New version of CIF Core dictionary (2.4)
Brian McMahon
bm at iucr.org
Tue Dec 18 10:06:13 GMT 2007
Dear COMCIFS
The Core Dictionary Management Group proposes a number of additions
to the core dictionary and a few minor revisions to existing content,
and requests the voting members of COMCIFS to approve these changes.
The changes are summarised below (the additional data items are
listed explicitly). The discussions of the coreDMG are available
at http://www.iucr.org/iucr-top/lists/coredmg/index.html
This draft has been approved following technical review by the
Dictionary Review Committee, who recommend that COMCIFS formally
approve this release. All members of this mailing list are welcome
to comment on the draft, but VOTING MEMBERS (I. D. Brown, H. M. Berman,
H. J. Bernstein, R. W. Grosse-Kunstleve, S. R. Hall, G. Madariaga,
B. McMahon and J. Westbrook) ARE REQUIRED TO SUBMIT A FORMAL VOTE for
or against the new version.
PLEASE SUBMIT YOUR VOTE BY JANUARY 20th 2008.
A complete draft of the dictionary incorporating these revisions may
be inspected at
ftp://ftp.iucr.org/cifdics/draft_cif_core_2.4.dic
with formatted versions (PDF and HTML respectively) at
ftp://ftp.iucr.org/cifdics/draft_core2.4.pdf
http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core_draft2.4.dic/index.html
If this version is approved, the relevant Chapters of International
Tables for Crystallography Volume G (Online) will be updated to
reflect and describe the new content.
Best wishes
Brian McMahon
Coordinating Secretary
#========================================================================
PROPOSED CHANGES IN CIF CORE DICTIONARY VERSION 2.4
2007-12-04 BMcM: Fixed typo in equation appearing in
_diffrn_reflns_av_sigmaI/netI and
_diffrn_reflns_av_unetI/netI
2007-12-04 IDB: Added new items approved by coreDMG:
SUMMARY
1. _atom_sites_solution_
Added new flags notdet, dual, other (Bruce Noll)
2. _chemical_enantioexcess_
Added items *_bulk, *_bulk_technique, *_crystal,
*_crystal_technique (H. D. Flack)
3. _diffrn_..._measured_fraction_
Added sentences to definitions of
_diffrn_reflns_resolution_full, *_theta_max and
*_resolution_max. Added new data items
_diffrn_reflns_Laue_measured_fraction_full, *_max
_diffrn_reflns_point_group_measured_fraction_full
and *_max
4. _diffrn_standards_decay_%
Clarified definition and added examples.
5. _distributed_density_
Added _atom_site_distributed_density_id and the new
DISTRIBUTED_DENSITY category following suggestions
from David Watkin.
6. _exptl_absorption_correction_T_max, *_T_min
Clarified definition and added items
exptl_transmission_factor_max and *_min
7. _geom_bond_multiplicity
New data item added.
8. _publ_section_keywords
New data name added.
9. _refine_ls_F_calc
Added _refine_ls_F_calc_details, *_formula and
*_precision.
10. _symmetry_equiv
Added _enumeration_default 1 to _space_group_symop_id
and _symmetry_equiv_pos_site_id; added
_enumeration_default x,y,z to
_symmetry_equiv_pos_as_xyz; added comment about the
need to have the identity as symop 1 to
_space_group_symop_operation_xyz, _space_group_symop_id,
_symmetry_equiv_pos_as_xyz and
_symmetry_equiv_pos_site_id
#------------------------------------------------------------------------
PROPOSED NEW DATA ITEMS:
#------------------------------------------------------------------------
data_atom_site_distributed_density_id
_name '_atom_site_distributed_density_id'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_list_mandatory no
_list_link_parent '_distributed_density_id'
_example an1
_example_detail 'see example in category DISTRIBUTED_DENSITY'
_definition
; An identifier that links the atom defined by _atom_site_label
with the distributed density of this atom defined in the
DISTRIBUTED_DENSITY category.
Note that all the atoms that give rise to a particular
distributed density, e.g. a ring, should be included in the
ATOM_SITE list, even when they, or the centroid of the
distribution, lie on a special position. That is, the
crystallographic site symmetry of the distribution is not
used to generate the full distributed density shape from the
crystallographic asymmetric portion.
The value of _atom_site_symmetry_multiplicity should be chosen
so that for each of the atoms in the ATOM_SITE list
(_atom_site_occupancy)*(_atom_site_symmetry_multiplicity) is
equal to its contribution to
(_chemical_formula_sum)*(_cell_formula_units_Z).
;
data_chemical_enantioexcess_bulk
_name '_chemical_enantioexcess_bulk'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_units .
_units_detail dimensionless
_definition
; The enantioexcess of the bulk material from which the
crystals were grown. A value of 0.0 indicates the
racemate. A value of 1.0 indicates that the compound
is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
(Moss et al., 1996). The composition of the crystal
and bulk must be the same.
Ref: Moss G. P. et al. (1996). Basic Terminology of
Stereochemistry. Pure Appl. Chem., 68, 2193-2222.
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
data_chemical_enantioexcess_bulk_technique
_name '_chemical_enantioexcess_bulk_technique'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail OA
; Enantioexcess determined by
measurement of the specific rotation
of the optical activity of the bulk
compound in solution.
;
CD
; Enantioexcess determined by
measurement of the visible/near UV
circular dichroism spectrum of the
bulk compound in solution.
;
EC
; Enantioexcess determined by
enantioselective chromatography of
the bulk compound in solution.
;
other
; Enantioexcess determined by
a technique not included elsewhere
in this list.
;
_definition
; The experimental technique used to determine the
enantioexcess of the bulk compound.
;
data_chemical_enantioexcess_crystal
_name '_chemical_enantioexcess_crystal'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_units .
_units_detail dimensionless
_definition
; The enantioexcess of the crystal used for the diffraction
study. A value of 0.0 indicates the racemate. A value of
1.0 indicates that the crystal is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
(Moss et al., 1996).
Ref: Moss G. P. et al. (1996). Basic Terminology of
Stereochemistry. Pure Appl. Chem., 68, 2193-2222.
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
data_chemical_enantioexcess_crystal_technique
_name '_chemical_enantioexcess_crystal_technique'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail CD
; Enantioexcess determined by
measurement of the visible/near UV
circular dichroism spectrum of the
crystal taken into solution.
;
EC
; Enantioexcess determined by
enantioselective chromatography of
the crystal taken into solution.
;
other
; Enantioexcess determined by
a technique not included elsewhere
in this list.
;
_definition
; The experimental technique used to determine the
enantioexcess of the crystal.
;
data_diffrn_reflns_Laue_measured_fraction_full
_name '_diffrn_reflns_Laue_measured_fraction_full'
_category diffrn_reflns
_type numb
_related_item '_diffrn_measured_fraction_theta_full'
_related_function alternate
_enumeration_range 0.95:1.0
_definition
; Fraction of Laue unique reflections (symmetry-independent in
the Laue group) measured out to the resolution given in
_diffrn_reflns_resolution_full or _diffrn_reflns_theta_full.
The Laue group always contains a centre of symmetry so that
the reflection h,k,l is always equivalent to the reflection
-h,-k,-l even in space groups without a centre of symmetry.
This number should not be less than 0.95, since it represents
the fraction of reflections measured in the part of the
diffraction pattern that is essentially complete.
;
data_diffrn_reflns_Laue_measured_fraction_max
_name '_diffrn_reflns_Laue_measured_fraction_max'
_category diffrn_reflns
_type numb
_related_item '_diffrn_measured_fraction_theta_max'
_related_function alternate
_enumeration_range 0:1.0
_definition
; Fraction of Laue unique reflections (symmetry-independent in
the Laue group) measured out to the resolution given in
_diffrn_reflns_resolution_max or _diffrn_reflns_theta_max.
The Laue group always contains a centre of symmetry so that the
reflection h,k,l is always equivalent to the reflection -h,-k,-l
even in space groups without a centre of symmetry.
;
data_diffrn_reflns_point_group_measured_fraction_full
_name '_diffrn_reflns_point_group_measured_fraction_full'
_category diffrn_reflns
_type numb
_related_item '_diffrn_measured_fraction_theta_full'
_related_function alternate
_enumeration_range 0.95:1.0
_definition
; Fraction of crystal point-group unique reflections (i.e.
symmetry-independent in the crystal point group) measured
out to the resolution given in _diffrn_reflns_resolution_full
or _diffrn_reflns_theta_full. For space groups that do not
contain a centre of symmetry the reflections h,k,l and
-h,-k,-l are independent. This number should not be less
than 0.95, since it represents the fraction of reflections
measured in the part of the diffraction pattern that is
essentially complete.
;
data_diffrn_reflns_point_group_measured_fraction_max
_name '_diffrn_reflns_point_group_measured_fraction_max'
_category diffrn_reflns
_type numb
_related_item '_diffrn_measured_fraction_theta_max'
_related_function alternate
_enumeration_range 0:1.0
_definition
; Fraction of crystal point-group unique reflections (i.e.
symmetry-independent in the crystal point group) measured
out to the resolution given in _diffrn_reflns_resolution_max
or _diffrn_reflns_theta_max. For space groups that do not
contain a centre of symmetry the reflections h,k,l and
-h,-k,-l are independent.
;
reflection count is close to complete. The fraction of unique
reflections measured out to this angle is given by
_diffrn_measured_fraction_theta_full.
diffraction pattern. The fraction of unique reflections
measured out to this angle is given by
_diffrn_measured_fraction_theta_max
The fraction of unique reflections measured out to this angle
is given by _diffrn_measured_fraction_theta_max
#########################
## DISTRIBUTED_DENSITY ##
#########################
data_distributed_density_[]
_name '_distributed_density_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_adp_type
_atom_site_distributed_density_id
_atom_site_calc_flag
# Inner ring of cyclopentadiene carbon atoms and borazole
C1 C -0.1362(8) -0.0974(8) -0.3116(10) 0.0662(18) 0.625(1) 4 Uiso . d
C2 C -0.1060(8) -0.2165(8) -0.1837(10) 0.071(2) 0.625(1) 4 Uiso . d
C3 C -0.1774(9) -0.1939(9) -0.0820(11) 0.082(2) 0.625(1) 4 Uiso . d
C4 C -0.2529(9) -0.0561(9) -0.1479(12) 0.084(2) 0.625(1) 4 Uiso . d
C5 C -0.2261(8) -0.0002(8) -0.2891(10) 0.072(2) 0.625(1) 4 Uiso . d
C1a C . . . . 0.208(1) 4 . an1 dum
C2a C . . . . 0.208(1) 4 . an1 dum
C3a C . . . . 0.208(1) 4 . an1 dum
C4a C . . . . 0.208(1) 4 . an1 dum
C5a C . . . . 0.208(1) 4 . an1 dum
N1 N -0.1375(8) -0.0968(8) -0.3201(10) 0.065(2) 0.167(1) 4 Uiso . d
B1 B -0.1002(8) -0.2265(8) -0.1728(10) 0.071(2) 0.167(1) 4 Uiso . d
N2 N -0.1402(8) -0.1034(8) -0.0765(10) 0.076(2) 0.167(1) 4 Uiso . d
B2 B -0.2370(9) -0.0364(9) -0.1832(10) 0.085(2) 0.167(1) 4 Uiso . d
N3 N -0.2893(8) 0.0034(8) -0.3621(10) 0.062(2) 0.167(1) 4 Uiso . d
B3 B -0.2246(9) -0.0452(9) -0.3004(11) 0.073(2) 0.167(1) 4 Uiso . d
# Outer ring of methyl groups
C11 C -0.0951 -0.0733 -0.4330 0.1901 0.625(1) 4 Uani . d
C12 C -0.0272 -0.3236 -0.1750 0.1990 0.625(1) 4 Uani . d
C13 C -0.1719 -0.2833 0.0404 0.2483 0.625(1) 4 Uani . d
C14 C -0.3291 -0.0080 -0.0844 0.2450 0.625(1) 4 Uani . d
C15 C -0.2817 0.1218 -0.3770 0.2219 0.625(1) 4 Uani . d
C11a C . . . . 0.208(1) 4 . an2 dum
C12a C . . . . 0.208(1) 4 . an2 dum
C13a C . . . . 0.208(1) 4 . an2 dum
C14a C . . . . 0.208(1) 4 . an2 dum
C15a C . . . . 0.208(1) 4 . an2 dum
# Details of the two rings of distributed density are given
# in the following loop
loop_
_distributed_density_id
_distributed_density_shape
_distributed_density_position_x
_distributed_density_position_y
_distributed_density_position_z
_distributed_density_radius
_distributed_density_direction_h
_distributed_density_direction_k
_distributed_density_direction_l
_distributed_density_Uiso
_distributed_density_symmetry_multiplicity
an1 ring -0.1810(8) -0.1133(8) -0.2058(8)
1.198(6) 1.35(2) 0.07(2) -0.45(2) 0.052(2) 4
an2 ring -0.1873(14) -0.1156(14) -0.2210(2)
2.626(6) 1.30(2) 0.10(2) -0.40(2) 0.131(3) 4
;
;
Example 1 - This example is fictitious (and chemically implausible) but
it is designed to illustrate how a complex system of
distributed density can be recorded. In this example
pentamethyl cyclopentadiene (Cp*) and borazole occupy the
same location in the crystal in the ratio 5:1. The atoms
of the borazole ring are fixed as are three quarters of
the atoms in the Cp* ring, but the remaining quarter of
the Cp* molecules are freely rotating around the cylindrical
Cp* axis. The rotating Cp* molecules give rise to two
concentric rings of density, one from the atoms in the
ring and the other from the methyl groups (hydrogen atoms
are ignored). On top of these rings lie the atoms of the
fixed Cp* molecules. The atoms of the borazole molecule also
lie over the inner Cp* ring. Full details of the chemical
composition are given in the ATOM_SITE loop together with
the positions of the fixed atoms. The coordinates of the
atoms that give rise to the distributed ring of density
are set to '.', meaning that they have no significance as
the atoms are dummy atoms. They are included to give the
correct composition when _atom_site_occupancy and
_atom_site_symmetry_multiplicity are given. The composition
defined in the ATOM_SITE loop is linked to the
DISTRIBUTED_DENSITY loop through the parent-child
identifiers, 'an1' and 'an2' (for annulus 1 and 2). The
one quarter of the Cp* molecules that are rotating have
the occupation number of 0.208 = 2/24 = 5/6 (the total
occupancy of the Cp*) x 1/4 (the portion rotating).
The three quarters that are in fixed positions have the
occupation number of 0.625 = 15/24 = 5/6 x 3/4.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the distributed_density category describe the
geometric arrangement of an atom or atoms when they are
distributed uniformly over a line or surface such as a ring,
cylindrical shell or spherical shell, the line or surface being
given a thickness through the application of an atomic
displacement parameter.
;
data_distributed_density_details
_name '_distributed_density_details'
_category distributed_density
_type char
_list both
_list_reference '_distributed_density_id'
_example
; The distribution was modelled using a disc of
density of the given radius.
;
_definition
; Information about the distribution of density not
given in other items.
;
data_distributed_density_direction_
loop_ _name '_distributed_density_direction_h'
'_distributed_density_direction_k'
'_distributed_density_direction_l'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_units rlu
_units_detail 'reciprocal lattice units'
_definition
; The (covariant) components on a reciprocal-lattice basis
of a vector of arbitrary length used to indicate the
direction of the unique axis of the distribution,
e.g. the axis of a cylindrical shell or the normal
to the plane of a ring.
;
data_distributed_density_id
_name '_distributed_density_id'
_category distributed_density
_type char
_list both
_list_mandatory yes
_list_link_child '_atom_site_distributed_density_id'
_definition
; An identifier that links the atom defined by
_atom_site_label with a distributed density
defined in the DISTRIBUTED_DENSITY category.
;
data_distributed_density_length
_name '_distributed_density_length'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A
_units_detail 'Angstrom units'
_definition
; The length of the line or cylindrical shell of distributed
density in angstroms.
;
data_distributed_density_position_
loop_ _name '_distributed_density_position_x'
'_distributed_density_position_y'
'_distributed_density_position_z'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_definition
; The position of the centroid of the distributed density in
fractions of the unit cell values.
;
data_distributed_density_radius
_name '_distributed_density_radius'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A
_units_detail 'Angstrom units'
_definition
; The radius of the ring, or of the cylindrical or spherical
shell, of distributed density in angstroms.
;
data_distributed_density_shape
_name '_distributed_density_shape'
_category distributed_density
_type char
_list both
_list_reference '_distributed_density_id'
loop_ _enumeration
_enumeration_detail
line 'line segment'
infline
; infinite line running through
the crystal
;
ring 'circular ring'
cylshell
; cylindrical shell of finite length
;
infcylshell
; cylindrical shell running through
the crystal
;
sphereshell 'spherical shell'
other
; give details in
_distributed_density_details
;
_definition
; A flag that indicates the shape of the distributed density.
The lines and ring are one-dimensional distributions of
atoms and the cylindrical shell and spherical shell are
two-dimensional distributions.
In each case the root-mean-square thickness of the distribution
is given by the atomic displacement parameter defined in
_distributed_density_Uiso.
;
data_distributed_density_symmetry_multiplicity
_name '_distributed_density_symmetry_multiplicity'
_category distributed_density
_type numb
_list both
_list_reference '_distributed_density_id'
_enumeration_range 1:192
_definition
; The number of images of the centroid of the distributed density
that the space-group symmetry generates in the unit cell
reported in the CELL category. It is the number that
appears in International Tables for Crystallography Vol. A
(2002) for the Wyckoff position occupied by the centroid.
In this treatment the symmetry of the distribution itself is
ignored, including any operations of its point group that are
part of the crystallographic site symmetry of the centroid.
All the atoms that give rise to the distributed density should
therefore be listed in the ATOM_SITE category even if they, or
the centroid of the distribution, lie on crystallographic
special positions.
For example, if the distribution is a ring and the centroid
of the ring lies on a crystallographic mirror plane, all
the atoms in the ring are listed if the ring lies either in or
perpendicular to the mirror plane since the mirror image of
the ring lies over the ring itself. If the ring is at some
arbitrary angle to the mirror plane, the mirror generates
a second ring and both rings should be described independently.
However, because both rings cannot be simultaneously occupied,
the occupation numbers given in the ATOM_SITE category must
have a value equal to or less than 0.5.
;
data_distributed_density_Uiso
_name '_distributed_density_Uiso'
_category distributed_density
_type numb
_type_conditions esd
_list both
_list_reference '_distributed_density_id'
_enumeration_range 0.0:
_units A^2^
_units_detail 'Angstrom units squared'
_example 0.018(3)
_definition
; The factor exp(-Ux^-2^) is applied to all parts of the
distribution, where U = _distributed_density_Uiso and
x is the distance from the ideal one- or two-dimensional
shape. This emulates the effects of thermal motion or
static displacement from the ideal positions described in this
category and has the effect of converting the simple one-
or two-dimensional geometric shapes into three-dimensional
objects of mean square thickness U.
;
data_exptl_transmission_factor_max
_name '_exptl_transmission_factor_max'
_category exptl
_type numb
_type_conditions su
_enumeration_range 0.0:1.0
_definition
; The calculated maximum value of the transmission factor for
the specimen. Its value does not include the effects of
absorption in the specimen mount. The presence of this
item does not imply that the structure factors have been
corrected for absorption. The applied correction should be
given by _exptl_absorpt_correction_T_max.
;
data_exptl_transmission_factor_min
_name '_exptl_transmission_factor_min'
_category exptl
_type numb
_type_conditions su
_enumeration_range 0.0:1.0
_definition
; The calculated minimum value of the transmission factor for
the specimen. Its value does not include the effects of
absorption in the specimen mount. The presence of this
item does not imply that the structure factors have been
corrected for absorption. The applied correction should be
given by _exptl_absorpt_correction_T_min.
;
data_geom_bond_multiplicity
_name '_geom_bond_multiplicity'
_category geom_bond
_type numb
_list yes
_list_reference '_geom_bond_atom_site_label_'
_enumeration_range 0:
_enumeration_default 1
_definition
; The number of times the given bond appears in the environment
of the atoms labelled _geom_bond_atom_site_label_1. In cases
where the full list of bonds is given, one of the series of
equivalent bonds may be assigned the appropriate multiplicity
while the others are assigned a value of 0.
;
data_refine_ls_F_calc_details
_name '_refine_ls_F_calc_details'
_category refine
_type char
loop_ _example 'Gaussian integration using 16 points'
; Bessel functions expansion up to 5th order.
Bessel functions estimated accuracy: better
than 0.001 electrons.
;
_definition
; Details concerning the evaluation of the structure
factors using the expression given in
_refine_ls_F_calc_formula.
;
data_refine_ls_F_calc_formula
_name '_refine_ls_F_calc_formula'
_category refine
_type char
_definition
; Analytical expression used to calculate the structure factors.
;
data_refine_ls_F_calc_precision
_name '_refine_ls_F_calc_precision'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; This item gives an estimate of the precision resulting
from the numerical approximations made during the evaluation
of the structure factors using the expression given in
_refine_ls_F_calc_formula following the method outlined
in _refine_ls_F_calc_details. For X-ray diffraction the
result is given in electrons.
;
#========================================================================
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