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templ_attr.cif
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#\#CIF_2.0
##############################################################################
# #
# TEMPLATE DEFINITION ATTRIBUTES DICTIONARY #
# #
##############################################################################
data_TEMPL_ATTR
_dictionary.title TEMPL_ATTR
_dictionary.class Template
_dictionary.version 1.4.11
_dictionary.date 2024-07-17
_dictionary.uri https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif
_dictionary.ddl_conformance 4.2.0
_description.text
;
This dictionary contains definition attribute sets that are common
to other CIF dictionaries and is imported by them.
;
#---------------------------------------------------------------------------
save_atom_site_label
_definition.update 2021-10-25
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell. It is made up of
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 underline character. Underline separators are
only used if higher-order components exist. If an intermediate
component is not used it may be omitted provided the underline
separators are inserted. For example the label 'C233__ggg' is
acceptable and represents the components C, 233, '', and ggg.
Each label may have a different number of components.
;
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Word
loop_
_description_example.case C12 Ca3g28 Fe3+17 H*251
C_a_phe_83_a_0 Zn_Zn_301_A_0
save_
save_restr_label
_definition.update 2021-10-25
_description.text
;
Labels of atom sites subtending distance or angle. Atom 2 is the apex for
angular restraints.
;
_name.linked_item_id '_atom_site.label'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_atom_site_id
_definition.update 2021-10-25
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_rho_coeff
_definition.update 2024-03-28
_description.text
;
Specifies a multipole population coefficient P(l,m) for
the atom identified in _atom_rho_multipole.atom_label.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_rho_kappa
_definition.update 2024-03-28
_description.text
;
A radial function expansion-contraction coefficient
(κ = _atom_rho_multipole_kappa.base and
κ'(l) = _atom_rho_multipole_kappa.prime[l])
for the atom specified in _atom_rho_multipole.atom_label.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_rho_slater
_definition.update 2024-03-28
_description.text
;
Items used when the radial dependence of the valence
electron density, R(κ'(l),l,r), of the atom specified in
_atom_rho_multipole.atom_label is expressed as a Slater-type
function [Hansen & Coppens (1978), equation (3)]
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_matrix_pdb
_definition.update 2021-03-18
_description.text
;
Element of the PDB ORIGX matrix or vector.
;
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_matrix_w
_definition.update 2023-09-11
_description.text
;
Element of the matrix W defined by van Smaalen (1991); (1995)
;
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
_units.code none
save_
save_ms_index
_definition.update 2014-06-27
_description.text
;
Additional Miller indices needed to write the reciprocal vector
in the definition of _diffrn_refln_index.m_list,
_diffrn_standard_refln.index_m_list, _exptl_crystal_face.index_m_list.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
save_
save_index_limit_max
_definition.update 2021-03-01
_description.text
;
Maximum value of the additional Miller indices appearing in
_diffrn_reflns.index_m_* and _reflns.index_m_*.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_units.code none
save_
save_index_limit_min
_definition.update 2021-03-01
_description.text
;
Minimum value of the additional Miller indices appearing in
_diffrn_reflns.index_m_* and _reflns.index_m_*.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_units.code none
save_
save_cell_angle
_definition.update 2023-07-01
_description.text
;
The angle between the bounding cell axes.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:180.0
_units.code degrees
save_
save_cell_angle_su
_definition.update 2023-07-01
_description.text
;
Standard uncertainty of the angle between the bounding cell axes.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code degrees
save_
save_cell_length
_definition.update 2024-07-17
_description.text
;
The length of each cell axis.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save_cell_length_su
_definition.update 2023-07-01
_description.text
;
Standard uncertainty of the length of each cell axis.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_site_symmetry
_definition.update 2023-06-19
_description.text
;
Data item specifying the symmetry operation codes applied to the atom
sites involved in a specific geometric configuration.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'pqr'. These numbers are
combined to form the code 'n pqr' or n_pqr.
The character string n_pqr is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match
a number given in _space_group_symop.id (or one of its
aliases, such as _symmetry_equiv_pos_site_id).
p, q and r 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 (p,q,r) by the relations
p = 5 + x
q = 5 + y
r = 5 + z
;
_type.purpose Composite
_type.source Derived
_type.container Single
_type.contents Symop
loop_
_description_example.case
_description_example.detail '4' '4th symmetry operation applied.'
'7_645' '7th symm. posn.; +a on x; -b on y.'
. 'No symmetry or translation to site.'
_enumeration.default 1_555
save_
save_cartn_coord
_definition.update 2012-05-07
_description.text
;
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.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_cartn_coord_su
_definition.update 2023-07-01
_description.text
;
Standard uncertainty values of 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.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_fract_coord
_definition.update 2012-05-07
_description.text
;
Atom site coordinates as fractions of the cell length values.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_fract_coord_su
_definition.update 2023-07-01
_description.text
;
Standard uncertainty value of the atom site coordinates
as fractions of the cell length values.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code none
save_
save_label_component
_definition.update 2021-10-21
_description.text
;
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 underline.
;
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_label_comp
_definition.update 2021-10-21
_description.text
;
See label_component_0 description.
;
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Word
save_
save_cartn_matrix
_definition.update 2021-07-21
_description.text
;
Matrix 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 3x1 translation is
defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial assignments with
cell vectors a,b,c aligned with orthogonal axes X,Y,Z so that c||Z and
b in plane YZ.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_cartn_vector
_definition.update 2021-07-21
_description.text
;
The 3x1 translation that is used with _atom_sites_cartn_transform.matrix
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.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_ncs_matrix_ij
_definition.update 2021-03-01
_description.text
;
The [I][J] element of the 3x3 matrix component of a
non-crystallographic symmetry operation.
;
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_rot_matrix_ij
_definition.update 2021-03-01
_description.text
;
The [I][J] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_fract_matrix
_definition.update 2021-07-21
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE category
to fractional coordinates. The axial alignments of this transformation are
described in _atom_sites_fract_transform.axes. The 3x1 translation is
defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial assignments with
cell vectors a,b,c aligned with orthogonal axes X,Y,Z so that c||Z and
b in plane YZ.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code reciprocal_angstroms
save_
save_fract_vector
_definition.update 2021-07-21
_description.text
;
The 3x1 translation that is used with _atom_sites_fract_transform.matrix
to transform Cartesian coordinates in the ATOM_SITE category to fractional
coordinates. The axial alignments of this transformation are described
in _atom_sites_fract_transform.axes.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_aniso_bij
_definition.update 2023-02-16
_description.text
;
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 [1].
Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1].
[1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstrom_squared
save_
save_aniso_bij_su
_definition.update 2023-07-01
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the B^ij^ anisotropic atomic displacement components (see
aniso_BIJ). Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the B^ij^ calculation.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstrom_squared
save_
save_aniso_betaij
_definition.update 2023-02-16
_description.text
;
These are the standard unitless anisotropic atomic displacement components
which appear in the structure factor term:
T = exp{-1 sum~i~ [ sum~j~ (β^ij^ h~i~ h~j~) ] }
h = the Miller indices
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of β for reporting atomic displacement parameters; U is preferred [1].
Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1].
[1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
save_
save_aniso_betaij_su
_definition.update 2023-02-15
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the β^ij^ anisotropic atomic displacement components (see
aniso_betaIJ). Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the β^ij^ calculation.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code none
save_
save_aniso_uij
_definition.update 2023-02-16
_description.text
;
These are the standard anisotropic atomic displacement components, in
angstroms squared, which appear in the structure factor term:
T = exp{ -2π^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.
The IUCr Commission on Nomenclature recommends the use of U for reporting
atomic displacement parameters [1].
Note that U^ij^ = β^ij^/(2 π^2^ a*~i~ a*~j~) = B^ij^/(8 π^2^) [1].
[1] Trueblood, K. N. et al. (1996). Acta Crystallogr. A52(5), 770-781.
;
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstrom_squared
save_
save_aniso_uij_su
_definition.update 2023-07-01
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the U^ij^ anisotropic atomic displacement components (see
aniso_UIJ). Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the U^ij^ calculation.
;
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstrom_squared
save_
save_general_su
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save_cromer_mann_coeff
_definition.update 2023-06-03
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of (0.0 < s < 2.0 Å^-1^) X-ray scattering factors.
f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
of the incident radiation in angstroms.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
save_
save_hi_ang_fox_coeffs
_definition.update 2023-06-03
_description.text
;
The set of data items used to define Fox et al. coefficients
for generation of high angle (2.0 < s < 6.0 Å^-1^) X-ray scattering factors.
f(s) = exp(Sum(c~i~ * s^i^, i=0:3))
where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
of the incident radiation in angstroms.
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
save_
save_miller_index
_definition.update 2013-04-16
_description.text
;
The index of a reciprocal space vector.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_units.code none
save_
save_orient_matrix
_definition.update 2012-05-07
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_units.code none
save_
save_transf_matrix
_definition.update 2012-05-07
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_units.code none
save_
save_face_angle
_definition.update 2013-04-15
_description.text
;
Diffractometer angle setting 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.
;
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range -180.0:180.0
_units.code degrees
save_
save_orient_angle
_definition.update 2013-04-15
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range -180.0:180.0
_units.code degrees
save_
save_diffr_angle
_definition.update 2013-04-15
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -180.0:180.0
_units.code degrees
save_
save_display_colour
_definition.update 2019-01-09
_description.text
;
Integer value between 0 and 255 giving the intensity of a
specific colour component (red, green or blue) for the RGB
display colour code.
;
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.range 0:255
_units.code none
save_
#=============================================================================
# The dictionary's attribute creation history.
#============================================================================
loop_
_dictionary_audit.version
_dictionary_audit.date
_dictionary_audit.revision
1.0.0 2005-12-12
;
Initial version of the TEMPLATES dictionary created from the
definitions used in CORE_3 dictionary version 3.5.02
;
1.0.1 2006-02-12
;
Remove dictionary attributes from a save frame.
Change category core_templates to template
;
1.2.1 2006-02-21
;
File structure to conform with prototype version dictionaries.
;
1.2.2 2006-03-07
;
Added the template _template.relational_id for the ddl3 dictionary.
;
1.2.3 2006-06-17
;
Apply DDL 3.6.01 changes
;
1.2.4 2006-06-29
;
Remove "_template" from the definition names.
Apply DDL 3.6.05 changes.
Change file name from templates.dic to com_att.dic
;
1.2.5 2006-09-07
;
Apply DDL 3.6.08 changes
;
1.2.6 2006-11-13
;
Apply DDL 3.6.10 changes
;
1.2.7 2006-12-14
;
Apply DDL 3.7.01 changes
;
1.2.8 2008-06-18
;
Change _type.purpose for Miller_index from Observed to Identify
;
1.3.1 2011-08-03
;
Remove definition.id lines in keeping with nested imports.
;
1.3.2 2011-12-01
;
Update the DDL version. No Matrix types present.
;
1.3.3 2012-05-07
;
Apply changes of 3.10.01 DDL version.
;
1.3.4 2012-10-16
;
Apply changes of 3.10.02 DDL version. "Label" becomes "Code".
;
1.3.5 2012-11-29
;
Add "_enumeration.def_index_id '_atom_type.symbol' "
to Cromer_Mann_coeff and hi_ang_Fox_coeffs.
;
1.3.6 2012-12-11
;
Add the templates Cartn_matrix and fract_matrix
;
1.4.1 2013-03-08
;
Changes arising from alerts issued by ALIGN.
;
1.4.2 2013-04-15
;
Removed description.common from all defs; inconsistent invocations
Changed types for 'diffrn_angle'
Added new frame for 'orient_angle'
;
1.4.3 2013-04-16
;
Changed type.source 'Measured' to 'Recorded'
Changed type.source 'Assigned' to 'Recorded' in Miller_index
;
1.4.4 2013-04-17
;
Changed type.source 'Quantity' to 'Number' or 'Encode'
;
1.4.5 2014-06-08
;
Added aniso_BIJ_su and aniso_UIJ_su
Added atom_site_fract_su and atom_site_cartn_su
;
1.4.6 2014-06-09
;
dummy top line added to all frames; this is skipped on import.
;
1.4.7 2014-06-12
;
Added attribute save frame "aniso_BIJ2"
Added attribute save frame "rot_matrix_IJ"
Added attribute save frame "ncs_matrix_IJ"
Added attribute save frame "atom_site_id"
Added attribute save frame "label_comp"
;
1.4.8 2014-06-27
;
Added attribute save frame "ms_index"
Added attribute save frame "matrix_w"
;
1.4.9 2019-09-25
;
Changed the '_type.purpose' from 'Encode' to 'Link' in the 'atom_site_id'
save frame.
Removed the '_name.linked_item_id' data item from the 'atom_site_label'
save frame.