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Re: Approval of CIF core changes for 2.3
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Re: Approval of CIF core changes for 2.3
- From: Brian McMahon <bm@iucr.org>
- Date: Thu, 10 Jul 2003 16:56:17 +0100 (BST)
Dear David I am sending as an attachment a revised copy of the document that was posted on your behalf a few days ago. It incorporates Howard's typos and minor rewordings. I haven't deleted the Z_prime entry, though you have indicated that you will pull it from consideration at this stage (though I remark that there have been requests from other sources for a record of Z', so finding a sound definition would be a useful priority for the next version). Nor have I included either of Howard's alternative definitions for _space_group_symop_operation_xyz I have also corrected a few syntax errors and incorrect DDL names, and made a few light editorial changes. The technical details are almost certainly of no interest to anyone, but can be inspected if necessary in the colour-coded file http://agate.iucr.org/cif/cif_core/minoredits.html If you prefer some different indication of the changes (e.g. a "diff" listing), please let me know. Best wishes Brian
##################################################
#
# REVISIONS TO CIF_CORE_2.3.DIC
# ITEMS SUBJECT TO APPROVAL BY CORE DMG AND COMCIFS
#
##################################################
#
# Accumulated list of tentatively approved items.
#
# The following new datanames are proposed in this draft of the revisions to
# the core CIF dictionary.
#
# ATOM SITE
# _atom_site_fract_ (modify)
# _atom_site_refinement_flags (replace with the following)
# _atom_site_refinement_flags_posn
# _atom_site_refinement_flags_adp
# _atom_site_refinement_flags_occupancy
# ATOM SITES
# _atom_sites_special_details
# CELL
# _cell_formula_units_Z_prime
# _cell_reciprocal_angle_alpha
# _cell_reciprocal_angle_beta
# _cell_reciprocal_angle_gamma
# _cell_reciprocal_length_a
# _cell_reciprocal_length_b
# _cell_reciprocal_length_c
# CHEMICAL
# _chemical_melting_point (modify)
# _chemical_melting_point_gt
# _chemical_melting_point_lt
# _chemical_properties_biological
# _chemical_properties_physical
# _chemical_temperature_decomposition
# _chemical_temperature_decomposition_gt
# _chemical_temperature_decomposition_lt
# _chemical_temperature_sublimation
# _chemical_temperature_sublimation_gt
# _chemical_temperature_sublimation_lt
# CITATION
# _citation_database_id_CSD
# DATABASE
# _database_code_depnum_ccdc_fiz
# _database_code_depnum_ccdc_journal
# _database_code_depnum_ccdc_archive
# _database_CSD_history
# DIFFRN
# _diffrn_ambient_pressure_gt
# _diffrn_ambient_pressure_lt
# _diffrn_ambient_temperature_gt
# _diffrn_ambient_temperature_lt
# DIFFRN_SOURCE
# _diffrn_source_take-off_angle
# DIFFRN_STANDARDS
# _diffrn_standards_decay_%_lt
# DIFFRN_REFLNS
# _diffrn_reflns_measured_fraction_resolution_full
# _diffrn_reflns_measured_fraction_resolution_max
# _diffrn_reflns_resolution_full
# _diffrn_reflns_resolution_max
# EXPTL_CRYSTAL
# _exptl_crystal_colour_primary
# _exptl_crystal_colour_modifier
# _exptl_crystal_colour_lustre
# _exptl_crystal_density_meas_gt
# _exptl_crystal_density_meas_lt
# _exptl_crystal_density_meas_temp_gt
# _exptl_crystal_density_meas_temp_lt
# _exptl_crystal_recrystallization_method
# PUBL
# _publ_contact_author_id_iucr
# PULB_AUTHOR
# _publ_author_id_iucr
# REFINE
# _refine_ls_shift/su_max_lt
# _refine_ls_shift/su_mean_lt
# SPACE_GROUP (General information on the space group)
# _space_group_crystal_system
# _space_group_id (Parent to various .sg_id's)
# _space_group_IT_number
# _space_group_name_Hall
# _space_group_name_H-M_alt
# SPACE_GROUP_SYMOP (Symmetry operations)
# _space_group_symop_id (parent to various .symop_id's)
# _space_group_symop_operation_xyz
# _space_group_symop_sg_id
#
##################################################
##################################################
#
# ATOM SITE
#
##################################################
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'
# _enumeration_default 0.0
_definition
; Atom site coordinates as fractions of the _cell_length_ values.
;
# COMMENT: The default should be deleted since it makes no sense. If the
# coordinates are defaulted it is, presumably, because they are not known, not
# because the atom is at the origin.
# STATUS: Preliminary approval 02-09-23
# COMMENT: The proposal is to replace the following item by the subsequent
# three items. The
# problem with the current definition is that it requires the character field
# to be parsed since any of the seven flags may appear in any order. The
# replacement items define unique flags for each possibility.
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
;
# STATUS: Preliminary approval 02-09-23
data_atom_site_refinement_flags_posn
_name '_atom_site_refinement_flags_posn'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
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.
;
# STATUS: Preliminary approval 02-09-23
data_atom_site_refinement_flags_adp
_name '_atom_site_refinement_flags_adp'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
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.
;
# COMMENT: Are these enumeration details clear? What is the difference
# between these two flags? Can both apply at the same time?
# STATUS: Preliminary approval 02-09-23
data_atom_site_refinement_flags_occupancy
_name '_atom_site_refinement_flags_occupancy'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
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.
;
# STATUS: Preliminary approval 02-09-23
##################################################
#
# ATOM SITES
#
##################################################
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.
;
# COMMENT: This could be useful in transcribing comments in databases.
# STATUS: Preliminary approval 02-09-23
##################################################
#
# CELL category
#
##################################################
data_cell_formula_units_Z_prime
_name '_cell_formula_units_Z_prime'
_category cell
_type numb
_enumeration_range 1:
_definition
; The number of the formula units as specified
by _chemical_formula_structural, _chemical_formula_moiety or
_chemical_formula_sum in the asymmetric unit of the
unit cell given in the CELL category and the
space group defined in the SYMMETRY or SPACE GROUP category.
This item is used to indicate the number of chemically
equivalent molecules in the asymmetric unit.
;
# COMMENT: Requested by CCDC
# STATUS: Preliminary approval 2002-10-14
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. 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))
(M.J.Buerger: X-ray Crystallography; New York, John Wiley & Sons Inc;
1942 p.360)
;
# COMMENT: Requested by CCDC
# STATUS: Preliminary approval 2002-10-14
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 the following equation:
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. (M.J.Buerger: X-ray Crystallography;
New York, John Wiley & Sons Inc; 1942 p.360)
;
# COMMENT: Requested by CCDC
# STATUS: Preliminary approval 2002-10-14
###################################################
#
# CHEMICAL category
#
###################################################
# CHANGE TO AN EXISTING ITEM
#
# _chemical_melting_point should have added:
#
# _type_conditions esd
#
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 'Kelvins'
_definition
; A temperature in Kelvins below which (_*_lt) or above
which (_*_gt) the melting point, the temperature at which a
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.
;
# COMMENT: These item are introduced to allow for a maximum or minimum
# limit, or a range of temperatures to be given. They are primarily designed
# to allow comments in exiting databases to be included in a CIF.
# STATUS: Preliminary approval 2002-10-14
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. a ureus 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 description of the biological properties of the
material.
;
# COMMENT: Suggested by CCDC for comments found in the CSD
# STATUS: Preliminary approval 2002-10-14
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 description of the physical properties of the material.
;
# COMMENT: Suggested by CCDC for comments found in the CSD
# STATUS: Preliminary approval 2002-10-14
data_chemical_temperature_decomposition
_name '_chemical_temperature_decomposition'
_category chemical
_type numb
_type_conditions esd
_units K
_units_detail Kelvin
_example 350
_definition
; The temperature in Kelvin at which a solid decomposes.
;
# COMMENT: Suggested by CCDC.
# STATUS: Preliminary approval 2002-10-14
data_chemical_temperature_decomposition_*
loop_ _name '_chemical_temperature_decomposition_gt'
'_chemical_temperature_decomposition_lt'
_category chemical
_type numb
_units K
_units_detail Kelvin
_related_item '_chemical_temperature_decomposition'
_related_function alternate
_example 350
_definition
; A temperature 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.
;
# COMMENT: Suggested by CCDC.
# STATUS: Preliminary approval 2002-10-14
data_chemical_temperature_sublimation
_name '_chemical_temperature_sublimation'
_category chemical
_type numb
_type_conditions esd
_units K
_units_detail Kelvin
_example 350
_definition
; The temperature in Kelvin at which a solid sublimes.
;
# COMMENT: Suggested by CCDC.
# STATUS: Preliminary approval 2002-10-14
data_chemical_temperature_sublimation_*
loop_ _name '_chemical_temperature_sublimation_gt'
'_chemical_temperature_sublimation_lt'
_category chemical
_type numb
_units K
_units_detail Kelvin
_related_item '_chemical_temperature_sublimation'
_related_function Alternate
_example 350
_definition
; A temperature below which (_*_lt) of 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.
;
# COMMENT: Suggested by CCDC.
# STATUS: Preliminary approval 2002-10-14
###################################################
#
# CITATION category
#
###################################################
# The following item has already been approved but still needs to be
# incorporated into the dictionary.
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 containing details of the cited structure.
;
# COMMENT: Submitted by Brian McMahon
# STATUS: Approved 2001-12-03
####################################################
#
# DATABASE Category
#
####################################################
data_database_code_depnum_ccdc_fiz
_name '_database_code_depnum_ccdc_fiz'
_category database
_type char
_definition
; Deposition numbers assigned by the Fachinformatsionszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Centre (CCDC)
;
# COMMENT: For use in the archives of CCDC. Submitted by CCDC
# STATUS: Preliminary approval 2002-02-28
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)
;
# COMMENT: For use in the archives of CCDC. Submitted by CCDC
# STATUS: Preliminary approval 2002-02-28
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.
;
# COMMENT: For use in the archives of CCDC. Submitted by CCDC
# STATUS: Preliminary approval 2002-02-28
data_database_CSD_history
_name '_database_CSD_history'
_category database
_type char
_list yes
_list_reference ?
_example ?
_definition
; A history of changes made by Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
;
# COMMENT: Requested by the CCDC
# STATUS: Preliminary approval 2002-11-11
###########################################
#
# DIFFRN category
#
###########################################
data_diffrn_ambient_pressure_
loop_ _name
'_diffrn_ambient_pressure_gt'
'_diffrn_ambient_pressure_lt'
_category diffrn
_type numb
_type_conditions esd
_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.
;
# COMMENT; Provides for a pressure range to be indicated.
# STATUS: Preliminary approval 2002-11-11
data_diffrn_ambient_temperature_
loop_ _name
'_diffrn_ambient_temperature_gt'
'_diffrn_ambient_temperature_lt'
_category diffrn
_type numb
_type_conditions esd
_related_item '_diffrn_ambient_temperature'
_related_function alternate
_enumeration_range 0.0:
_units K
_units_detail 'kelvins'
_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.
;
# COMMENT: Provides for a range of temperatures to be specified.
# STATUS: Preliminary approval 2002-11-11
################################################
#
# DIFFRN_SOURCE
#
################################################
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 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.
;
# COMMENT: Suggested by the powder DMG.
# 2003.06.26 Definition modified by BM
# 2003-06-26 Definition further modified by Howard Flack
# STATUS: Preliminary approval 2002-11-11
######################################
#
# DIFFRN_STANDARDS category
#
######################################
data_diffrn_standards_decay_%_lt
_name '_diffrn_standards_decay_%_lt'
_category diffrn_standards
_type numb
_related_item '_diffrn_standards_decay_%'
_related_function alternate
_enumeration_range :100
_definition
; An upper limit on the percentage decrease in the mean
intensity of the set of standard reflections measured at the
start of the measurement of the diffraction pattern and at the
end. This value is used when the decay is too small to be
detected.
;
# COMMENT: Many experiments show no detectable decay and there is no provision
# for this at the moment other than to enter 0.0.
# STATUS: Preliminary approval 2002-11-11
#################################################
#
# DIFFRN_REFLNS
#
#################################################
data_diffrn_reflns_measured_fraction_resolution_full
_name '_diffrn_reflns_measured_fraction_resolution_full'
_category diffrn_reflns
_list yes
_type numb
_enumeration_range 0:1.0
_related_item '_diffrn_measured_fraction_theta_full'
_related_function alternate
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to the resolution given in _diffrn_reflns_resolution_full.
This number should be very close to 1.0, since it represents the
fraction of reflections measured in the part of the diffraction
pattern that is essentially complete.
;
# COMMENT: Replacement for _diffrn_measured_fraction_theta_full, moved to a
# more appropriate category and defined in terms of resolution rather than
# angle which depends on the radiation used.
# 2003-06-26 _related_function 'replace' changed to 'alternate'
# STATUS: Preliminary approval 2002-11-11
data__diffrn_reflns_measured_fraction_resolution_max
_name '_diffrn_reflns_measured_fraction_resolution_max'
_category diffrn_reflns
_list yes
_type numb
_enumeration_range 0:1.0
_related_item '_diffrn_measured_fraction_theta_max'
_related_function alternate
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to the resolution given in _diffrn_reflns_resolution_max.
;
# COMMENT: Replacement for _diffrn_measured_fraction_theta_max, moved to a
# more appropriate category and defined in terms of resolution rather than
# angle which depends on the radiation used.
# 2003-06-26 _related_function 'replace' changed to 'alternate'
# STATUS: Preliminary approval 2002-11-11
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. The fraction of unique
reflections measured out to this resolution is given by
_diffrn_reflns_measured_fraction_resolution_full
;
# COMMENT: Replacement for _diffrn_reflns_theta_full expressed in terms of
# resolution rather than an angle that depends on the radiation used.
# 2003-06-26 _related_function 'replace' changed to 'alternate'
# STATUS: Preliminary approval 2002-11-11
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 of the measured diffraction pattern.
;
# COMMENT: Replacement for _diffrn_reflns_theta_max expressed in terms of
# resolution rather than an angle that depends on the radiation used.
# 2003-06-26 _related_function 'replace' changed to 'alternate'
# STATUS: Preliminary approval 2002-11-11
#################################################
#
# EXPTL_CRYSTAL
#
#################################################
#
# The following three items replace _exptl_crystal_colour, replacing the free
# description allowed there by a more structured colour description based on
# the standardized names adopted by the International Center for Diffraction
# Data. This scheme allows for three standardized colour descriptors, each
# with its own enumeration list.
#
data_exptl_crystal_colour_primary
_name '_exptl_crystal_colour_primary'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Center 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',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
data_exptl_crystal_colour_modifier
_name '_exptl_crystal_colour_modifier'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Center 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',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
data_exptl_crystal_colour_lustre
_name '_exptl_crystal_colour_lustre'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Center 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',
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
loop_
_enumeration
metallic
dull
clear
#
# STATUS: Preliminary approval 2003-06-17
data_exptl_crystal_density_meas_
loop_ _name
'_exptl_crystal_density_meas_gt'
'_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_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
_definition
; The value above which (_*_gt) or below which (_*_lt) the
density measured using standard chemical and physical
methods lies. The units are megagrams per cubic metre (grams per
cubic centimetre). These items should not be used to report
new experimental work where _exptl_crystal_density_meas should
be used. They are intended for use in reporting information in
existing databases and archives which would be misleading if
reported under _exptl_crystal_density_meas.
;
loop_
_example
_example_detail
'_exptl_crystal_density_meas_lt 1.0' 'specimen floats in water'
; _exptl_crystal_density_meas_gt 2.5
_exptl_crystal_density_meas_lt 5.0
;
'Only the range within which the density lies was given in the original paper'
#
# STATUS: Preliminary approval 2003-06-16
data_exptl_crystal_density_meas_temp_*
loop_
_name '_exptl_crystal_density_meas_temp_gt'
'_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail 'Kelvins'
_related_item '_exptl_crystal_density_meas_temp'
_related_function alternate
_definition
; Temperature in kelvins above which (_*_gt) or below which
(_*_lt) _exptl_crystal_density_meas was determined. These
items should not be used for reporting new work where the
correct temperature of measurement should be given. They are
intended for use in reporting information stored in databases
or archives which would be misleading if reported under
_exptl_crystal_density_meas_temp.
;
loop_
_example
_example_detail
'_exptl_crystal_density_meas_temp_lt 300'
; The density was measured at some unspecified temperature below room
temperature.
;
# COMMENT: The above two items suggested by CCDC.
#
# STATUS: Preliminary approval 2003-06-16
data_exptl_crystal_recrystallization_method
_name '_exptl_crystal_recrystallization_method'
_category exptl_crystal
_type char
_example ?
_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.
;
# COMMENT: Suggested by CCDC.
# Definition elaborated to give details of what should be included.
# STATUS: Preliminary approval 2003-06-16
##########################################################
#
# PUBL category
#
##########################################################
data_publ_contact_author_id_iucr
_name '_publ_contact_author_id_iucr'
_category publ
_type char
_list yes
_example 2985
_definition
; Identifier in the IUCr contact database of the author
submitting the manuscript and datablock. This identifier may
be available from the World Directory of Crystallographers
(http://wdc.iucr.org).
;
# COMMENT: Submitted by Brian McMahon This identifier will allow linking to
# other publications or files by the contact author.
# (Linking based on name alone is inefficient because
# individuals change their names or spelling of the names. A complementary
# data name is proposed for the authors in the PUBL_AUTHOR category.
# STATUS: Preliminary approval 2003-01-07
#########################################################
#
# PUBL_AUTHOR category
#
#########################################################
data_publ_author_id_iucr
_name '_publ_author_id_iucr'
_category publ_author
_type char
_list yes
_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).
;
# COMMENT: Submitted by Brian McMahon. See _publ_contact_author_id_iucr for
# further details.
# STATUS: Preliminary approval 2003-01-07
#########################################
#
# REFINE category
#
#########################################
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 divided by 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.
;
# STATUS: Preliminary approval 2003-01-07
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 divided by 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.
;
# STATUS: Preliminary approval 2003-01-07
################################################
#
# CATEGORY: SPACE_GROUP
#
################################################
data_SPACE_GROUP
_name space_group
_category category_overview
_type null
_definition
; Contains all the data items that refer to the space group as a
whole, such as its name, crystal system etc. It 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 cif_sym
dictionary.
Space group types are identified by their International Tables
for Crystallography Vol A number or Schoenflies symbol.
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. It 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 cif_sym dictionary.
;
_example
;
_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
;
# STATUS: Preliminary approval 2003-03-11
data_space_group_crystal_system
_name '_space_group_crystal_system'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_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.
;
_type char
loop_
_enumeration
triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
# STATUS: Preliminary approval 2003-03-11
#
# THE PREVIOUS ITEM REPLACES _symmetry_cell_setting. The definition of the old
# item should be modified to make it clear that the old name is discontinued
# (the name is crystallographically incorrect and therefore misleading). The
# following items should be added to the dictionary entry for
# _symmetry_cell_setting:
#
# _related_item '_space_group_crystal_system'
# _related_function replace
#
# Incidentally I have removed the _related_item and _related_function from the
# definition of _space_group_crystal_system because they are incorrect. It is
# the _related_item that should 'replace' the item being defined, not the other
# way around.
#
data_space_group_id
_name '_space_group_id'
_category space_group
_list yes
_list_mandatory yes
_definition
; This is an identifier needed if _space_group_* items are looped.
;
_type char
loop_
_list_link_child
'_space_group_symop_sg_id'
# STATUS: Preliminary approval 2003-03-11
data_space_group_IT_number
_name '_space_group_IT_number'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_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.
;
_type numb
_enumeration_range 1:230
#
# As above _symmetry_Int_Tables_number should have:
#
# _related_item '_space_group_IT_number'
# _related_function replace
#
# added, and the _related_item and _related_function lines should be removed
# from the cif_sym dictionary.
#
# STATUS: Preliminary approval 2003-03-11
data_space_group_name_Hall
_name '_space_group_name_Hall'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
loop_
_example
_example_detail 'P 2c -2ac' 'Equivalent to Pca21'
'-I 4bd 2ab 3' 'Equivalent to Ia3d'
_definition
; Space group symbol defined by Hall (Acta Cryst. (1981) A37,
517-525) (See also International Tables for Crystallography
Vol.B (1993) 1.4 Appendix B).
Each component of the space group name is separated by a
space or an underscore. The use of space is strongly
recommended. The underscore is only retained because it
was used in earlier archived 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.
;
_type char
#
# As above '_symmetry_space_group_name_Hall' should have the following items
# added:
#
# _related_item '_space_group_name_Hall'
# _related_function replace
#
# and the _related_item and _related_function items should be removed
# from _space_group_name_Hall in the cif_sym dictionary.
#
# STATUS: Preliminary approval 2003-03-11
data_space_group_name_H-M_alt
_name '_space_group_name_H-M_alt'
_category space_group
_list both
_list_mandatory no
_list_reference '_space_group_id'
_type char
loop_
_example
_example_detail
;
loop_
_space_group_name_H-M_alt
'C m c m'
'C 2/c 2/m 21/m'
'A m a m'
;
'three examples for the space group number 63.'
_definition
; *_name_H-M_alt allows for 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 4.3.1 of International Tables for Crystallography
Vol A (1995) or a Hermann-Mauguin symbol for a conventional or
unconventional setting.
Each component of the space group name is separated by a
space or underscore. The use of space is strongly
recommended. The underscore is only retained because it
was used in earlier archived 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 the *_IT_number or *_name_Schoenflies.
The Hermann-Mauguin symbol may contain information on the
choice of basis though not on the choice of origin. To
define the setting uniquely use *_name_Hall or list the
symmetry operations.
;
#
# As above '_symmetry_space_group_name_H-M' should have the following items
# added:
#
# _related_item _space_group_name_H-M_alt
# _related_function replacement
#
# and the _related_item and _related_function should be removed from this item
# in the cif_sym dictionary.
#
# STATUS: Preliminary approval 2003-03-11
###########################################################
#
# SPACE GROUP SYMOP
#
###########################################################
data_SPACE_GROUP_SYMOP
_category category_overview
_type null
_definition
; Contains information about the symmetry operations of the
space group.
;
loop_
_example_detail
_example
;
The symmetry operations for the space group P21/c
;
; 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
;
# STATUS: Preliminary approval 2003-03-11
data_space_group_symop_id
_definition
; An arbitrary identifier that uniquely labels each symmetry
operation in the list.
;
_type char
_name '_space_group_symop_id'
_category space_group_symop
_list yes
_list_mandatory yes
#
# The following should be added to '_symmetry_equiv_pos_site_id' for the
# reasons described above:
#
# _related_item '_space_group_symop_id'
# _related_function replace
#
# and the _related_item and _related_function items should be removed from the
# cif_sym dictionary.
#
# STATUS: Preliminary approval 2003-03-11
data_space_group_symop_operation_xyz
_name '_space_group_symop_operation_xyz'
_category space_group_symop
_list both
_list_mandatory no
_list_reference '_space_group_symop_id'
loop_
_example
_example_detail
'x,1/2-y,1/2+z' 'c glide reflection through the plane (x,1/4,z)'
_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 the 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, Section 5)
When a list of symmetry operations is given, it is assumed
that the list contains all the operations of the space
group (including the identity operation) as given by the
representatives of the general position in International
Tables for Crystallography Vol. A.
;
_type char
_enumeration_default 'x,y,z'
# STATUS: Preliminary approval 2003-03-11
data_space_group_symop_sg_id
_name '_space_group_symop_sg_id'
_category space_group_symop
_list both
_list_mandatory no
_list_reference '_space_group_symop_id'
loop_
_example
_example_detail
? ?
_definition
; This must match a particular value of _space_group_id allowing
the symmetry operation to be identified with a particular space
group.
;
_type numb
_list_link_parent '_space_group_id'
# COMMENT: The _space_group items above have all been approved by
# COMCIFS. The only question we have to decide is which ones are to be included
# in the revised dictionary. Some changes have been made in the descriptions
# and examples to make them more appropriate for the core dictionary.
#
# STATUS: Preliminary approval 2003-03-11
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