensities
are greater than the initial ones.
;
data_diffrn_standards_interval_
loop_ _name '_diffrn_standards_interval_count'
'_diffrn_standards_interval_time'
_category diffrn_standards
_type numb
_enumeration_range 0:
_definition
; The number of reflection intensities, or the time in minutes,
between the measurement of standard reflection intensities.
;
data_diffrn_standards_number
_name '_diffrn_standards_number'
_category diffrn_standards
_type numb
_enumeration_range 0:
_definition
; The number of unique standard reflections used during the
measurement of the diffraction intensities.
;
data_diffrn_standards_scale_sigma
_name '_diffrn_standards_scale_sigma'
_category diffrn_standards
_type numb
_related_item '_diffrn_standards_scale_u'
_related_function replace
_enumeration_range 0.0:
_definition
; The standard uncertainty (e.s.d.) of the individual mean
standard scales applied to the intensity data.
;
data_diffrn_standards_scale_u
_name '_diffrn_standards_scale_u'
_category diffrn_standards
_type numb
_related_item '_diffrn_standards_scale_sigma'
_related_function alternate
_enumeration_range 0.0:
_definition
; The standard uncertainty of the individual mean
standard scales applied to the intensity data.
;
###########
## EXPTL ##
###########
data_exptl_[]
_name '_exptl_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_exptl_absorpt_coefficient_mu 0.962
_exptl_absorpt_correction_type psi-scan
_exptl_absorpt_process_details
'North, Phillips & Mathews (1968)'
_exptl_absorpt_correction_T_min 0.929
_exptl_absorpt_correction_T_max 0.997
;
;
Example 1 - based on a paper by Steiner [Acta Cryst. (1996), C52,
2554-2556].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
;
data_exptl_absorpt_coefficient_mu
_name '_exptl_absorpt_coefficient_mu'
_category exptl
_type numb
_enumeration_range 0.0:
_units mm^-1^
_units_detail 'reciprocal millimetres'
_definition
; The absorption coefficient mu in reciprocal millimetres
calculated from the atomic content of the cell, the density and
the radiation wavelength.
;
data_exptl_absorpt_correction_T_
loop_ _name '_exptl_absorpt_correction_T_max'
'_exptl_absorpt_correction_T_min'
_category exptl
_type numb
_enumeration_range 0.0:1.0
_definition
; The maximum and minimum transmission factors for the crystal
and radiation. These factors are also referred to as the
absorption correction A or 1/A*.
;
data_exptl_absorpt_correction_type
_name '_exptl_absorpt_correction_type'
_category exptl
_type char
loop_ _enumeration
_enumeration_detail analytical 'analytical from crystal shape'
cylinder 'cylindrical'
empirical 'empirical from intensities'
gaussian 'Gaussian from crystal shape'
integration 'integration from crystal shape'
multi-scan 'symmetry-related measurements'
none 'no absorption correction applied'
numerical 'numerical from crystal shape'
psi-scan 'psi-scan corrections'
refdelf 'refined from delta-F'
sphere 'spherical'
_definition
; The absorption-correction type and method. The value 'empirical'
should NOT be used unless more detailed information is not
available.
;
data_exptl_absorpt_process_details
_name '_exptl_absorpt_process_details'
_category exptl
_type char
loop_ _example 'Tompa analytical'
'MolEN (Fair, 1990)'
'(North, Phillips & Mathews, 1968)'
_definition
; Description of the absorption process applied to the
intensities. A literature reference should be supplied
for psi-scan techniques.
;
data_exptl_crystals_number
_name '_exptl_crystals_number'
_category exptl
_type numb
_enumeration_range 1:
_definition
; The total number of crystals used for the measurement of
intensities.
;
data_exptl_special_details
_name '_exptl_special_details'
_category exptl
_type char
_definition
; Any special information about the experimental work prior to the
intensity measurements. See also _exptl_crystal_preparation.
;
###################
## EXPTL_CRYSTAL ##
###################
data_exptl_crystal_[]
_name '_exptl_crystal_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_exptl_crystal_description prism
_exptl_crystal_colour colourless
_exptl_crystal_size_max 0.32
_exptl_crystal_size_mid 0.27
_exptl_crystal_size_min 0.10
_exptl_crystal_density_diffrn 1.146
_exptl_crystal_density_meas ?
_exptl_crystal_density_method 'not measured'
_exptl_crystal_F_000 656
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _exptl_crystal_density_meas_gt 2.5
_exptl_crystal_density_meas_lt 5.0
;
;
Example 2 - using separate items to define upper and lower
limits for a value.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _exptl_crystal_density_meas_temp_lt 300
;
;
Example 3 - here the density was measured at some
unspecified temperature below room temperature.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL_CRYSTAL category record details about
experimental measurements on the crystal or crystals used,
such as shape, size or density.
;
data_exptl_crystal_colour
_name '_exptl_crystal_colour'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_
_related_item
_related_function '_exptl_crystal_colour_lustre' alternate
'_exptl_crystal_colour_modifier' alternate
'_exptl_crystal_colour_primary' alternate
_example 'dark green'
_definition
; The colour of the crystal.
;
data_exptl_crystal_colour_lustre
_name '_exptl_crystal_colour_lustre'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration metallic
dull
clear
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_colour_modifier
_name '_exptl_crystal_colour_modifier'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_colour_primary
_name '_exptl_crystal_colour_primary'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_density_diffrn
_name '_exptl_crystal_density_diffrn'
_category exptl_crystal
_type numb
_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 the crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
;
data_exptl_crystal_density_meas
_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
cubic centimetre).
;
data_exptl_crystal_density_meas_gt
_name '_exptl_crystal_density_meas_gt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_related_item '_exptl_crystal_density_meas'
_related_function alternate
loop_ _example
_example_detail
2.5
; lower limit for the density (only the range
within which the density lies was given in the
original paper)
;
_definition
; The value above which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal_density_meas_gt and
_exptl_crystal_density_meas_lt should not be used to
report new experimental work, for which
_exptl_crystal_density_meas should be used. These items
are intended for use in reporting information in
existing databases and archives which would be misleading if
reported under _exptl_crystal_density_meas.
;
data_exptl_crystal_density_meas_lt
_name '_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_related_item '_exptl_crystal_density_meas'
_related_function alternate
loop_ _example
_example_detail
1.0
'specimen floats in water'
5.0
; upper limit for the density (only the range
within which the density lies was given in the
original paper)
;
_definition
; The value below which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal_density_meas_gt and
_exptl_crystal_density_meas_lt should not be used to
report new experimental work, for which
_exptl_crystal_density_meas should be used. These items
are intended for use in reporting information in
existing databases and archives which would be misleading if
reported under _exptl_crystal_density_meas.
;
data_exptl_crystal_density_meas_temp
_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 kelvin
_definition
; Temperature in kelvins at which _exptl_crystal_density_meas
was determined.
;
data_exptl_crystal_density_meas_temp_gt
_name '_exptl_crystal_density_meas_temp_gt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_exptl_crystal_density_meas_temp'
_related_function alternate
_definition
; Temperature in kelvins above which _exptl_crystal_density_meas
was determined. _exptl_crystal_density_meas_temp_gt and
_exptl_crystal_density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases
or archives which would be misleading if reported under
_exptl_crystal_density_meas_temp.
;
data_exptl_crystal_density_meas_temp_lt
_name '_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_exptl_crystal_density_meas_temp'
_related_function alternate
loop_ _example
_example_detail
300
; The density was measured at some unspecified
temperature below room temperature.
;
_definition
; Temperature in kelvins below which _exptl_crystal_density_meas
was determined. _exptl_crystal_density_meas_temp_gt and
_exptl_crystal_density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases
or archives which would be misleading if reported under
_exptl_crystal_density_meas_temp.
;
data_exptl_crystal_density_method
_name '_exptl_crystal_density_method'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _example 'flotation in aqueous KI'
'not measured'
'Berman density torsion balance'
_definition
; The method used to measure _exptl_crystal_density_meas.
;
data_exptl_crystal_description
_name '_exptl_crystal_description'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; A description of the quality and habit of the crystal.
The crystal dimensions should not normally be reported here;
use instead _exptl_crystal_size_ for the gross dimensions of
the crystal and _exptl_crystal_face_ to describe the
relationship between individual faces.
;
data_exptl_crystal_F_000
_name '_exptl_crystal_F_000'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_definition
; The effective number of electrons in the crystal unit cell
contributing to F(000). This may contain dispersion contributions
and is calculated as
F(000) = [ (sum f~r~)^2^ + (sum 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
the sum is taken over each atom in the unit cell
;
data_exptl_crystal_id
_name '_exptl_crystal_id'
_category exptl_crystal
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_diffrn_refln_crystal_id'
'_refln_crystal_id'
_definition
; Code identifying each crystal if multiple crystals are used. It
is used to link with _diffrn_refln_crystal_id in the intensity
measurements and with _refln_crystal_id in the _refln_ list.
;
data_exptl_crystal_preparation
_name '_exptl_crystal_preparation'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_example 'mounted in an argon-filled quartz capillary'
_definition
; Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the intensity measurements.
;
data_exptl_crystal_pressure_history
_name '_exptl_crystal_pressure_history'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; Relevant details concerning the pressure history of the
sample.
;
data_exptl_crystal_recrystallization_method
_name '_exptl_crystal_recrystallization_method'
_category exptl_crystal
_type char
_definition
; Describes the method used to recrystallize the sample.
Sufficient details should be given for the procedure to be
repeated. The temperature or temperatures should be given as
well as details of the solvent, flux or carrier gas with
concentrations or pressures and ambient atmosphere.
;
data_exptl_crystal_size_
loop_ _name '_exptl_crystal_size_length'
'_exptl_crystal_size_max'
'_exptl_crystal_size_mid'
'_exptl_crystal_size_min'
'_exptl_crystal_size_rad'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; The maximum, medial and minimum dimensions in millimetres of
the crystal. If the crystal is a sphere, then the *_rad item is
its radius. If the crystal is a cylinder, then the *_rad item
is its radius and the *_length item is its length. These may
appear in a list with _exptl_crystal_id if multiple crystals
are used in the experiment.
;
data_exptl_crystal_thermal_history
_name '_exptl_crystal_thermal_history'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; Relevant details concerning the thermal history of the
sample.
;
########################
## EXPTL_CRYSTAL_FACE ##
########################
data_exptl_crystal_face_[]
_name '_exptl_crystal_face_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_exptl_crystal_face_index_h
_exptl_crystal_face_index_k
_exptl_crystal_face_index_l
_exptl_crystal_face_perp_dist
0 -1 -2 .18274
1 0 -2 .17571
-1 1 -2 .17845
-2 1 0 .21010
-1 0 2 .18849
1 -1 2 .20605
2 -1 0 .24680
-1 2 0 .19688
0 1 2 .15206
;
;
Example 1 - based on structure PAWD2 of Vittal & Dean [Acta
Cryst. (1996), C52, 1180-1182].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
;
data_exptl_crystal_face_diffr_
loop_ _name '_exptl_crystal_face_diffr_chi'
'_exptl_crystal_face_diffr_kappa'
'_exptl_crystal_face_diffr_phi'
'_exptl_crystal_face_diffr_psi'
_category exptl_crystal_face
_type numb
_list yes
_list_reference '_exptl_crystal_face_index_'
_units deg
_units_detail 'degrees'
_definition
; The goniometer angle settings in degrees when the perpendicular
to the specified crystal face is aligned along a specified
direction (e.g. the bisector of the incident and reflected beams
in an optical goniometer).
;
data_exptl_crystal_face_index_
loop_ _name '_exptl_crystal_face_index_h'
'_exptl_crystal_face_index_k'
'_exptl_crystal_face_index_l'
_category exptl_crystal_face
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of the crystal face associated with the value
_exptl_crystal_face_perp_dist.
;
data_exptl_crystal_face_perp_dist
_name '_exptl_crystal_face_perp_dist'
_category exptl_crystal_face
_type numb
_list yes
_list_reference '_exptl_crystal_face_index_'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; The perpendicular distance in millimetres from the face to the
centre of rotation of the crystal.
;
##########
## GEOM ##
##########
data_geom_[]
_name '_geom_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_geom_special_details
; All esds (except the esd in the dihedral angle between
two l.s. planes) are estimated using the full covariance
matrix. The cell esds are taken into account individually
in the estimation of esds in distances, angles and
torsion angles; correlations between esds in cell
parameters are only used when they are defined by crystal
symmetry. An approximate (isotropic) treatment of cell
esds is used for estimating esds involving l.s. planes.
;
;
;
Example 1 - based on data set bagan of Yamane & DiSalvo [Acta
Cryst. (1996), C52, 760-761].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION)
categories record details about the molecular and crystal
geometry as calculated from the ATOM,
CELL and SYMMETRY data.
Geometry data are usually redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they serve the dual purposes of providing a
check on the correctness of both sets of data and of enabling
the most important geometric data to be identified for
publication by setting the appropriate publication flag.
;
data_geom_special_details
_name '_geom_special_details'
_category geom
_type char
_definition
; The description of geometrical information not covered by the
existing data names in the geometry categories, such as
least-squares planes.
;
################
## GEOM_ANGLE ##
################
data_geom_angle_[]
_name '_geom_angle_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_2
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C2 O1 C5 111.6(2) 1_555 1_555 1_555 yes
O1 C2 C3 110.9(2) 1_555 1_555 1_555 yes
O1 C2 O21 122.2(3) 1_555 1_555 1_555 yes
C3 C2 O21 127.0(3) 1_555 1_555 1_555 yes
C2 C3 N4 101.3(2) 1_555 1_555 1_555 yes
C2 C3 C31 111.3(2) 1_555 1_555 1_555 yes
C2 C3 H3 107(1) 1_555 1_555 1_555 no
N4 C3 C31 116.7(2) 1_555 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_ANGLE category record details about the
bond angles as calculated from the ATOM,
CELL and SYMMETRY data.
;
data_geom_angle
_name '_geom_angle'
_category geom_angle
_type numb
_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. The site at *_2
is at the apex of the angle.
;
data_geom_angle_atom_site_label_
loop_ _name '_geom_angle_atom_site_label_1'
'_geom_angle_atom_site_label_2'
'_geom_angle_atom_site_label_3'
_category geom_angle
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of the three atom sites which define the angle
given by _geom_angle. These must match labels specified as
_atom_site_label in the atom list. Label 2 identifies the site at
the apex of the angle.
;
data_geom_angle_publ_flag
_name '_geom_angle_publ_flag'
_category geom_angle
_type char
_list yes
_list_reference '_geom_angle_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the angle is referred to in a
publication or should be placed in a table of significant
angles.
;
data_geom_angle_site_symmetry_
loop_ _name '_geom_angle_site_symmetry_1'
'_geom_angle_site_symmetry_2'
'_geom_angle_site_symmetry_3'
_category geom_angle
_type char
_list yes
_list_reference '_geom_angle_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
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
_space_group_symop_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.
;
###############
## GEOM_BOND ##
###############
data_geom_bond_[]
_name '_geom_bond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
O1 C2 1.342(4) 1_555 1_555 yes
O1 C5 1.439(3) 1_555 1_555 yes
C2 C3 1.512(4) 1_555 1_555 yes
C2 O21 1.199(4) 1_555 1_555 yes
C3 N4 1.465(3) 1_555 1_555 yes
C3 C31 1.537(4) 1_555 1_555 yes
C3 H3 1.00(3) 1_555 1_555 no
N4 C5 1.472(3) 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_BOND category record details about
bonds as calculated from the ATOM, CELL
and SYMMETRY data.
;
data_geom_bond_atom_site_label_
loop_ _name '_geom_bond_atom_site_label_1'
'_geom_bond_atom_site_label_2'
_category geom_bond
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of two atom sites that form a bond. These must match
labels specified as _atom_site_label in the atom list.
;
data_geom_bond_distance
_name '_geom_bond_distance'
_category geom_bond
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_bond_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The intramolecular bond distance in angstroms.
;
data_geom_bond_publ_flag
_name '_geom_bond_publ_flag'
_category geom_bond
_type char
_list yes
_list_reference '_geom_bond_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the bond distance is referred to in a
publication or should be placed in a list of significant bond
distances.
;
data_geom_bond_site_symmetry_
loop_ _name '_geom_bond_site_symmetry_1'
'_geom_bond_site_symmetry_2'
_category geom_bond
_type char
_list yes
_list_reference '_geom_bond_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
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
_space_group_symop_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.
;
data_geom_bond_valence
_name '_geom_bond_valence'
_category geom_bond
_type numb
_list yes
_list_reference '_geom_bond_atom_site_label_'
_definition
; The bond valence calculated from _geom_bond_distance.
;
##################
## GEOM_CONTACT ##
##################
data_geom_contact_[]
_name '_geom_contact_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_contact_atom_site_label_1
_geom_contact_atom_site_label_2
_geom_contact_distance
_geom_contact_site_symmetry_1
_geom_contact_site_symmetry_2
_geom_contact_publ_flag
O(1) O(2) 2.735(3) . . yes
H(O1) O(2) 1.82 . . no
;
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_CONTACT category record details about
interatomic contacts as calculated from the
ATOM, CELL and SYMMETRY data.
;
data_geom_contact_atom_site_label_
loop_ _name '_geom_contact_atom_site_label_1'
'_geom_contact_atom_site_label_2'
_category geom_contact
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of two atom sites that are within contact distance.
The labels must match _atom_site_label codes in the atom list.
;
data_geom_contact_distance
_name '_geom_contact_distance'
_category geom_contact
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_contact_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The interatomic contact distance in angstroms.
;
data_geom_contact_publ_flag
_name '_geom_contact_publ_flag'
_category geom_contact
_type char
_list yes
_list_reference '_geom_contact_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include distance in special list'
n 'abbreviation for "no"'
yes 'do include distance in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
;
data_geom_contact_site_symmetry_
loop_ _name '_geom_contact_site_symmetry_1'
'_geom_contact_site_symmetry_2'
_category geom_contact
_type char
_list yes
_list_reference '_geom_contact_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
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
_space_group_symop_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.
;
################
## GEOM_HBOND ##
################
data_geom_hbond_[]
_name '_geom_hbond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_publ_flag
N6 HN6 OW 0.888(8) 1.921(12) 2.801(8) 169.6(8) yes
OW HO2 O7 0.917(6) 1.923(12) 2.793(8) 153.5(8) yes
OW HO1 N10 0.894(8) 1.886(11) 2.842(8) 179.7(9) yes
;
;
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the ATOM,
CELL and SYMMETRY data.
;
data_geom_hbond_angle_DHA
_name '_geom_hbond_angle_DHA'
_category geom_hbond
_type numb
_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. The site at *_H
(the hydrogen atom participating in the interaction) is at
the apex of the angle.
;
data_geom_hbond_atom_site_label_
loop_ _name '_geom_hbond_atom_site_label_D'
'_geom_hbond_atom_site_label_H'
'_geom_hbond_atom_site_label_A'
_category geom_hbond
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of three atom sites (respectively, the donor atom,
hydrogen atom and acceptor atom) participating in a hydrogen
bond. These must match labels specified as _atom_site_label
in the atom list.
;
data_geom_hbond_distance_
loop_ _name '_geom_hbond_distance_DH'
'_geom_hbond_distance_HA'
'_geom_hbond_distance_DA'
_category geom_hbond
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_hbond_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Distances in angstroms between the donor and hydrogen (*_DH),
hydrogen and acceptor (*_HA) and donor and acceptor (*_DA)
sites in a hydrogen bond.
;
data_geom_hbond_publ_flag
_name '_geom_hbond_publ_flag'
_category geom_hbond
_type char
_list yes
_list_reference '_geom_hbond_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the hydrogen-bond information
is referred to in a publication or should be placed in a
table of significant hydrogen-bond geometry.
;
data_geom_hbond_site_symmetry_
loop_ _name '_geom_hbond_site_symmetry_D'
'_geom_hbond_site_symmetry_H'
'_geom_hbond_site_symmetry_A'
_category geom_hbond
_type char
_list yes
_list_reference '_geom_hbond_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
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
_space_group_symop_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.
;
##################
## GEOM_TORSION ##
##################
data_geom_torsion_[]
_name '_geom_torsion_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
C(9) O(2) C(7) C(2) 71.8(2) . . . . yes
C(7) O(2) C(9) C(10) -168.0(3) . . . 2_666 yes
C(10) O(3) C(8) C(6) -167.7(3) . . . . yes
C(8) O(3) C(10) C(9) -69.7(2) . . . 2_666 yes
O(1) C(1) C(2) C(3) -179.5(4) . . . . no
O(1) C(1) C(2) C(7) -0.6(1) . . . . no
;
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_TORSION category record details about
interatomic torsion angles as calculated from
the ATOM, CELL and SYMMETRY data.
;
data_geom_torsion
_name '_geom_torsion'
_category geom_torsion
_type numb
_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
must match labels specified as _atom_site_label in the atom list.
The torsion-angle definition should be that of Klyne and Prelog.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
data_geom_torsion_atom_site_label_
loop_ _name '_geom_torsion_atom_site_label_1'
'_geom_torsion_atom_site_label_2'
'_geom_torsion_atom_site_label_3'
'_geom_torsion_atom_site_label_4'
_category geom_torsion
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of the four atom sites which define the torsion angle
specified by _geom_torsion. These must match codes specified as
_atom_site_label in the atom list. The torsion-angle definition
should be that of Klyne and Prelog. The vector direction
*_label_2 to *_label_3 is the viewing direction, and the torsion
angle is the angle of twist required to superimpose the
projection of the vector between site 2 and site 1 onto the
projection of the vector between site 3 and site 4. Clockwise
torsions are positive, anticlockwise torsions are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
data_geom_torsion_publ_flag
_name '_geom_torsion_publ_flag'
_category geom_torsion
_type char
_list yes
_list_reference '_geom_torsion_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the torsion angle is referred to in a
publication or should be placed in a table of significant
torsion angles.
;
data_geom_torsion_site_symmetry_
loop_ _name '_geom_torsion_site_symmetry_1'
'_geom_torsion_site_symmetry_2'
'_geom_torsion_site_symmetry_3'
'_geom_torsion_site_symmetry_4'
_category geom_torsion
_type char
_list yes
_list_reference '_geom_torsion_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
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
_space_group_symop_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.
;
#############
## JOURNAL ##
#############
data_journal_[]
_name '_journal_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_journal_date_recd_electronic 91-04-15
_journal_date_from_coeditor 91-04-18
_journal_date_accepted 91-04-18
_journal_date_printers_first 91-08-07
_journal_date_proofs_out 91-08-07
_journal_coeditor_code HL0007
_journal_techeditor_code C910963
_journal_coden_ASTM ACSCEE
_journal_name_full 'Acta Crystallographica Section C'
_journal_year 1991
_journal_volume 47
_journal_issue NOV91
_journal_page_first 2276
_journal_page_last 2277
;
;
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith
& Tozer (1991). Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the JOURNAL category record details about the
book-keeping by the journal staff when processing
a CIF submitted for publication.
The creator of a CIF will not normally specify these data items.
The data names are not defined in the dictionary because they are
for journal use only.
;
data_journal_
loop_ _name '_journal_coden_ASTM'
'_journal_coden_Cambridge'
'_journal_coeditor_address'
'_journal_coeditor_code'
'_journal_coeditor_email'
'_journal_coeditor_fax'
'_journal_coeditor_name'
'_journal_coeditor_notes'
'_journal_coeditor_phone'
'_journal_data_validation_number'
'_journal_date_accepted'
'_journal_date_from_coeditor'
'_journal_date_to_coeditor'
'_journal_date_printers_final'
'_journal_date_printers_first'
'_journal_date_proofs_in'
'_journal_date_proofs_out'
'_journal_date_recd_copyright'
'_journal_date_recd_electronic'
'_journal_date_recd_hard_copy'
'_journal_issue'
'_journal_language'
'_journal_name_full'
'_journal_page_first'
'_journal_page_last'
'_journal_paper_category'
'_journal_suppl_publ_number'
'_journal_suppl_publ_pages'
'_journal_techeditor_address'
'_journal_techeditor_code'
'_journal_techeditor_email'
'_journal_techeditor_fax'
'_journal_techeditor_name'
'_journal_techeditor_notes'
'_journal_techeditor_phone'
'_journal_volume'
'_journal_year'
_category journal
_type char
_definition
; 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
[Acta Cryst. (1994), C50, 2067-2069].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the JOURNAL_INDEX category are used to list
terms used to generate the journal indexes.
The creator of a CIF will not normally 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 the journal staff.
;
##########
## PUBL ##
##########
data_publ_[]
_name '_publ_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _publ_section_title
; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-
1,3-oxazolidin-5-one
;
_publ_section_abstract
; The oxazolidinone ring is a shallow envelope
conformation with the tert-butyl and iso-butyl groups
occupying trans-positions with respect to the ring. The
angles at the N atom sum to 356.2\%, indicating a very
small degree of pyramidalization at this atom. This is
consistent with electron delocalization between the N
atom and the carbonyl centre [N-C=O = 1.374(3)\%A].
;
;
;
Example 1 - based on Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _publ_section_title
; Hemiasterlin methyl ester
;
_publ_section_title_footnote
; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl-
2-methylamino-3-(N-methylbenzo[b]pyrrol-
3-yl)butanamido]-3,3-dimethyl-N-methyl-
butanamido}-2-hexenoate.
;
;
;
Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick,
Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL category are used when submitting a
manuscript for publication. They refer either to the paper as
a 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 text
of other submissions. Typically, each journal will
supply a list of the specific items it requires in its Notes
for Authors.
;
data_publ_contact_author
_name '_publ_contact_author'
_category publ
_type char
loop_
_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
data block. This is the person contacted by the journal
editorial staff. It is preferable to use the separate data items
_publ_contact_author_name and _publ_contact_author_address.
;
data_publ_contact_author_address
_name '_publ_contact_author_address'
_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
data block. This is the person contacted by the journal
editorial staff.
;
data_publ_contact_author_email
_name '_publ_contact_author_email'
_category publ
_type char
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; E-mail address in a form recognizable to international networks.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
data_publ_contact_author_fax
_name '_publ_contact_author_fax'
_category publ
_type char
loop_
_example '12(34)9477334'
'12()349477334'
_definition
; Facsimile telephone number of the author submitting the
manuscript and data block.
The recommended style is the international dialing
prefix, followed by the area code in parentheses, followed by
the local number with no spaces. The earlier convention of
including the international dialing prefix in parentheses is
no longer recommended.
;
data_publ_contact_author_id_iucr
_name '_publ_contact_author_id_iucr'
_category publ
_type char
_example 2985
_definition
; Identifier in the IUCr contact database of the author
submitting the manuscript and data block. This identifier may
be available from the World Directory of Crystallographers
(http://wdc.iucr.org).
;
data_publ_contact_author_name
_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
editorial staff.
;
data_publ_contact_author_phone
_name '_publ_contact_author_phone'
_category publ
_type char
loop_
_example '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
_definition
; Telephone number of the author submitting the manuscript and
data block.
The recommended style is the international dialing
prefix, followed by 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 prefix in parentheses is no longer
recommended.
;
data_publ_contact_letter
_name '_publ_contact_letter'
_category publ
_type char
_definition
; A letter submitted to the journal editor by the contact author.
;
data_publ_manuscript_creation
_name '_publ_manuscript_creation'
_category publ
_type char
_example 'Tex file created by FrameMaker on a Sun 3/280'
_definition
; A description of the word-processor package and computer used to
create the word-processed manuscript stored as
_publ_manuscript_processed.
;
data_publ_manuscript_processed
_name '_publ_manuscript_processed'
_category publ
_type char
_definition
; The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item _publ_manuscript_creation.
;
data_publ_manuscript_text
_name '_publ_manuscript_text'
_category publ
_type char
_definition
; The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
;
data_publ_requested_category
_name '_publ_requested_category'
_category publ
_type char
loop_ _enumeration
_enumeration_detail
FA 'Full article'
FI 'Full submission - inorganic (Acta C)'
FO 'Full submission - organic (Acta C)'
FM 'Full submission - metal-organic (Acta C)'
CI 'CIF-access paper - inorganic (Acta C) (no longer in use)'
CO 'CIF-access paper - organic (Acta C) (no longer in use)'
CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)'
EI 'Electronic submission - inorganic (Acta E)'
EO 'Electronic submission - organic (Acta E)'
EM 'Electronic submission - metal-organic (Acta E)'
AD 'Addenda and Errata (Acta C, Acta E)'
SC 'Short communication'
_enumeration_default FA
_definition
; The category of paper submitted. For submission to Acta
Crystallographica Section C or Acta Crystallographica
Section E, ONLY those codes indicated for use with those
journals should be used.
;
data_publ_requested_coeditor_name
_name '_publ_requested_coeditor_name'
_category publ
_type char
_definition
; The name of the co-editor whom the authors would like to
handle the submitted manuscript.
;
data_publ_requested_journal
_name '_publ_requested_journal'
_category publ
_type char
_definition
; The name of the journal to which the manuscript is being
submitted.
;
data_publ_section_
loop_ _name '_publ_section_title'
'_publ_section_title_footnote'
'_publ_section_synopsis'
'_publ_section_abstract'
'_publ_section_comment'
'_publ_section_introduction'
'_publ_section_experimental'
'_publ_section_exptl_prep'
'_publ_section_exptl_refinement'
'_publ_section_exptl_solution'
'_publ_section_discussion'
'_publ_section_acknowledgements'
'_publ_section_references'
'_publ_section_figure_captions'
'_publ_section_table_legends'
_category publ
_type char
_definition
; The sections of a manuscript if submitted in parts. As
an alternative, see _publ_manuscript_text and
_publ_manuscript_processed.
The _publ_section_exptl_prep, _publ_section_exptl_refinement
and _publ_section_exptl_solution items are preferred for
separating the chemical preparation, refinement and structure
solution aspects of the experimental description.
;
#################
## PUBL_AUTHOR ##
#################
data_publ_author_[]
_name '_publ_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_author_name
_publ_author_address
'Willis, Anthony C.'
; Research School of Chemistry
Australian National University
GPO Box 4
Canberra, ACT
Australia 2601
;
;
;
Example 1 - based on Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
;
data_publ_author_address
_name '_publ_author_address'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The address of a publication author. If there is more than one
author, this will be looped with _publ_author_name.
;
data_publ_author_footnote
_name '_publ_author_footnote'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
loop_ _example 'On leave from U. Western Australia'
'Also at Department of Biophysics'
_definition
; A footnote accompanying an author's name in the list of authors
of a paper. Typically indicates sabbatical address, additional
affiliations or date of decease.
;
data_publ_author_email
_name '_publ_author_email'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; The e-mail address of a publication author. If there is more
than one author, this will be looped with _publ_author_name.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
data_publ_author_id_iucr
_name '_publ_author_id_iucr'
_category publ_author
_type char
_list both
_example 2985
_definition
; Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
;
data_publ_author_name
_name '_publ_author_name'
_category publ_author
_type char
_list both
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of a publication author. If there are multiple authors,
this will be looped with _publ_author_address. The family
name(s), followed by a comma and including any dynastic
components, precedes the first names or initials.
;
###############
## PUBL_BODY ##
###############
data_publ_body_[]
_name '_publ_body_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_body_element
_publ_body_label
_publ_body_title
_publ_body_format
_publ_body_contents
section 1 Introduction cif
; X-ray diffraction from a crystalline material provides
information on the thermally and spatially averaged
electron density in the crystal...
;
section 2 Theory tex
; In the rigid-atom approximation, the dynamic electron
density of an atom is described by the convolution
product of the static atomic density and a probability
density function,
$\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$
;
;
;
Example 1 - based on a paper by R. Restori & D. Schwarzenbach
[Acta Cryst. (1996), A52, 369-378].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_body_element
_publ_body_label
_publ_body_title
_publ_body_contents
section 3
; The two-channel method for retrieval of the deformation
electron density
;
.
subsection 3.1 'The two-channel entropy S[\D\r(r)]'
; As the wide dynamic range involved in the total electron
density...
;
subsection 3.2
'Uniform vs informative prior model densities' .
subsubsection 3.2.1 'Use of uniform models'
; Straightforward algebra leads to expressions analogous
to...
;
;
;
Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens
[Acta Cryst. (1996), A52, 397-407].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL_BODY category permit the labelling of
different text sections within the body of a 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
_name '_publ_body_contents'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
_definition
; A text section of a paper.
;
data_publ_body_element
_name '_publ_body_element'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
loop_ _enumeration
section
subsection
subsubsection
appendix
footnote
_definition
; The functional role of the associated text section.
;
data_publ_body_format
_name '_publ_body_format'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
loop_ _enumeration
_enumeration_detail
ascii 'no coding for special symbols'
cif 'CIF convention'
latex 'LaTeX'
rtf 'Rich Text Format'
sgml 'SGML (ISO 8879)'
tex 'TeX'
troff 'troff or nroff'
_enumeration_default cif
_definition
; Code indicating the appropriate typesetting conventions
for accented characters and special symbols in the text
section.
;
data_publ_body_label
_name '_publ_body_label'
_category publ_body
_type char
_list yes
_list_mandatory yes
_list_uniqueness '_publ_body_element'
loop_ _example 1 1.1 2.1.3
_definition
; Code identifying the section of text. The combination of this
with _publ_body_element must be unique.
;
data_publ_body_title
_name '_publ_body_title'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
_definition
; Title of the associated section of text.
;
##########################
## PUBL_MANUSCRIPT_INCL ##
##########################
data_publ_manuscript_incl_[]
_name '_publ_manuscript_incl_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_manuscript_incl_extra_item
_publ_manuscript_incl_extra_info
_publ_manuscript_incl_extra_defn
#
# Include Hydrogen Bonding Geometry Description
# =============================================
# Name explanation standard?
# ---- ----------- ---------
'_geom_hbond_atom_site_label_D' 'H-bond donor' yes
'_geom_hbond_atom_site_label_H' 'H-bond hydrogen' yes
'_geom_hbond_atom_site_label_A' 'H-bond acceptor' yes
'_geom_hbond_distance_DH' 'H-bond D-H' yes
'_geom_hbond_distance_HA' 'H-bond H...A' yes
'_geom_hbond_distance_DA' 'H-bond D...A' yes
'_geom_hbond_angle_DHA' 'H-bond D-H...A' yes
;
;
Example 1 - directive to include a hydrogen-bonding table, including
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
used by the 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'
n 'abbreviation for "no"'
yes 'a standard CIF data name'
y 'abbreviation for "yes"'
_enumeration_default yes
_definition
; Flags whether the corresponding data item marked for inclusion
in a journal request list is a standard CIF definition or not.
;
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 are 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 ##
############
data_refine_[]
_name '_refine_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_refine_special_details sfls:_F_calc_weight_full_matrix
_refine_ls_structure_factor_coef F
_refine_ls_matrix_type full
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details 'w=1/(u^2^(F)+0.0004F^2^)'
_refine_ls_hydrogen_treatment refxyz
_refine_ls_extinction_method Zachariasen
_refine_ls_extinction_coef 3514(42)
_refine_ls_extinction_expression
; Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
;
_refine_ls_abs_structure_details
; The absolute configuration was assigned to agree with that
of its precursor l-leucine at the chiral centre C3.
;
_refine_ls_number_reflns 1408
_refine_ls_number_parameters 272
_refine_ls_number_restraints 0
_refine_ls_number_constraints 0
_refine_ls_R_factor_all .038
_refine_ls_R_factor_gt .034
_refine_ls_wR_factor_all .044
_refine_ls_wR_factor_gt .042
_refine_ls_goodness_of_fit_all 1.462
_refine_ls_goodness_of_fit_gt 1.515
_refine_ls_shift/su_max .535
_refine_ls_shift/su_mean .044
_refine_diff_density_min -.108
_refine_diff_density_max .131
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFINE category record details about the
structure-refinement parameters.
;
data_refine_diff_density_
loop_ _name '_refine_diff_density_max'
'_refine_diff_density_min'
'_refine_diff_density_rms'
_category refine
_type numb
_type_conditions esd
_units e_A^-3^
_units_detail 'electrons per cubic angstrom'
_definition
; The largest and smallest values and the root-mean-square
deviation, in electrons per angstrom cubed, of the final
difference electron density. The *_rms value is measured with
respect to the arithmetic mean density and is derived from
summations over each grid point in the asymmetric unit of
the cell. This quantity is useful for assessing the
significance of *_min and *_max values, and also for
defining suitable contour levels.
;
data_refine_ls_abs_structure_details
_name '_refine_ls_abs_structure_details'
_category refine
_type char
_definition
; The nature of the absolute structure and how it was determined.
;
data_refine_ls_abs_structure_Flack
_name '_refine_ls_abs_structure_Flack'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_definition
; The measure of absolute structure as defined by Flack (1983).
For centrosymmetric structures, the only permitted value, if the
data name is present, is 'inapplicable', represented by '.' .
For noncentrosymmetric structures, the value must lie in the
99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a
standard uncertainty (e.s.d.) u must be supplied. The
_enumeration_range of 0.0:1.0 is correctly interpreted as
meaning (0.0 - 3u) =< x =< (1.0 + 3u).
Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
;
data_refine_ls_abs_structure_Rogers
_name '_refine_ls_abs_structure_Rogers'
_category refine
_type numb
_type_conditions esd
_enumeration_range -1.0:1.0
_definition
; The measure of absolute structure as defined by Rogers (1981).
The value must lie in the 99.97% Gaussian confidence interval
-1 -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must
be supplied. The _enumeration_range of -1.0:1.0 is correctly
interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u).
Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
;
data_refine_ls_d_res_high
_name '_refine_ls_d_res_high'
_category refine
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The smallest value in angstroms of the interplanar spacings
of the reflections used in the refinement. This is called
the highest resolution.
;
data_refine_ls_d_res_low
_name '_refine_ls_d_res_low'
_category refine
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The largest value in angstroms of the interplanar spacings
of the reflections used in the refinement. This is called
the lowest resolution.
;
data_refine_ls_extinction_coef
_name '_refine_ls_extinction_coef'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine_ls_extinction_expression and
_refine_ls_extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
data_refine_ls_extinction_expression
_name '_refine_ls_extinction_expression'
_category refine
_type char
_example
; Larson, A. C. (1970). "Crystallographic Computing",
edited by F. R. Ahmed. Eq. (22), p. 292.
Copenhagen: Munksgaard.
;
_definition
; A description of or reference to the extinction-correction
equation used to apply the data item _refine_ls_extinction_coef.
This information must be sufficient to reproduce the
extinction-correction factors applied to the structure factors.
;
data_refine_ls_extinction_method
_name '_refine_ls_extinction_method'
_category refine
_type char
_enumeration_default 'Zachariasen'
loop_ _example 'B-C type 2 Gaussian isotropic'
'none'
_definition
; A description of the extinction-correction method applied.
This description should
include information about the correction method, either
'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
referred to as the 'Larson' method even though it employs
Zachariasen's formula.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; and as 'mixed'
when there is a mixture of types 1 and 2.
For the Becker-Coppens method, it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' and
the nature of the extinction as 'isotropic' or 'anisotropic'.
Note that if either the 'mixed' or 'anisotropic' corrections
are applied, the multiple coefficients cannot be contained in
*_extinction_coef and must be listed in _refine_special_details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
data_refine_ls_goodness_of_fit_all
_name '_refine_ls_goodness_of_fit_all'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for all
reflections after the final cycle of refinement.
Ideally, account should be taken of parameters restrained
in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = the standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_gt
_name '_refine_ls_goodness_of_fit_gt'
_category refine
_type numb
_type_conditions esd
_related_item '_refine_ls_goodness_of_fit_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for
significantly intense reflections (see
_reflns_threshold_expression) after the final cycle of
refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_obs
_name '_refine_ls_goodness_of_fit_obs'
_category refine
_type numb
_type_conditions esd
_related_item '_refine_ls_goodness_of_fit_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for observed
reflections (see _reflns_observed_criterion) after the final
cycle of refinement. Ideally, account should be taken of
parameters restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty (e.s.d.)
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_ref
_name '_refine_ls_goodness_of_fit_ref'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for all
reflections included in the refinement after the final cycle
of refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_hydrogen_treatment
_name '_refine_ls_hydrogen_treatment'
_category refine
_type char
loop_ _enumeration
_enumeration_detail refall 'refined all H-atom parameters'
refxyz 'refined H-atom coordinates only'
refU 'refined H-atom U's only'
noref 'no refinement of H-atom parameters'
constr 'H-atom parameters constrained'
mixed 'some constrained, some independent'
undef 'H-atom parameters not defined'
_enumeration_default undef
_definition
; Treatment of hydrogen atoms in the least-squares refinement.
;
data_refine_ls_matrix_type
_name '_refine_ls_matrix_type'
_category refine
_type char
loop_ _enumeration
_enumeration_detail full 'full'
fullcycle 'full with fixed elements per cycle'
atomblock 'block diagonal per atom'
userblock 'user-defined blocks'
diagonal 'diagonal elements only'
sparse 'selected elements only'
_enumeration_default full
_definition
; Type of matrix used to accumulate the least-squares derivatives.
;
data_refine_ls_number_constraints
_name '_refine_ls_number_constraints'
_category refine
_type numb
_enumeration_range 0:
_enumeration_default 0
_definition
; The number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site_constraints and _atom_site_refinement_flags. A general
description of constraints may appear in _refine_special_details.
;
data_refine_ls_number_parameters
_name '_refine_ls_number_parameters'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of parameters refined in the least-squares process.
If possible, this number should include some contribution from
the restrained parameters. The restrained parameters are
distinct from the constrained parameters (where one or more
parameters are linearly dependent on the refined value of
another). Least-squares restraints often depend on geometry or
energy considerations and this makes their direct contribution
to this number, and to the goodness-of-fit calculation,
difficult to assess.
;
data_refine_ls_number_reflns
_name '_refine_ls_number_reflns'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of unique reflections contributing to the
least-squares refinement calculation.
;
data_refine_ls_number_restraints
_name '_refine_ls_number_restraints'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of restrained parameters. These are parameters which
are not directly dependent on another refined parameter.
Restrained parameters often involve geometry or energy
dependencies.
See also _atom_site_constraints and _atom_site_refinement_flags.
A general description of refinement constraints may appear in
_refine_special_details.
;
data_refine_ls_R_factor_all
_name '_refine_ls_R_factor_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor for all reflections satisfying the
resolution limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_factor_gt
_name '_refine_ls_R_factor_gt'
_category refine
_type numb
_related_item '_refine_ls_R_factor_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; Residual factor for the reflections (with number given by
_reflns_number_gt) judged significantly intense (i.e. satisfying
the threshold specified by _reflns_threshold_expression)
and included in the refinement. The reflections also satisfy
the resolution limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_factor_obs
_name '_refine_ls_R_factor_obs'
_category refine
_type numb
_related_item '_refine_ls_R_factor_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; Residual factor for the reflections classified as 'observed'
(see _reflns_observed_criterion) and included in the
refinement. The reflections also satisfy the resolution limits
established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_Fsqd_factor
_name '_refine_ls_R_Fsqd_factor'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor R(Fsqd), calculated on the squared amplitudes
of the observed and calculated structure factors, for
significantly intense reflections (satisfying
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_d_res_high and _refine_ls_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_I_factor
_name '_refine_ls_R_I_factor'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor R(I) for significantly intense reflections
(satisfying _reflns_threshold_expression) and included in
the refinement.
This is most often calculated in Rietveld refinements against
powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the specified reflections
;
data_refine_ls_restrained_S_all
_name '_refine_ls_restrained_S_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for all
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied in the
least-squares process. See also _refine_ls_goodness_of_fit_
definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_restrained_S_gt
_name '_refine_ls_restrained_S_gt'
_category refine
_type numb
_related_item '_refine_ls_restrained_S_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for
significantly intense reflections (satisfying
_reflns_threshold_expression) after the final cycle
of least-squares refinement. This parameter explicitly includes
the restraints applied in the least-squares process.
See also _refine_ls_goodness_of_fit_ definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_restrained_S_obs
_name '_refine_ls_restrained_S_obs'
_category refine
_type numb
_related_item '_refine_ls_restrained_S_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for observed
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied in the
least-squares process. See also _refine_ls_goodness_of_fit_
definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_shift/esd_max
_name '_refine_ls_shift/esd_max'
_category refine
_type numb
_related_item '_refine_ls_shift/su_max'
_related_function replace
_enumeration_range 0.0:
_definition
; The largest ratio of the final least-squares parameter
shift to the final standard uncertainty (s.u.,
formerly described as estimated standard deviation, e.s.d.).
;
data_refine_ls_shift/esd_mean
_name '_refine_ls_shift/esd_mean'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_function replace
_enumeration_range 0.0:
_definition
; The average ratio of the final least-squares parameter
shift to the final standard uncertainty (s.u.,
formerly described as estimated standard deviation, e.s.d.).
;
data_refine_ls_shift/su_max
_name '_refine_ls_shift/su_max'
_category refine
_type numb
_related_item '_refine_ls_shift/esd_max'
_related_function alternate
_enumeration_range 0.0:
_definition
; The largest ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
data_refine_ls_shift/su_max_lt
_name '_refine_ls_shift/su_max_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_max'
_related_function alternate
_enumeration_range 0.0:
_definition
; An upper limit for the largest ratio of the final
least-squares parameter shift to the final
standard uncertainty. This item is used when the largest
value of the shift divided by the final standard uncertainty
is too small to measure.
;
data_refine_ls_shift/su_mean
_name '_refine_ls_shift/su_mean'
_category refine
_type numb
_related_item '_refine_ls_shift/esd_mean'
_related_function alternate
_enumeration_range 0.0:
_definition
; The average ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
data_refine_ls_shift/su_mean_lt
_name '_refine_ls_shift/su_mean_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_function alternate
_enumeration_range 0.0:
_definition
; An upper limit for the average ratio of the final
least-squares parameter shift to the
final standard uncertainty. This
item is used when the average value of the shift divided by
the final standard uncertainty is too small to measure.
;
data_refine_ls_structure_factor_coef
_name '_refine_ls_structure_factor_coef'
_category refine
_type char
loop_ _enumeration
_enumeration_detail F 'structure-factor magnitude'
Fsqd 'structure factor squared'
Inet 'net intensity'
_enumeration_default F
_definition
; Structure-factor coefficient |F|, F^2^ or I used in the
least-squares refinement process.
;
data_refine_ls_weighting_details
_name '_refine_ls_weighting_details'
_category refine
_type char
_example
; Sigdel model of Konnert-Hendrickson:
Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6)
Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0 at the end of refinement.
;
_definition
; A description of special aspects of the weighting scheme used
in the least-squares refinement. Used to describe the weighting
when the value of _refine_ls_weighting_scheme is specified
as 'calc'.
;
data_refine_ls_weighting_scheme
_name '_refine_ls_weighting_scheme'
_category refine
_type char
loop_ _enumeration
_enumeration_detail sigma "based on measured s.u.'s"
unit 'unit or no weights applied'
calc 'calculated weights applied'
_enumeration_default sigma
_definition
; The weighting scheme applied in the least-squares process. The
standard code may be followed by a description of the weight
(but see _refine_ls_weighting_details for a preferred approach).
;
data_refine_ls_wR_factor_all
_name '_refine_ls_wR_factor_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for all reflections.
The reflections also satisfy the resolution limits established
by _refine_ls_d_res_high and _refine_ls_d_res_low.
See also the _refine_ls_R_factor_ definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_gt
_name '_refine_ls_wR_factor_gt'
_category refine
_type numb
_related_item '_refine_ls_wR_factor_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; Weighted residual factors for significantly intense reflections
(satisfying _reflns_threshold_expression) included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_obs
_name '_refine_ls_wR_factor_obs'
_category refine
_type numb
_related_item '_refine_ls_wR_factor_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; Weighted residual factors for the reflections classified as
'observed' (see _reflns_observed_criterion) and included
in the refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_ref
_name '_refine_ls_wR_factor_ref'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for all reflections included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_special_details
_name '_refine_special_details'
_category refine
_type char
_definition
; Description of special aspects of the refinement process.
;
#####################
## REFINE_LS_CLASS ##
#####################
data_refine_ls_class_[]
_name '_refine_ls_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refine_ls_class_R_factor_gt
_refine_ls_class_code
0.057 'Main'
0.074 'Com'
0.064 'NbRefls'
0.046 'LaRefls'
0.112 'Sat1'
0.177 'Sat2'
;
;
Example 1 - example for a modulated structure extracted from van Smaalen
[J. Phys. Condens. Matter (1991), 3, 1247-1263.]
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFINE_LS_CLASS category record details
(for each reflection class separately) about the reflections
used for the structure refinement.
;
data_refine_ls_class_code
_name '_refine_ls_class_code'
_category refine_ls_class
_type char
_list yes
_list_link_parent '_reflns_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class. This code must
match a _reflns_class_code.
;
data_refine_ls_class_d_res_high
_name '_refine_ls_class_d_res_high'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the highest resolution in angstroms
for the reflections used in the refinement. This is
the lowest d value in a reflection class.
;
data_refine_ls_class_d_res_low
_name '_refine_ls_class_d_res_low'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the lowest resolution in angstroms
for the reflections used in the refinement. This is
the highest d value in a reflection class.
;
data_refine_ls_class_R_factor_
loop_ _name '_refine_ls_class_R_factor_all'
'_refine_ls_class_R_factor_gt'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factors for all
reflections, and for significantly intense reflections (see
_reflns_threshold_expression), included in the refinement.
The reflections also satisfy the resolution limits established by
_refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
This is the conventional R factor.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class. See also
_refine_ls_class_wR_factor_all definitions.
;
data_refine_ls_class_R_Fsqd_factor
_name '_refine_ls_class_R_Fsqd_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
data_refine_ls_class_R_I_factor
_name '_refine_ls_class_R_I_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns_threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
data_refine_ls_class_wR_factor_all
_name '_refine_ls_class_wR_factor_all'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitudes specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitudes specified by
_refine_ls_structure_factor_coef
w = the least-squares weights
and the sum is taken over the reflections of this class. See
also _refine_ls_class_R_factor_ definitions.
;
###########
## REFLN ##
###########
data_refln_[]
_name '_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_squared_calc
_refln_F_squared_meas
_refln_F_squared_sigma
_refln_include_status
2 0 0 85.57 58.90 1.45 o
3 0 0 15718.18 15631.06 30.40 o
4 0 0 55613.11 49840.09 61.86 o
5 0 0 246.85 241.86 10.02 o
6 0 0 82.16 69.97 1.93 o
7 0 0 1133.62 947.79 11.78 o
8 0 0 2558.04 2453.33 20.44 o
9 0 0 283.88 393.66 7.79 o
10 0 0 283.70 171.98 4.26 o
;
;
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[Acta Cryst. (1993), C49, 1352-1354].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_meas
_refln_F_calc
_refln_F_sigma
_refln_include_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. University
of 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
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
data_refln_A_
loop_ _name '_refln_A_calc'
'_refln_A_meas'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated and measured structure-factor component A
(in electrons for X-ray diffraction).
A =|F|cos(phase)
;
data_refln_B_
loop_ _name '_refln_B_calc'
'_refln_B_meas'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated and measured structure-factor component B
(in electrons for X-ray diffraction).
B =|F|sin(phase)
;
data_refln_class_code
_name '_refln_class_code'
_category refln
_type char
_list yes
_list_reference '_refln_index_'
_list_link_parent '_reflns_class_code'
_definition
; The code identifying the class to which this reflection has been
assigned. This code must match a value of _reflns_class_code.
Reflections may be grouped into classes for a variety of
purposes. For example, for modulated structures each reflection
class may be defined by the number m=sum|m~i~|, where the m~i~
are the integer coefficients that, in addition to h,k,l, index
the corresponding diffraction vector in the basis defined
for the reciprocal lattice.
;
data_refln_d_spacing
_name '_refln_d_spacing'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The d spacing in angstroms for this reflection. This is related
to the (sin theta)/lambda value by the expression
_refln_d_spacing = 2/(_refln_sint/lambda)
;
data_refln_crystal_id
_name '_refln_crystal_id'
_category refln
_type char
_list yes
_list_link_parent '_exptl_crystal_id'
_list_reference '_refln_index_'
_definition
; Code identifying each crystal if multiple crystals are used. Is
used to link with _exptl_crystal_id in the _exptl_crystal_ list.
;
data_refln_F_
loop_ _name '_refln_F_calc'
'_refln_F_meas'
'_refln_F_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated, measured and standard uncertainty (derived from
measurement) of the structure factors (in electrons for
X-ray diffraction).
;
data_refln_F_squared_
loop_ _name '_refln_F_squared_calc'
'_refln_F_squared_meas'
'_refln_F_squared_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; Calculated, measured and estimated standard uncertainty (derived
from measurement) of the squared structure factors (in electrons
squared for X-ray diffraction).
;
data_refln_include_status
_name '_refln_include_status'
_category refln
_type char
_related_item '_refln_observed_status'
_related_function alternate
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail o
; (lower-case letter o for 'observed')
satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
exceeds _reflns_threshold_expression
;
<
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
does not exceed
_reflns_threshold_expression
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine_ls_d_res_high'
l 'does not satisfy _refine_ls_d_res_low'
_enumeration_default o
_definition
; Classification of a reflection indicating its status with
respect to inclusion in the refinement and the calculation
of R factors.
;
data_refln_index_
loop_ _name '_refln_index_h'
'_refln_index_k'
'_refln_index_l'
_category refln
_type numb
_list yes
_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 the cell lengths and cell angles in the CELL category.
;
data_refln_intensity_
loop_ _name '_refln_intensity_calc'
'_refln_intensity_meas'
'_refln_intensity_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated, measured and standard uncertainty (derived from
measurement) of the intensity, all in the same arbitrary units
as _refln_intensity_meas.
;
data_refln_mean_path_length_tbar
_name '_refln_mean_path_length_tbar'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; Mean path length in millimetres through the crystal for this
reflection.
;
data_refln_observed_status
_name '_refln_observed_status'
_category refln
_type char
_related_item '_refln_include_status'
_related_function replace
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail o
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
observed by _reflns_observed_criterion
;
<
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
unobserved by _reflns_observed_criterion
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine_ls_d_res_high'
l 'does not satisfy _refine_ls_d_res_low'
_enumeration_default o
_definition
; Classification of a reflection indicating its status with
respect to inclusion in the refinement and the 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
_type char
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail incl 'included in ls process'
excl 'excluded from ls process'
extn 'excluded due to extinction'
_enumeration_default incl
_definition
; Status of a reflection in the structure-refinement process.
;
data_refln_scale_group_code
_name '_refln_scale_group_code'
_category refln
_type char
_list yes
_list_link_parent '_reflns_scale_group_code'
_list_reference '_refln_index_'
loop_ _example 1 2 3 s1 A B c1 c2 c3
_definition
; Code identifying the structure-factor scale. This code must
correspond to one of the _reflns_scale_group_code values.
;
data_refln_sint/lambda
_name '_refln_sint/lambda'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
;
data_refln_symmetry_epsilon
_name '_refln_symmetry_epsilon'
_category refln
_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
space-group symmetry operations.
;
data_refln_symmetry_multiplicity
_name '_refln_symmetry_multiplicity'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 1:48
_definition
; The number of reflections symmetry-equivalent under the Laue
symmetry to the present reflection. In the Laue symmetry, Friedel
opposites (h k l and -h -k -l) are equivalent. Tables of
symmetry-equivalent reflections are available in International
Tables for Crystallography Volume A (2002), Chapter 10.1.
;
data_refln_wavelength
_name '_refln_wavelength'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The mean wavelength in angstroms of the radiation used to measure
this reflection. This is an important parameter for data
collected using energy-dispersive detectors or the Laue method.
;
data_refln_wavelength_id
_name '_refln_wavelength_id'
_category refln
_type char
_list yes
_list_link_parent '_diffrn_radiation_wavelength_id'
_list_reference '_refln_index_'
_definition
; Code identifying the wavelength in the _diffrn_radiation_ list.
See _diffrn_radiation_wavelength_id.
;
############
## REFLNS ##
############
data_reflns_[]
_name '_reflns_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_reflns_limit_h_min 0
_reflns_limit_h_max 6
_reflns_limit_k_min 0
_reflns_limit_k_max 17
_reflns_limit_l_min 0
_reflns_limit_l_max 22
_reflns_number_total 1592
_reflns_number_gt 1408
_reflns_threshold_expression 'F > 6.0u(F)'
_reflns_d_resolution_high 0.8733
_reflns_d_resolution_low 11.9202
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
data_reflns_d_resolution_
loop_ _name '_reflns_d_resolution_high'
'_reflns_d_resolution_low'
_category reflns
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The highest and lowest resolution in angstroms for the
reflections. These are the smallest and largest d values.
;
data_reflns_Friedel_coverage
_name '_reflns_Friedel_coverage'
_category reflns
_type numb
_enumeration_range 0.0:1.0
_definition
; The proportion of Friedel-related reflections present in
the number of 'independent' reflections specified by
the item _reflns_number_total.
This proportion is calculated as the ratio:
[N(crystal class) - N(Laue symmetry)] / N(Laue symmetry)
where, working from the _diffrn_refln_ list,
N(crystal class) is the number of reflections obtained on
averaging under the symmetry of the crystal class
N(Laue symmetry) is the number of reflections obtained on
averaging under the Laue symmetry.
Examples:
(a) For centrosymmetric structures, _reflns_Friedel_coverage
is necessarily equal to 0.0 as the crystal class
is identical to the Laue symmetry.
(b) For whole-sphere data for a crystal in the space
group P1, _reflns_Friedel_coverage is equal to 1.0,
as no reflection h k l is equivalent to -h -k -l
in the crystal class and all Friedel pairs
{h k l; -h -k -l} have been measured.
(c) For whole-sphere data in space group Pmm2,
_reflns_Friedel_coverage will be < 1.0 because
although reflections h k l and
-h -k -l are not equivalent when h k l indices are
nonzero, they are when l=0.
(d) For a crystal in the space group Pmm2, measurements of the
two inequivalent octants h >= 0, k >=0, l lead to the
same value as in (c), whereas measurements of the
two equivalent octants h >= 0, k, l >= 0 will lead to
a value of zero for _reflns_Friedel_coverage.
;
data_reflns_limit_
loop_ _name '_reflns_limit_h_max'
'_reflns_limit_h_min'
'_reflns_limit_k_max'
'_reflns_limit_k_min'
'_reflns_limit_l_max'
'_reflns_limit_l_min'
_category reflns
_type numb
_definition
; Miller indices limits for the reported reflections. These need
not be the same as the _diffrn_reflns_limit_ values.
;
data_reflns_number_gt
_name '_reflns_number_gt'
_category reflns
_type numb
_related_item '_reflns_number_observed'
_related_function alternate
_enumeration_range 0:
_definition
; The number of reflections in the _refln_ list (not the
_diffrn_refln_ list) that are significantly intense, satisfying
the criterion specified by _reflns_threshold_expression. This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_number_observed
_name '_reflns_number_observed'
_category reflns
_type numb
_related_item '_reflns_number_gt'
_related_function replace
_enumeration_range 0:
_definition
; The number of 'observed' reflections in the _refln_ list (not
the _diffrn_refln_ list). The observed reflections satisfy the
threshold criterion specified by _reflns_threshold_expression
(or the deprecated item _reflns_observed_criterion). They may
include Friedel-equivalent reflections according to the nature
of the structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_number_total
_name '_reflns_number_total'
_category reflns
_type numb
_enumeration_range 0:
_definition
; The total number of reflections in the _refln_ list (not the
_diffrn_refln_ list). This may include Friedel-equivalent
reflections (i.e. those which are symmetry-equivalent under the
Laue symmetry but inequivalent under the crystal class)
according to the nature of the structure and the procedures
used. Special characteristics of the reflections included
in the _refln_ list should be given in the item
_reflns_special_details.
;
data_reflns_observed_criterion
_name '_reflns_observed_criterion'
_category reflns
_type char
_related_item '_reflns_threshold_expression'
_related_function replace
_example 'I>2u(I)'
_definition
; The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or sigma(F)
threshold.
;
data_reflns_special_details
_name '_reflns_special_details'
_category reflns
_type char
_definition
; Description of the properties of the reported reflection list
that are not given in other data items. In particular, this
should include information about the averaging (or not) of
symmetry-equivalent reflections including Friedel pairs.
;
data_reflns_threshold_expression
_name '_reflns_threshold_expression'
_category reflns
_type char
_related_item '_reflns_observed_criterion'
_related_function alternate
_example 'I>2u(I)'
_definition
; The threshold, usually based on multiples of u(I), u(F^2^)
or u(F), that serves to identify significantly intense
reflections, the number of which is given by _reflns_number_gt.
These reflections are used in the calculation of
_refine_ls_R_factor_gt.
;
##################
## REFLNS_CLASS ##
##################
data_reflns_class_[]
_name '_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_class_number_gt
_reflns_class_code
584 'Main'
226 'Sat1'
50 'Sat2'
;
;
Example 1 - corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_CLASS category record details, for
each reflection class, about the reflections used to determine
the structural parameters.
;
data_reflns_class_code
_name '_reflns_class_code'
_category reflns_class
_type char
_list yes
loop_ _list_link_child '_refln_class_code'
'_refine_ls_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class.
;
data_reflns_class_description
_name '_reflns_class_description'
_category reflns_class
_type char
_list yes
_list_reference '_reflns_class_code'
loop_ _example 'm=1 first order satellites'
'H0L0 common projection reflections'
_definition
; Description of each reflection class.
;
data_reflns_class_d_res_high
_name '_reflns_class_d_res_high'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the highest resolution in angstroms
for the reflections used in the refinement. This is the smallest
d value.
;
data_reflns_class_d_res_low
_name '_reflns_class_d_res_low'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the lowest resolution in angstroms
for the reflections used in the refinement. This is the largest
d value.
;
data_reflns_class_number_gt
_name '_reflns_class_number_gt'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the number of significantly intense
reflections (see _reflns_threshold_expression) in the _refln_
list (not the _diffrn_refln_ list). This may include Friedel-
equivalent reflections (i.e. those which are symmetry-equivalent
under the Laue symmetry but inequivalent under the crystal
class) according to the nature of the structure and the
procedures used. Special characteristics of the reflections
included in the _refln_ list should be given in the item
_reflns_special_details.
;
data_reflns_class_number_total
_name '_reflns_class_number_total'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the total number of reflections
in the _refln_ list (not the _diffrn_refln_ list). This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_class_R_factor_
loop_ _name '_reflns_class_R_factor_all'
'_reflns_class_R_factor_gt'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factors for all
reflections, and for significantly intense reflections (see
_reflns_threshold_expression), included in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class_d_res_high and _reflns_class_d_res_low.
This is the conventional R factor.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class. See also
_reflns_class_wR_factor_all definitions.
;
data_reflns_class_R_Fsqd_factor
_name '_reflns_class_R_Fsqd_factor'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors, for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _reflns_class_d_res_high and _reflns_class_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
data_reflns_class_R_I_factor
_name '_reflns_class_R_I_factor'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns_threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
data_reflns_class_wR_factor_all
_name '_reflns_class_wR_factor_all'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_reflns_class_d_res_high and _reflns_class_d_res_low.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitudes specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitudes specified by
_refine_ls_structure_factor_coef
w = the least-squares weights
and the sum is taken over the reflections of this class. See
also _reflns_class_R_factor_ definitions.
;
##################
## REFLNS_SCALE ##
##################
data_reflns_scale_[]
_name '_reflns_scale_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_scale_group_code
_reflns_scale_meas_F
1 .895447
2 .912743
;
;
Example 1 - based on standard test data set p6122 of the Xtal distribution
[Hall, King & Stewart (1995). Xtal3.4 User's Manual. University
of 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.
;
data_reflns_scale_group_code
_name '_reflns_scale_group_code'
_category reflns_scale
_type char
_list yes
_list_mandatory yes
_list_link_child '_refln_scale_group_code'
_definition
; The code identifying a scale _reflns_scale_meas_. These are
linked to the _refln_ list by the _refln_scale_group_code. These
codes need not correspond to those in the _diffrn_scale_ list.
;
data_reflns_scale_meas_
loop_ _name '_reflns_scale_meas_F'
'_reflns_scale_meas_F_squared'
'_reflns_scale_meas_intensity'
_category reflns_scale
_type numb
_type_conditions esd
_enumeration_range 0.0:
_list yes
_list_reference '_reflns_scale_group_code'
_definition
; Scales associated with _reflns_scale_group_code.
;
##################
## REFLNS_SHELL ##
##################
data_reflns_shell_[]
_name '_reflns_shell_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_shell_d_res_high
_reflns_shell_d_res_low
_reflns_shell_meanI_over_uI_gt
_reflns_shell_number_measured_gt
_reflns_shell_number_unique_gt
_reflns_shell_percent_possible_gt
_reflns_shell_Rmerge_F_gt
31.38 3.82 69.8 9024 2540 96.8 1.98
3.82 3.03 26.1 7413 2364 95.1 3.85
3.03 2.65 10.5 5640 2123 86.2 6.37
2.65 2.41 6.4 4322 1882 76.8 8.01
2.41 2.23 4.3 3247 1714 70.4 9.86
2.23 2.10 3.1 1140 812 33.3 13.99
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_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.
;
data_reflns_shell_d_res_high
_name '_reflns_shell_d_res_high'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The highest resolution in angstroms for the reflections in
this shell. This is the smallest d value.
;
data_reflns_shell_d_res_low
_name '_reflns_shell_d_res_low'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The lowest resolution in angstroms for the
reflections in this shell. This is the largest d value.
;
data_reflns_shell_meanI_over_sigI_all
_name '_reflns_shell_meanI_over_sigI_all'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_uI_all'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in the resolution shell.
;
data_reflns_shell_meanI_over_sigI_gt
_name '_reflns_shell_meanI_over_sigI_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_uI_gt'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns_threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in the
resolution shell.
;
data_reflns_shell_meanI_over_sigI_obs
_name '_reflns_shell_meanI_over_sigI_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_sigI_gt'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of the reflections
classified as 'observed' (see _reflns_observed_criterion) in
this shell to the mean of the standard uncertainties of the
intensities of the 'observed' reflections in the resolution
shell.
;
data_reflns_shell_meanI_over_uI_all
_name '_reflns_shell_meanI_over_uI_all'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_sigI_all'
_related_function alternate
_list yes
_definition
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in the resolution shell.
;
data_reflns_shell_meanI_over_uI_gt
_name '_reflns_shell_meanI_over_uI_gt'
_category reflns_shell
_type numb
loop_ _related_item
_related_function '_reflns_shell_meanI_over_sigI_gt' alternate
'_reflns_shell_meanI_over_sigI_obs' alternate
_list yes
_definition
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns_threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in the
resolution shell.
;
data_reflns_shell_number_measured_all
_name '_reflns_shell_number_measured_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The total number of reflections measured for this
resolution shell.
;
data_reflns_shell_number_measured_gt
_name '_reflns_shell_number_measured_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_measured_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The number of significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_number_measured_obs
_name '_reflns_shell_number_measured_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_measured_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The number of reflections classified as 'observed'
(see _reflns_observed_criterion) measured for this
resolution shell.
;
data_reflns_shell_number_possible
_name '_reflns_shell_number_possible'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0:
_definition
; The number of unique reflections it is possible to measure in
this reflection shell.
;
data_reflns_shell_number_unique_all
_name '_reflns_shell_number_unique_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0:
_definition
; The total number of measured reflections resulting from
merging measured symmetry-equivalent reflections for this
resolution shell.
;
data_reflns_shell_number_unique_gt
_name '_reflns_shell_number_unique_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_unique_obs'
_related_function alternate
_list yes
_enumeration_range 0:
_definition
; The total number of significantly intense reflections
(see _reflns_threshold_expression) resulting from merging
measured symmetry-equivalent reflections for this resolution
shell.
;
data_reflns_shell_number_unique_obs
_name '_reflns_shell_number_unique_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_unique_gt'
_related_function replace
_list yes
_enumeration_range 0:
_definition
; The total number of reflections classified as
'observed' (see _reflns_observed_criterion) resulting from
merging measured symmetry-equivalent reflections for this
resolution shell.
;
data_reflns_shell_percent_possible_all
_name '_reflns_shell_percent_possible_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by all reflections measured for this
resolution shell.
;
data_reflns_shell_percent_possible_gt
_name '_reflns_shell_percent_possible_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_percent_possible_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_percent_possible_obs
_name '_reflns_shell_percent_possible_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_percent_possible_gt'
_related_function replace
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by reflections classified as 'observed'
(see _reflns_observed_criterion) measured for this
resolution shell.
;
data_reflns_shell_Rmerge_F_all
_name '_reflns_shell_Rmerge_F_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for all reflections in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_F_gt
_name '_reflns_shell_Rmerge_F_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_F_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_F_obs
_name '_reflns_shell_Rmerge_F_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_F_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_all
_name '_reflns_shell_Rmerge_I_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for all reflections in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_gt
_name '_reflns_shell_Rmerge_I_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_I_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_obs
_name '_reflns_shell_Rmerge_I_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_I_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
#################
## SPACE_GROUP ##
#################
data_space_group_[]
_name '_space_group_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_space_group_id 1
_space_group_name_H-M_alt 'C 2/c'
_space_group_IT_number 15
_space_group_name_Hall '-C 2yc'
_space_group_crystal_system monoclinic
;
;
Example 1 - the monoclinic space group No. 15 with unique axis b.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Contains all the data items that refer to the space group as a
whole, such as its name or crystal system. They may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in the
core dictionary. The remainder are found in the symmetry CIF
dictionary.
Space-group types are identified by their number as given in
International Tables for Crystallography Vol. A. Specific
settings of the space groups can be identified either by their
Hall symbol or by specifying their symmetry operations.
The commonly used Hermann-Mauguin symbol determines the
space-group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space-group type. A
Hermann-Mauguin symbol contains information on the choice of
the basis, but not on the choice of origin. Different formats
for the Hermann-Mauguin symbol are found in the symmetry CIF
dictionary.
;
data_space_group_crystal_system
_name '_space_group_crystal_system'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_cell_setting'
_related_function alternate
loop_ _enumeration triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
_definition
; The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that rhombohedral space groups belong to the
trigonal system.
;
data_space_group_id
_name '_space_group_id'
_category space_group
_type char
_list yes
_list_mandatory yes
_list_link_child '_space_group_symop_sg_id'
_definition
; This is an identifier needed if _space_group_ items are looped.
;
data_space_group_IT_number
_name '_space_group_IT_number'
_category space_group
_type numb
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_Int_Tables_number'
_related_function alternate
_enumeration_range 1:230
_definition
; The number as assigned in International Tables for
Crystallography Vol. A, specifying the proper affine class (i.e.
the orientation-preserving affine class) of space groups
(crystallographic space-group type) to which the space group
belongs. This number defines the space-group type but not
the coordinate system in which it is expressed.
;
data_space_group_name_Hall
_name '_space_group_name_Hall'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_space_group_name_Hall'
_related_function alternate
loop_ _example
_example_detail 'P 2c -2ac' 'equivalent to Pca21'
'-I 4bd 2ab 3' 'equivalent to Ia-3d'
_definition
; Space-group symbol defined by Hall.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in older files. It should not be
used in new CIFs.
_space_group_name_Hall uniquely defines the space group and
its reference to a particular coordinate system.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
[See also International Tables for Crystallography,
Vol. B (2001), Chapter 1.4, Appendix 1.4.2]
;
data_space_group_name_H-M_alt
_name '_space_group_name_H-M_alt'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_space_group_name_H-M'
_related_function alternate
loop_ _example
_example_detail
; loop_
_space_group_id
_space_group_name_H-M_alt
1 'C m c m'
2 'C 2/c 2/m 21/m'
3 'A m a m'
;
'three examples for space group No. 63'
_definition
; _space_group_name_H-M_alt allows any Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and in general is not intended to be interpreted by
computer. It may, for example, be used to give one of the
extended Hermann-Mauguin symbols given in Table 4.3.2.1 of
International Tables for Crystallography Vol. A (2002) or
a Hermann-Mauguin symbol for a conventional or unconventional
setting.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in older files. It should not be
used in new CIFs. Subscripts should appear without special
symbols. Bars should be given as negative signs before the
numbers to which they apply.
The commonly used Hermann-Mauguin symbol determines the space-
group type uniquely but a given space-group type may be
described by more than one Hermann-Mauguin symbol. The space-
group type is best described using _space_group_IT_number.
The Hermann-Mauguin symbol may contain information on the
choice of basis, but not on the choice of origin. To
define the setting uniquely, use _space_group_name_Hall or
list the symmetry operations.
;
#######################
## SPACE_GROUP_SYMOP ##
#######################
data_space_group_symop_[]
_name '_space_group_symop_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 -x,-y,-z
3 -x,1/2+y,1/2-z
4 x,1/2-y,1/2+z
;
;
Example 1 - the symmetry operations for the space group P21/c.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Contains information about the symmetry operations of the
space group.
;
data_space_group_symop_id
_name '_space_group_symop_id'
_type char
_category space_group_symop
_list yes
_list_mandatory yes
_related_item '_symmetry_equiv_pos_site_id'
_related_function alternate
_definition
; An arbitrary identifier that uniquely labels each symmetry
operation in the list.
;
data_space_group_symop_operation_xyz
_name '_space_group_symop_operation_xyz'
_category space_group_symop
_type char
_list both
_list_reference '_space_group_symop_id'
_enumeration_default 'x,y,z'
_related_item '_symmetry_equiv_pos_as_xyz'
_related_function alternate
loop_ _example
_example_detail 'x,1/2-y,1/2+z'
; glide reflection through the plane (x,1/4,z),
with glide vector (1/2)c
;
_definition
; A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by fractions, an equivalent position
X' is generated from a given position X by the equation
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Part 5)
When a list of symmetry operations is given, it must contain
a complete set of coordinate representatives which generates
all the operations of the space group by the addition of
all primitive translations of the space group. Such
representatives are to be found as the coordinates of
the general-equivalent position in International Tables for
Crystallography Vol. A (2002), to which it is necessary to
add any centring translations shown above the
general-equivalent position.
That is to say, it is necessary to list explicitly all the
symmetry operations required to generate all the atoms in
the unit cell defined by the setting used.
;
data_space_group_symop_sg_id
_name '_space_group_symop_sg_id'
_category space_group_symop
_type numb
_list both
_list_mandatory no
_list_reference '_space_group_symop_id'
_list_link_parent '_space_group_id'
_definition
; This must match a particular value of _space_group_id, allowing
the symmetry operation to be identified with a particular space
group.
;
##############
## SYMMETRY ##
##############
data_symmetry_[]
_name '_symmetry_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_H-M 'P 21 21 21'
_symmetry_space_group_name_Hall 'P 2ac 2ab'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the SYMMETRY category record details about the
space-group symmetry.
;
data_symmetry_cell_setting
_name '_symmetry_cell_setting'
_category symmetry
_type char
loop_ _enumeration triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
_related_item '_space_group_crystal_system'
_related_function replace
_definition
; The cell settings for this space-group symmetry.
;
data_symmetry_Int_Tables_number
_name '_symmetry_Int_Tables_number'
_category symmetry
_type numb
_enumeration_range 1:230
_related_item '_space_group_IT_number'
_related_function replace
_definition
; Space-group number from International Tables for Crystallography
Vol. A (2002).
;
data_symmetry_space_group_name_Hall
_name '_symmetry_space_group_name_Hall'
_category symmetry
_type char
_related_item '_space_group_name_Hall'
_related_function replace
loop_ _example '-P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
_definition
; Space-group symbol as described by Hall. This symbol gives the
space-group setting explicitly. Leave spaces between the separate
components of the symbol.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
;
data_symmetry_space_group_name_H-M
_name '_symmetry_space_group_name_H-M'
_category symmetry
_type char
_related_item '_space_group_name_H-M_alt'
_related_function replace
loop_ _example 'P 1 21/m 1'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'
_definition
; Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin
symbol does not necessarily contain complete information
about the symmetry and the space-group origin. If used, always
supply the FULL symbol from International Tables for
Crystallography Vol. A (2002) and indicate the origin and
the setting if it is not implicit. If there is any doubt
that the equivalent positions can be uniquely deduced from
this symbol, specify the _symmetry_equiv_pos_as_xyz
or *_Hall data items as well. Leave spaces between
symbols referring to different axes.
;
####################
## SYMMETRY_EQUIV ##
####################
data_symmetry_equiv_[]
_name '_symmetry_equiv_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_symmetry_equiv_pos_as_xyz
+x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
3 1/2+x,1/2-y,-z
4 -x,1/2+y,1/2-z
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277]. Formally, the value of
_symmetry_equiv_pos_site_id can be any unique character string;
it is recommended that it be assigned the sequence number of
the list of equivalent positions for compatibility with
older files in which it did not appear.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the SYMMETRY_EQUIV category list the
symmetry-equivalent positions for the space group.
;
data_symmetry_equiv_pos_as_xyz
_name '_symmetry_equiv_pos_as_xyz'
_category symmetry_equiv
_type char
_list both
_example -y+x,-y,1/3+z
_related_item '_space_group_symop_operation_xyz'
_related_function replace
_definition
; Symmetry-equivalent position in the 'xyz' representation. Except
for the space group P1, these data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography Vol. A. (2002). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
data_symmetry_equiv_pos_site_id
_name '_symmetry_equiv_pos_site_id'
_category symmetry_equiv
_type numb
_list yes
_list_reference '_symmetry_equiv_pos_as_xyz'
_related_item '_space_group_symop_id'
_related_function replace
_definition
; A code identifying each entry in the _symmetry_equiv_pos_as_xyz
list. It is normally 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'.
;
###################
## VALENCE_PARAM ##
###################
data_valence_param_[]
_name '_valence_param_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_valence_param_id
_valence_param_atom_1
_valence_param_atom_1_valence
_valence_param_atom_2
_valence_param_atom_2_valence
_valence_param_Ro
_valence_param_B
_valence_param_ref_id
_valence_param_details
1 Cu 2 O -2 1.679 0.37 a .
2 Cu 2 O -2 1.649 0.37 j .
3 Cu 2 N -3 1.64 0.37 m '2-coordinate N'
4 Cu 2 N -3 1.76 0.37 m '3-coordinate N'
loop_
_valence_ref_id
_valence_ref_reference
a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247'
j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205'
m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375'
;
;
Example 1 - a bond-valence parameter list with accompanying references.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the VALENCE_PARAM category define the
parameters used for calculating bond valences from bond
lengths. In addition to the parameters, a pointer
is given to the reference (in VALENCE_REF) from which
the bond-valence parameters were taken.
;
data_valence_param_atom_1
_name '_valence_param_atom_1'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; The element symbol of the first atom forming the bond whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_1_valence
_name '_valence_param_atom_1_valence'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_definition
; The valence (formal charge) of the first atom whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_2
_name '_valence_param_atom_2'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; The element symbol of the second atom forming the bond whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_2_valence
_name '_valence_param_atom_2_valence'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_definition
; The valence (formal charge) of the second atom whose
bond-valence parameters are given in this category.
;
data_valence_param_B
_name '_valence_param_B'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_units A
_units_detail Angstrom
_definition
; The bond-valence parameter B used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
data_valence_param_details
_name '_valence_param_details'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; Details of or comments on the bond-valence parameters.
;
data_valence_param_id
_name '_valence_param_id'
_category valence_param
_type char
_list yes
_definition
; An identifier for the valence parameters of a bond between
the given atoms.
;
data_valence_param_ref_id
_name '_valence_param_ref_id'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_list_link_parent '_valence_ref_id'
_definition
; An identifier which links to the reference to the source
from which the bond-valence parameters are taken. A child
of _valence_ref_id, which it must match.
;
data_valence_param_Ro
_name '_valence_param_Ro'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_units A
_units_detail Angstrom
_definition
; The bond-valence parameter Ro used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
#################
## VALENCE_REF ##
#################
data_valence_ref_[]
_name '_valence_ref_[]'
_category category_overview
_type null
_definition
; Data items in the VALENCE_REF category list the references
from which the bond-valence parameters have been taken.
;
data_valence_ref_id
_name '_valence_ref_id'
_category valence_ref
_type char
_list yes
_list_reference '_valence_ref_id'
_list_link_child '_valence_param_ref_id'
_definition
; An identifier for items in this category. Parent of
_valence_param_ref_id, which must have the same value.
;
data_valence_ref_reference
_name '_valence_ref_reference'
_type char
_category valence_ref
_list yes
_list_reference '_valence_ref_id'
_definition
; Literature reference from which the valence parameters
identified by _valence_param_id were taken.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
