Generated with dic2owl from cif_core.dic
_atom_analytical.analyte
Symbol of the element for which a particular composition refers to, as given by _atom_analytical.analyte_mass_percent.
['Actinium', 'Silver', 'Aluminum', 'Americium', 'Argon', 'Arsenic', 'Astatine', 'Gold', 'Boron', 'Barium', 'Beryllium', 'Bohrium', 'Bismuth', 'Berkelium', 'Bromine', 'Carbon', 'Calcium', 'Cadmium', 'Cerium', 'Californium', 'Chlorine', 'Curium', 'Copernicium', 'Cobalt', 'Chromium', 'Cesium', 'Copper', 'Deuterium', 'Dubnium', 'Darmstadtium', 'Dysprosium', 'Erbium', 'Einsteinium', 'Europium', 'Fluorine', 'Iron', 'Flerovium', 'Fermium', 'Francium', 'Gallium', 'Gadolinium', 'Germanium', 'Hydrogen', 'Helium', 'Hafnium', 'Mercury', 'Holmium', 'Hassium', 'Iodine', 'Indium', 'Iridium', 'Potassium', 'Krypton', 'Lanthanum', 'Lithium', 'Lawrencium', 'Lutetium', 'Livermorium', 'Moscovium', 'Mendelevium', 'Magnesium', 'Manganese', 'Molybdenum', 'Meitnerium', 'Nitrogen', 'Sodium', 'Niobium', 'Neodymium', 'Neon', 'Nihonium', 'Nickel', 'Nobelium', 'Neptunium', 'Oxygen', 'Oganesson', 'Osmium', 'Phosphorus', 'Protactinium', 'Lead', 'Palladium', 'Promethium', 'Polonium', 'Praseodymium', 'Platinum', 'Plutonium', 'Radium', 'Rubidium', 'Rhenium', 'Rutherfordium', 'Roentgenium', 'Rhodium', 'Radon', 'Ruthenium', 'Sulfur', 'Antimony', 'Scandium', 'Selenium', 'Seaborgium', 'Silicon', 'Samarium', 'Tin', 'Strontium', 'Tantalum', 'Terbium', 'Technetium', 'Tellurium', 'Thorium', 'Titanium', 'Thallium', 'Thulium', 'Tennessine', 'Uranium', 'Vanadium', 'Tungsten', 'Xenon', 'Yttrium', 'Ytterbium', 'Zinc', 'Zirconium']
['Ac', 'Ag', 'Al', 'Am', 'Ar', 'As', 'At', 'Au', 'B', 'Ba', 'Be', 'Bh', 'Bi', 'Bk', 'Br', 'C', 'Ca', 'Cd', 'Ce', 'Cf', 'Cl', 'Cm', 'Cn', 'Co', 'Cr', 'Cs', 'Cu', 'D', 'Db', 'Ds', 'Dy', 'Er', 'Es', 'Eu', 'F', 'Fe', 'Fl', 'Fm', 'Fr', 'Ga', 'Gd', 'Ge', 'H', 'He', 'Hf', 'Hg', 'Ho', 'Hs', 'I', 'In', 'Ir', 'K', 'Kr', 'La', 'Li', 'Lr', 'Lu', 'Lv', 'Mc', 'Md', 'Mg', 'Mn', 'Mo', 'Mt', 'N', 'Na', 'Nb', 'Nd', 'Ne', 'Nh', 'Ni', 'No', 'Np', 'O', 'Og', 'Os', 'P', 'Pa', 'Pb', 'Pd', 'Pm', 'Po', 'Pr', 'Pt', 'Pu', 'Ra', 'Rb', 'Re', 'Rf', 'Rg', 'Rh', 'Rn', 'Ru', 'S', 'Sb', 'Sc', 'Se', 'Sg', 'Si', 'Sm', 'Sn', 'Sr', 'Ta', 'Tb', 'Tc', 'Te', 'Th', 'Ti', 'Tl', 'Tm', 'Ts', 'U', 'V', 'W', 'Xe', 'Y', 'Yb', 'Zn', 'Zr']
atom_analytical
analyte
Single
Word
State
Assigned
_atom_analytical.analyte_mass_percent
Mass percentage of the analyte element derived from elemental analysis.
analyte_mass_percent
Real
Measurand
Derived
none
_atom_analytical.analyte_mass_percent_su
Standard uncertainty of _atom_analytical.analyte_mass_percent.
analyte_mass_percent_su
Related
_atom_analytical.chemical_species
Chemical formula of the species for which the corresponding _atom_analytical.chemical_species_mass_percent refers. The following rules apply in the construction of the formula: 1. Only recognized element symbols may be used. 2. The first element corresponds to the analyte. The remaining elements should be given in alphabetical order by symbol. 3. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 4. A space or parenthesis must separate each cluster of (element symbol + count). A formula cannot begin with a paranthesis. 5. Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers.
['Fe2 O3', 'Li', 'Si O2', 'Ca S O4 (H2 O)2']
chemical_species
Text
Encode
_atom_analytical.chemical_species_mass_percent
Mass percentage of the chemical species given in _atom_analytical.chemical_species as derived from elemental analysis. This is most often used in elemental compositions determined by XRF, where elements are reported as equivalent mass percentages of their relevant oxide. For example: Al is reported as Al2O3, P is reported as P2O5.
chemical_species_mass_percent
_atom_analytical.chemical_species_mass_percent_su
Standard uncertainty of _atom_analytical.chemical_species_mass_percent.
chemical_species_mass_percent_su
_atom_analytical.id
Arbitrary label uniquely identifying a single composition value.
Key
_atom_analytical.meas_id
Arbitrary label identifying the source of an elemental composition. This code must match the _atom_analytical_source.id of the associated technique in the analytical source list.
_atom_analytical_source.id
meas_id
Link
_atom_analytical_mass_loss.id
Arbitrary label uniquely identifying the source of an elemental composition value. This value is used by _atom_analytical.meas_id to link individual composition values to their corresponding technique of determination.
atom_analytical_mass_loss
_atom_analytical_mass_loss.meas_id
_atom_analytical_mass_loss.percent
Mass lost by the specimen during specimen preparation expressed as a percentage. The temperature at which the mass loss was recorded is given by _atom_analytical_mass_loss.temperature. A mass gain is represented by a negative value. This data name would be used to record mass loss on drying, or mass loss on ignition, during, for example, fusion bead preparation for XRF analysis.
['\n Represents a mass loss of 12.5 wt% upon exposure of the specimen\n to the temperature given in _atom_analytical_mass_loss.temperature.', '\n Represents a mass gain of 7.2 wt% upon exposure of the specimen\n to the temperature given in _atom_analytical_mass_loss.temperature.']
percent
_atom_analytical_mass_loss.percent_su
Standard uncertainty of _atom_analytical_mass_loss.percent.
percent_su
_atom_analytical_mass_loss.special_details
Text describing the conditions under which the data were collected that are not able to be captured using other data names within the ATOM_ANALYTICAL_MASS_LOSS category.
special_details
Describe
Recorded
_atom_analytical_mass_loss.temperature
The temperature, in kelvin, at which the mass loss was recorded as given by _atom_analytical_mass_loss.percent. This would be used to record the temperature of drying or ignition, during, for example, fusion bead preparation for XRF analysis.
temperature
kelvins
_atom_analytical_mass_loss.temperature_su
Standard uncertainty of _atom_analytical_mass_loss.temperature.
analysis_temperature_su
_atom_analytical_source.equipment_make
The make, model or name of the equipment used to determine the elemental composition.
['Bruker', 'ELEMISSION', 'Thermo Fisher Scientific']
atom_analytical_source
equipment_make
_atom_analytical_source.special_details
Text describing the equipment or conditions under which the data were collected that are not able to be captured using _atom_analytical_source.equipment_make or _atom_analytical_source.technique.
['\n XRF utilising a WDS detector system calibrated for the analysis\n of iron ores.', '\n Laser Induced Breakdown Spectroscopy. Measurements carried out\n by commercial laboratory, report #P90.', '\n Detector calibrated following Smith (2018).']
_atom_analytical_source.technique
Succinct text or acronym describing the experimental technique used to find the elemental composition. If further details are required to properly describe the experimental technique, or the given acronym is not in common use, use _atom_analytical_source.special_details.
['XRF', 'LIBS', 'ICP OES']
technique
_atom_scat_versus_stol.atom_type
The identity of the atom specie(s) representing this atom type. See _atom_type.symbol for further details.
atom_scat_versus_stol
_atom_type.symbol
atom_type
_atom_scat_versus_stol.scat_value
The value of the scattering factor of a particular atom type at a particular stol value.
scat_value
electrons
_atom_scat_versus_stol.scat_value_su
Standard uncertainty of _atom_scat_versus_stol.scat_value.
scat_value_su
_atom_scat_versus_stol.stol_value
The value of sin(θ)/λ (sin theta over lambda, stol) to which the accompanying atom symbol and scattering factor value correspond to. A regularly spaced grid is strongly recommended.
stol_value
Number
reciprocal_angstroms
_atom_site.ADP_type
['_atom_site_ADP_type', '_atom_site_thermal_displace_type', '_atom_site.thermal_displace_type']
Code for type of atomic displacement parameters used for the site.
['Anisotropic Uij.', 'Isotropic U.', 'Overall U.', 'Multipole expansion U.', 'Anisotropic Bij.', 'Isotropic B.', 'Overall B.', 'Anisotropic betaij.']
['Uani', 'Uiso', 'Uovl', 'Umpe', 'Bani', 'Biso', 'Bovl', 'betaani']
atom_site
ADP_type
_atom_site.B_equiv_geom_mean
_atom_site_B_equiv_geom_mean
Equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B(equiv) = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalised B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
B_equiv_geom_mean
angstrom_squared
_atom_site.B_equiv_geom_mean_su
['_atom_site_B_equiv_geom_mean_su', '_atom_site.B_equiv_geom_mean_esd']
Standard uncertainty of the equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters.
B_equiv_geom_mean_su
_atom_site.B_iso_or_equiv
_atom_site_B_iso_or_equiv
Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated from anisotropic atomic displacement parameters. B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~.a~j~)] a = the real-space cell vectors a* = the reciprocal-space cell lengths B^ij^ = 8 π^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.
B_iso_or_equiv
_atom_site.B_iso_or_equiv_su
['_atom_site_B_iso_or_equiv_su', '_atom_site.B_iso_or_equiv_esd']
Standard uncertainty of the isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated from anisotropic atomic displacement parameters.
B_iso_or_equiv_su
_atom_site.Cartn_x
_atom_site_Cartn_x
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.
Cartn_x
angstroms
_atom_site.Cartn_x_su
['_atom_site_Cartn_x_su', '_atom_site.Cartn_x_esd']
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.
Cartn_x_su
_atom_site.Cartn_xyz
Vector of Cartesian (orthogonal angstrom) atom site coordinates.
With a as atom_site _atom_site.Cartn_xyz = [a.Cartn_x, a.Cartn_y, a.Cartn_z]
Evaluation
Cartn_xyz
Matrix
_atom_site.Cartn_xyz_su
Standard uncertainty of _atom_site.Cartn_xyz.
Cartn_xyz_su
_atom_site.Cartn_y
_atom_site_Cartn_y
Cartn_y
_atom_site.Cartn_y_su
['_atom_site_Cartn_y_su', '_atom_site.Cartn_y_esd']
Cartn_y_su
_atom_site.Cartn_z
_atom_site_Cartn_z
Cartn_z
_atom_site.Cartn_z_su
['_atom_site_Cartn_z_su', '_atom_site.Cartn_z_esd']
Cartn_z_su
_atom_site.U_equiv_geom_mean
_atom_site_U_equiv_geom_mean
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 orthogonalised U^ij^
U_equiv_geom_mean
_atom_site.U_equiv_geom_mean_su
['_atom_site_U_equiv_geom_mean_su', '_atom_site.U_equiv_geom_mean_esd']
Standard uncertainty values (esds) of the U(equiv).
U_equiv_geom_mean_su
_atom_site.U_iso_or_equiv
_atom_site_U_iso_or_equiv
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 vectors a* = the reciprocal-space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
U_iso_or_equiv
_atom_site.U_iso_or_equiv_su
['_atom_site_U_iso_or_equiv_su', '_atom_site.U_iso_or_equiv_esd']
Standard uncertainty values (esds) of the U(iso) or U(equiv).
U_iso_or_equiv_su
_atom_site.Wyckoff_symbol
_atom_site_Wyckoff_symbol
The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987).
Wyckoff_symbol
_atom_site.attached_hydrogens
_atom_site_attached_hydrogens
Number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given.
['Water oxygen.', 'Hydroxyl oxygen.', 'Ammonium nitrogen.']
attached_hydrogens
Integer
_atom_site.calc_attached_atom
_atom_site_calc_attached_atom
The _atom_site.label of the atom site to which the 'geometry-calculated' atom site is attached.
_atom_site.label
calc_attached_atom
_atom_site.calc_flag
_atom_site_calc_flag
A standard code to signal if the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy coordinates.
['Determined from diffraction measurements.', 'Calculated from molecular geometry.', 'Abbreviation for "calc".', 'Dummy site with meaningless coordinates.']
['d', 'calc', 'c', 'dum']
calc_flag
_atom_site.chemical_conn_number
_atom_site_chemical_conn_number
This number links an atom site to the chemical connectivity list. It must match a number specified by _chemical_conn_atom.number.
_chemical_conn_atom.number
chemical_conn_number
_atom_site.constraints
_atom_site_constraints
A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags_* and _refine_ls.number_constraints.
pop=1.0-pop(Zn3)
constraints
_atom_site.description
['_atom_site_description', '_atom_site.details']
A description of special aspects of this site. See also _atom_site.refinement_flags_*.
Ag/Si disordered
description
_atom_site.disorder_assembly
_atom_site_disorder_assembly
A code which identifies a cluster of atoms that show long range 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.
['\n Disordered methyl assembly with groups 1 and 2.', '\n Disordered sites related by a mirror.', '\n Assembly with groups that describe alternative compositions of a\n compositionally disordered site.', '\n Disordered sites independent of symmetry.']
disorder_assembly
_atom_site.disorder_group
_atom_site_disorder_group
A code that identifies a group of disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the H atoms of a methyl group that exists in two orientations) should be assigned to two or more groups. Similarly, atoms that describe a specific alternative composition of a compositionally disordered site should be assigned to a distinct disorder group (e.g. a site that is partially occupied by Mg and Mn atoms should be described by assigning the Mg atom to one group and the Mn atom to another group). 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.
['\n Unique disordered site in group 1.', '\n Unique disordered site in group 2.', '\n Group describes a specific alternative composition of a compositionally\n disordered site.', "\n Symmetry-independent disordered site.'"]
disorder_group
_atom_site.fract_x
_atom_site_fract_x
Atom site coordinates as fractions of the cell length values.
fract_x
_atom_site.fract_x_su
['_atom_site_fract_x_su', '_atom_site.fract_x_esd']
Standard uncertainty value of the atom site coordinates as fractions of the cell length values.
fract_x_su
_atom_site.fract_xyz
Vector of atom site coordinates projected onto the crystal unit cell as fractions of the cell lengths.
With a as atom_site _atom_site.fract_xyz = [a.fract_x, a.fract_y, a.fract_z]
fract_xyz
_atom_site.fract_xyz_su
Standard uncertainty of _atom_site.fract_xyz.
fract_xyz_su
_atom_site.fract_y
_atom_site_fract_y
fract_y
_atom_site.fract_y_su
['_atom_site_fract_y_su', '_atom_site.fract_y_esd']
fract_y_su
_atom_site.fract_z
_atom_site_fract_z
fract_z
_atom_site.fract_z_su
['_atom_site_fract_z_su', '_atom_site.fract_z_esd']
fract_z_su
['_atom_site_label', '_atom_site.id']
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.
label
_atom_site.label_component_0
_atom_site_label_component_0
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.
label_component_0
_atom_site.label_component_1
_atom_site_label_component_1
See label_component_0 description.
label_component_1
_atom_site.label_component_2
_atom_site_label_component_2
label_component_2
_atom_site.label_component_3
_atom_site_label_component_3
label_component_3
_atom_site.label_component_4
_atom_site_label_component_4
label_component_4
_atom_site.label_component_5
_atom_site_label_component_5
label_component_5
_atom_site.label_component_6
_atom_site_label_component_6
label_component_6
_atom_site.occupancy
_atom_site_occupancy
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).
occupancy
_atom_site.occupancy_su
['_atom_site_occupancy_su', '_atom_site.occupancy_esd']
Standard uncertainty of the fraction of the atom type present at this site.
occupancy_su
_atom_site.refinement_flags
_atom_site_refinement_flags
['_atom_site.refinement_flags_posn', '_atom_site.refinement_flags_ADP', '_atom_site.refinement_flags_occupancy']
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.
['Special position constraint on site.', 'Rigid group refinement of site.', 'Riding-atom site attached to non-riding atom.', 'Distance or angle restraint on site.', 'Thermal displacement constraints.', 'Uiso or Uij restraint (rigid bond).', 'Partial occupancy constraint.', 'No refinement constraints.']
refinement_flags
_atom_site.refinement_flags_ADP
_atom_site_refinement_flags_ADP
A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.
['No constraints on atomic displacement parameters.', 'Special-position constraints on atomic displacement parameters.', 'Uiso or Uij restraint (rigid bond).', 'Both constraints applied.']
refinement_flags_ADP
_atom_site.refinement_flags_occupancy
_atom_site_refinement_flags_occupancy
A code which indicates the refinement restraints or constraints applied to the occupancy of this site.
['No constraints on site-occupancy parameters.', 'Site-occupancy constraint.']
refinement_flags_occupancy
_atom_site.refinement_flags_posn
_atom_site_refinement_flags_posn
A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.
['No constraints on positional coordinates.', 'Distance or angle restraint on positional coordinates.', 'Rigid-group refinement of positional coordinates.', 'Riding-atom site attached to non-riding atom.', 'Special-position constraint on positional coordinates.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.', 'Combination of the above constraints.']
['.', 'D', 'G', 'R', 'S', 'DG', 'DR', 'DS', 'GR', 'GS', 'RS', 'DGR', 'DGS', 'DRS', 'GRS', 'DGRS']
refinement_flags_posn
_atom_site.restraints
_atom_site_restraints
A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags_* and _refine_ls.number_restraints.
restrained to planar ring
restraints
_atom_site.site_symmetry_multiplicity
['_atom_site_site_symmetry_multiplicity', '_atom_site_symmetry_multiplicity', '_atom_site.symmetry_multiplicity']
The number of different sites that are generated by the application of the space-group symmetry to the coordinates given for this site. It is equal to the multiplicity given for this Wyckoff site in International Tables for Cryst. Vol. A (2002). It is equal to the multiplicity of the general position divided by the order of the site symmetry given in _atom_site.site_symmetry_order. The _atom_site_symmetry_multiplicity form of this data name is deprecated because of historical inconsistencies in practice among structure refinement software packages and should not be used.
With a as atom_site mul = 0 xyz = a.fract_xyz Loop s as space_group_symop { sxyz = s.R * xyz + s.T diff = Mod( 99.5 + xyz - sxyz, 1.0) - 0.5 If ( Norm ( diff ) < 0.1 ) mul += 1 } _atom_site.site_symmetry_multiplicity = _space_group.multiplicity / mul
site_symmetry_multiplicity
_atom_site.site_symmetry_order
_atom_site_site_symmetry_order
The number of times application of the crystallographic symmetry to the coordinates for this site generates the same coordinates. That is: multiplicity of the general position ------------------------------------ _atom_site.site_symmetry_multiplicity
site_symmetry_order
_atom_site.type_symbol
_atom_site_type_symbol
A code to identify the atom specie(s) 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.
_atom_site.type_symbol = AtomType ( _atom_site.label )
type_symbol
_atom_site_aniso.B_11
['_atom_site_aniso_B_11', '_atom_site.aniso_B[1][1]', '_atom_site_anisotrop.B[1][1]']
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.
atom_site_aniso
_atom_site_aniso.B_11_su
['_atom_site_aniso_B_11_su', '_atom_site.aniso_B[1][1]_esd', '_atom_site_anisotrop.B[1][1]_esd']
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.
B_11_su
_atom_site_aniso.B_12
['_atom_site_aniso_B_12', '_atom_site.aniso_B[1][2]', '_atom_site_anisotrop.B[1][2]']
_atom_site_aniso.B_12_su
['_atom_site_aniso_B_12_su', '_atom_site.aniso_B[1][2]_esd', '_atom_site_anisotrop.B[1][2]_esd']
B_12_su
_atom_site_aniso.B_13
['_atom_site_aniso_B_13', '_atom_site.aniso_B[1][3]', '_atom_site_anisotrop.B[1][3]']
_atom_site_aniso.B_13_su
['_atom_site_aniso_B_13_su', '_atom_site.aniso_B[1][3]_esd', '_atom_site_anisotrop.B[1][3]_esd']
B_13_su
_atom_site_aniso.B_22
['_atom_site_aniso_B_22', '_atom_site.aniso_B[2][2]', '_atom_site_anisotrop.B[2][2]']
_atom_site_aniso.B_22_su
['_atom_site_aniso_B_22_su', '_atom_site.aniso_B[2][2]_esd', '_atom_site_anisotrop.B[2][2]_esd']
B_22_su
_atom_site_aniso.B_23
['_atom_site_aniso_B_23', '_atom_site.aniso_B[2][3]', '_atom_site_anisotrop.B[2][3]']
_atom_site_aniso.B_23_su
['_atom_site_aniso_B_23_su', '_atom_site.aniso_B[2][3]_esd', '_atom_site_anisotrop.B[2][3]_esd']
B_23_su
_atom_site_aniso.B_33
['_atom_site_aniso_B_33', '_atom_site.aniso_B[3][3]', '_atom_site_anisotrop.B[3][3]']
_atom_site_aniso.B_33_su
['_atom_site_aniso_B_33_su', '_atom_site.aniso_B[3][3]_esd', '_atom_site_anisotrop.B[3][3]_esd']
B_33_su
_atom_site_aniso.U_11
['_atom_site_aniso_U_11', '_atom_site.aniso_U[1][1]', '_atom_site_anisotrop.U[1][1]']
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.
_atom_site_aniso.U_11_su
['_atom_site_aniso_U_11_su', '_atom_site.aniso_U[1][1]_esd', '_atom_site_anisotrop.U[1][1]_esd']
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.
U_11_su
_atom_site_aniso.U_12
['_atom_site_aniso_U_12', '_atom_site.aniso_U[1][2]', '_atom_site_anisotrop.U[1][2]']
_atom_site_aniso.U_12_su
['_atom_site_aniso_U_12_su', '_atom_site.aniso_U[1][2]_esd', '_atom_site_anisotrop.U[1][2]_esd']
U_12_su
_atom_site_aniso.U_13
['_atom_site_aniso_U_13', '_atom_site.aniso_U[1][3]', '_atom_site_anisotrop.U[1][3]']
_atom_site_aniso.U_13_su
['_atom_site_aniso_U_13_su', '_atom_site.aniso_U[1][3]_esd', '_atom_site_anisotrop.U[1][3]_esd']
U_13_su
_atom_site_aniso.U_22
['_atom_site_aniso_U_22', '_atom_site.aniso_U[2][2]', '_atom_site_anisotrop.U[2][2]']
_atom_site_aniso.U_22_su
['_atom_site_aniso_U_22_su', '_atom_site.aniso_U[2][2]_esd', '_atom_site_anisotrop.U[2][2]_esd']
U_22_su
_atom_site_aniso.U_23
['_atom_site_aniso_U_23', '_atom_site.aniso_U[2][3]', '_atom_site_anisotrop.U[2][3]']
_atom_site_aniso.U_23_su
['_atom_site_aniso_U_23_su', '_atom_site.aniso_U[2][3]_esd', '_atom_site_anisotrop.U[2][3]_esd']
U_23_su
_atom_site_aniso.U_33
['_atom_site_aniso_U_33', '_atom_site.aniso_U[3][3]', '_atom_site_anisotrop.U[3][3]']
_atom_site_aniso.U_33_su
['_atom_site_aniso_U_33_su', '_atom_site.aniso_U[3][3]_esd', '_atom_site_anisotrop.U[3][3]_esd']
U_33_su
_atom_site_aniso.beta_11
_atom_site_aniso_beta_11
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.
beta_11
_atom_site_aniso.beta_11_su
_atom_site_aniso_beta_11_su
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.
beta_11_su
_atom_site_aniso.beta_12
_atom_site_aniso_beta_12
beta_12
_atom_site_aniso.beta_12_su
_atom_site_aniso_beta_12_su
beta_12_su
_atom_site_aniso.beta_13
_atom_site_aniso_beta_13
beta_13
_atom_site_aniso.beta_13_su
_atom_site_aniso_beta_13_su
beta_13_su
_atom_site_aniso.beta_22
_atom_site_aniso_beta_22
beta_22
_atom_site_aniso.beta_22_su
_atom_site_aniso_beta_22_su
beta_22_su
_atom_site_aniso.beta_23
_atom_site_aniso_beta_23
beta_23
_atom_site_aniso.beta_23_su
_atom_site_aniso_beta_23_su
beta_23_su
_atom_site_aniso.beta_33
_atom_site_aniso_beta_33
beta_33
_atom_site_aniso.beta_33_su
_atom_site_aniso_beta_33_su
beta_33_su
_atom_site_aniso.label
['_atom_site_aniso_label', '_atom_site_anisotrop.id']
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.
_atom_site_aniso.matrix_B
The symmetric anisotropic atomic displacement matrix B.
With a as atom_site_aniso a.matrix_B = [[ a.B_11, a.B_12, a.B_13 ], [ a.B_12, a.B_22, a.B_23 ], [ a.B_13, a.B_23, a.B_33 ]]
matrix_B
_atom_site_aniso.matrix_B_su
Standard uncertainty of _atom_site_aniso.matrix_B.
matrix_B_su
_atom_site_aniso.matrix_U
The symmetric anisotropic atomic displacement matrix U.
With a as atom_site_aniso a.matrix_U = [[ a.U_11, a.U_12, a.U_13 ], [ a.U_12, a.U_22, a.U_23 ], [ a.U_13, a.U_23, a.U_33 ]]
matrix_U
_atom_site_aniso.matrix_U_su
Standard uncertainty of _atom_site_aniso.matrix_U.
matrix_U_su
_atom_site_aniso.matrix_beta
_atom_site.tensor_beta
The symmetric anisotropic atomic displacement parameter (ADP) matrix, β, which appears in a structure factor expression. The contribution of the ADPs to the calculation of the structure factor is given as: T = exp(-1 * Sum(Sum(β^ij^ * h~i~ * h~j~, j=1:3), i=1:3)) where β^ij^ are the matrix elements, and h~m~ are the Miller indices. The ADP matrix β, is related to the ADP matrices U and B, as follows: |a~1~* 0 0 | |t^11^ t^12^ t^13^| |a~1~* 0 0 | β = C * | 0 a~2~* 0 | * |t^12^ t^22^ t^23^| * | 0 a~2~* 0 | | 0 0 a~3~*| |t^13^ t^23^ t^33^| | 0 0 a~3~*| where C is a constant (2 * π^2^ for U, and 0.25 for B), a~i~* is the length of the respective reciprocal unit cell vector, and t represents the individual anisotropic values, U^ij^ or B^ij^.
With a as atom_site_aniso label = a.label If (a.ADP_type == 'betaani') { a.matrix_beta = [[ a.beta_11, a.beta_12, a.beta_13 ], [ a.beta_12, a.beta_22, a.beta_23 ], [ a.beta_13, a.beta_23, a.beta_33 ]] } Else { If (a.ADP_type == 'Uani') { UIJ = b.matrix_U } Else If (a.ADP_type == 'Bani') { UIJ = b.matrix_B / (8 * Pi**2) } Else { If (a.ADP_type == 'Uiso') { Loop b as atom_site { If(label == b.label) { U = b.U_iso_or_equiv Break } } } Else If (a.ADP_type == 'Biso') { Loop b as atom_site { If(label == b.label) { U = b.B_iso_or_equiv / (8 * Pi**2) Break } } } UIJ = U * _cell.convert_Uiso_to_Uij } CUB = _cell.convert_Uij_to_betaij a.matrix_beta = CUB * UIJ * CUB }
matrix_beta
_atom_site_aniso.matrix_beta_su
_atom_site.tensor_beta_su
Standard uncertainty of _atom_site_aniso.matrix_beta.
matrix_beta_su
_atom_site_aniso.ratio
['_atom_site_aniso_ratio', '_atom_site_anisotrop.ratio', '_atom_site.aniso_ratio']
Ratio of the maximum to minimum eigenvalues of the atomic displacement ellipsoids.
ratio
_atom_site_aniso.type_symbol
['_atom_site_aniso_type_symbol', '_atom_site_anisotrop.type_symbol']
This _atom_type.symbol code links the anisotropic atomic displacement parameters to the atom type data associated with this site and must match one of the _atom_type.symbol codes in this list.
_atom_site_aniso.type_symbol = AtomType ( _atom_site_aniso.label )
_atom_sites.solution_hydrogens
_atom_sites_solution_hydrogens
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. Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. and Usón, I. (2001). Ab initio phasing. In International Tables for Crystallography, Vol. F. Crystallography of biological macromolecules, edited by M. G. Rossmann and E. Arnold, ch. 16.1. Dordrecht: Kluwer Academic Publishers.
['\n Difference Fourier map.', '\n Real-space vector search.', '\n Heavy-atom method.', '\n Structure-invariant direct methods.', '\n Inferred from neighbouring sites.', '\n Anomalous-dispersion techniques.', '\n Isomorphous structure methods.', '\n A mixture of "geom" and "difmap".', '\n Coordinates were not determined.', '\n Dual-space method (Sheldrick et al., 2001).', '\n Iterative e.g. charge flipping [Oszlányi, G. and Süto, A. (2004).\n Acta Cryst. A60, 134-141].', '\n A method not included elsewhere in this list.']
['difmap', 'vecmap', 'heavy', 'direct', 'geom', 'disper', 'isomor', 'mixed', 'notdet', 'dual', 'iterative', 'other']
atom_sites
solution_hydrogens
_atom_sites.solution_primary
_atom_sites_solution_primary
['\n Difference Fourier map.', '\n Real-space vector search.', '\n Heavy-atom method.', '\n Structure-invariant direct methods.', '\n Inferred from neighbouring sites.', '\n Anomalous-dispersion techniques.', '\n Isomorphous structure methods.', '\n Coordinates were not determined.', '\n Dual-space method (Sheldrick et al., 2001).', '\n Iterative e.g. charge flipping [Oszlányi, G. and Süto, A. (2004).\n Acta Cryst. A60, 134-141].', '\n A method not included elsewhere in this list.']
['difmap', 'vecmap', 'heavy', 'direct', 'geom', 'disper', 'isomor', 'notdet', 'dual', 'iterative', 'other']
solution_primary
_atom_sites.solution_secondary
_atom_sites_solution_secondary
solution_secondary
_atom_sites.special_details
_atom_sites_special_details
Information about atomic coordinates not coded elsewhere in the CIF.
_atom_sites_Cartn_transform.axes
['_atom_sites_Cartn_transform_axes', '_atom_sites.Cartn_transform_axes']
Description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites_Cartn_transform.matrix.
a parallel to x; b in the plane of x & y
atom_sites_Cartn_transform
axes
_atom_sites_Cartn_transform.mat_11
['_atom_sites_Cartn_tran_matrix_11', '_atom_sites.Cartn_transf_matrix[1][1]']
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.
With c as cell _enumeration.default = c.length_a*Sind(c.angle_beta)*Sind(c.reciprocal_angle_gamma)
Definition
mat_11
_atom_sites_Cartn_transform.mat_11_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_11.
mat_11_su
_atom_sites_Cartn_transform.mat_12
['_atom_sites_Cartn_tran_matrix_12', '_atom_sites.Cartn_transf_matrix[1][2]']
_enumeration.default = 0.
mat_12
_atom_sites_Cartn_transform.mat_12_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_12.
mat_12_su
_atom_sites_Cartn_transform.mat_13
['_atom_sites_Cartn_tran_matrix_13', '_atom_sites.Cartn_transf_matrix[1][3]']
mat_13
_atom_sites_Cartn_transform.mat_13_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_13.
mat_13_su
_atom_sites_Cartn_transform.mat_21
['_atom_sites_Cartn_tran_matrix_21', '_atom_sites.Cartn_transf_matrix[2][1]']
with c as cell _enumeration.default = -c.length_a*Sind(c.angle_beta)*Cosd(c.reciprocal_angle_gamma)
mat_21
_atom_sites_Cartn_transform.mat_21_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_21.
mat_21_su
_atom_sites_Cartn_transform.mat_22
['_atom_sites_Cartn_tran_matrix_22', '_atom_sites.Cartn_transf_matrix[2][2]']
With c as cell _enumeration.default = c.length_b * Sind(c.angle_alpha)
mat_22
_atom_sites_Cartn_transform.mat_22_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_22.
mat_22_su
_atom_sites_Cartn_transform.mat_23
['_atom_sites_Cartn_tran_matrix_23', '_atom_sites.Cartn_transf_matrix[2][3]']
mat_23
_atom_sites_Cartn_transform.mat_23_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_23.
mat_23_su
_atom_sites_Cartn_transform.mat_31
['_atom_sites_Cartn_tran_matrix_31', '_atom_sites.Cartn_transf_matrix[3][1]']
With c as cell _enumeration.default = c.length_a * Cosd(c.angle_beta)
mat_31
_atom_sites_Cartn_transform.mat_31_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_31.
mat_31_su
_atom_sites_Cartn_transform.mat_32
['_atom_sites_Cartn_tran_matrix_32', '_atom_sites.Cartn_transf_matrix[3][2]']
With c as cell _enumeration.default = c.length_b * Cosd(c.angle_alpha)
mat_32
_atom_sites_Cartn_transform.mat_32_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_32.
mat_32_su
_atom_sites_Cartn_transform.mat_33
['_atom_sites_Cartn_tran_matrix_33', '_atom_sites.Cartn_transf_matrix[3][3]']
_enumeration.default = _cell.length_c
mat_33
_atom_sites_Cartn_transform.mat_33_su
Standard uncertainty of _atom_sites_Cartn_transform.mat_33.
mat_33_su
_atom_sites_Cartn_transform.matrix
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 3 x 1 translation is defined in _atom_sites_Cartn_transform.vector. x' |11 12 13| x | 1 | ( y' ) Cartesian = |21 22 23| * ( y ) fractional + v| 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.
With a as atom_sites_Cartn_transform _atom_sites_Cartn_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13], [a.mat_21, a.mat_22, a.mat_23], [a.mat_31, a.mat_32, a.mat_33]]
matrix
_atom_sites_Cartn_transform.matrix_su
Standard uncertainty of _atom_sites_Cartn_transform.matrix.
matrix_su
_atom_sites_Cartn_transform.vec_1
['_atom_sites_Cartn_tran_vector_1', '_atom_sites.Cartn_transf_vector[1]']
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.
vec_1
_atom_sites_Cartn_transform.vec_1_su
Standard uncertainty of _atom_sites_Cartn_transform.vec_1.
vec_1_su
_atom_sites_Cartn_transform.vec_2
['_atom_sites_Cartn_tran_vector_2', '_atom_sites.Cartn_transf_vector[2]']
vec_2
_atom_sites_Cartn_transform.vec_2_su
Standard uncertainty of _atom_sites_Cartn_transform.vec_2.
vec_2_su
_atom_sites_Cartn_transform.vec_3
['_atom_sites_Cartn_tran_vector_3', '_atom_sites.Cartn_transf_vector[3]']
vec_3
_atom_sites_Cartn_transform.vec_3_su
Standard uncertainty of _atom_sites_Cartn_transform.vec_3.
vec_3_su
_atom_sites_Cartn_transform.vector
The 3x1 translation is used with _atom_sites_Cartn_transform.matrix used to transform fractional coordinates to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform.axes.
With t as atom_sites_Cartn_transform _atom_sites_Cartn_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ]
vector
_atom_sites_Cartn_transform.vector_su
Standard uncertainty of _atom_sites_Cartn_transform.vector.
vector_su
_atom_sites_fract_transform.axes
['_atom_sites_fract_transform_axes', '_atom_sites.fract_transform_axes']
Description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites_fract_transform.matrix.
atom_sites_fract_transform
_atom_sites_fract_transform.mat_11
['_atom_sites_fract_tran_matrix_11', '_atom_sites.fract_transf_matrix[1][1]']
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.
_atom_sites_fract_transform.mat_11_su
Standard uncertainty of _atom_sites_fract_transform.mat_11.
_atom_sites_fract_transform.mat_12
['_atom_sites_fract_tran_matrix_12', '_atom_sites.fract_transf_matrix[1][2]']
_atom_sites_fract_transform.mat_12_su
Standard uncertainty of _atom_sites_fract_transform.mat_12.
_atom_sites_fract_transform.mat_13
['_atom_sites_fract_tran_matrix_13', '_atom_sites.fract_transf_matrix[1][3]']
_atom_sites_fract_transform.mat_13_su
Standard uncertainty of _atom_sites_fract_transform.mat_13.
_atom_sites_fract_transform.mat_21
['_atom_sites_fract_tran_matrix_21', '_atom_sites.fract_transf_matrix[2][1]']
_atom_sites_fract_transform.mat_21_su
Standard uncertainty of _atom_sites_fract_transform.mat_21.
_atom_sites_fract_transform.mat_22
['_atom_sites_fract_tran_matrix_22', '_atom_sites.fract_transf_matrix[2][2]']
_atom_sites_fract_transform.mat_22_su
Standard uncertainty of _atom_sites_fract_transform.mat_22.
_atom_sites_fract_transform.mat_23
['_atom_sites_fract_tran_matrix_23', '_atom_sites.fract_transf_matrix[2][3]']
_atom_sites_fract_transform.mat_23_su
Standard uncertainty of _atom_sites_fract_transform.mat_23.
_atom_sites_fract_transform.mat_31
['_atom_sites_fract_tran_matrix_31', '_atom_sites.fract_transf_matrix[3][1]']
_atom_sites_fract_transform.mat_31_su
Standard uncertainty of _atom_sites_fract_transform.mat_31.
_atom_sites_fract_transform.mat_32
['_atom_sites_fract_tran_matrix_32', '_atom_sites.fract_transf_matrix[3][2]']
_atom_sites_fract_transform.mat_32_su
Standard uncertainty of _atom_sites_fract_transform.mat_32.
_atom_sites_fract_transform.mat_33
['_atom_sites_fract_tran_matrix_33', '_atom_sites.fract_transf_matrix[3][3]']
_atom_sites_fract_transform.mat_33_su
Standard uncertainty of _atom_sites_fract_transform.mat_33.
_atom_sites_fract_transform.matrix
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 3 x 1 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.
With a as atom_sites_fract_transform _atom_sites_fract_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13], [a.mat_21, a.mat_22, a.mat_23], [a.mat_31, a.mat_32, a.mat_33]]
_atom_sites_fract_transform.matrix_su
Standard uncertainty of _atom_sites_fract_transform.matrix.
_atom_sites_fract_transform.vec_1
['_atom_sites_fract_tran_vector_1', '_atom_sites.fract_transf_vector[1]']
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.
_atom_sites_fract_transform.vec_1_su
Standard uncertainty of _atom_sites_fract_transform.vec_1.
_atom_sites_fract_transform.vec_2
['_atom_sites_fract_tran_vector_2', '_atom_sites.fract_transf_vector[2]']
_atom_sites_fract_transform.vec_2_su
Standard uncertainty of _atom_sites_fract_transform.vec_2.
_atom_sites_fract_transform.vec_3
['_atom_sites_fract_tran_vector_3', '_atom_sites.fract_transf_vector[3]']
_atom_sites_fract_transform.vec_3_su
Standard uncertainty of _atom_sites_fract_transform.vec_3.
_atom_sites_fract_transform.vector
The 3x1 translation is used with _atom_sites_fract_transform.matrix used to transform Cartesian coordinates to fractional coordinates. The axial alignments of this transformation are described in _atom_sites_fract_transform.axes.
With t as atom_sites_fract_transform _atom_sites_fract_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ]
_atom_sites_fract_transform.vector_su
Standard uncertainty of _atom_sites_fract_transform.vector.
_atom_type.analytical_mass_percent
['_atom_type_analytical_mass_%', '_atom_type.analytical_mass_%']
Mass percentage of this atom type derived from chemical analysis.
analytical_mass_percent
_atom_type.analytical_mass_percent_su
Standard uncertainty of _atom_type.analytical_mass_percent.
analytical_mass_percent_su
_atom_type.atomic_mass
Mass of this atom type.
['H', 'D', 'H1-', 'He', 'Li', 'Li1+', 'Be', 'Be2+', 'B', 'C', 'N', 'O', 'O1-', 'F', 'F1-', 'Ne', 'Na', 'Na1+', 'Mg', 'Mg2+', 'Al', 'Al3+', 'Si', 'Si4+', 'P', 'S', 'Cl', 'Cl1-', 'Ar', 'K', 'K1+', 'Ca', 'Ca2+', 'Sc', 'Sc3+', 'Ti', 'Ti2+', 'Ti3+', 'Ti4+', 'V', 'V2+', 'V3+', 'V5+', 'Cr', 'Cr2+', 'Cr3+', 'Mn', 'Mn2+', 'Mn3+', 'Mn4+', 'Fe', 'Fe2+', 'Fe3+', 'Co', 'Co2+', 'Co3+', 'Ni', 'Ni2+', 'Ni3+', 'Cu', 'Cu1+', 'Cu2+', 'Zn', 'Zn2+', 'Ga', 'Ga3+', 'Ge', 'Ge4+', 'As', 'Se', 'Br', 'Br1-', 'Kr', 'Rb', 'Rb1+', 'Sr', 'Sr2+', 'Y', 'Y3+', 'Zr', 'Zr4+', 'Nb', 'Nb3+', 'Nb5+', 'Mo', 'Mo3+', 'Mo5+', 'Mo6+', 'Tc', 'Ru', 'Ru3+', 'Ru4+', 'Rh', 'Rh3+', 'Rh4+', 'Pd', 'Pd2+', 'Pd4+', 'Ag', 'Ag1+', 'Ag2+', 'Cd', 'Cd2+', 'In', 'In3+', 'Sn', 'Sn2+', 'Sn4+', 'Sb', 'Sb3+', 'Sb5+', 'Te', 'I', 'I1-', 'Xe', 'Cs', 'Cs1+', 'Ba', 'Ba2+', 'La', 'La3+', 'Ce', 'Ce3+', 'Ce4+', 'Pr', 'Pr3+', 'Pr4+', 'Nd', 'Nd3+', 'Pm', 'Sm', 'Sm3+', 'Eu', 'Eu2+', 'Eu3+', 'Gd', 'Gd3+', 'Tb', 'Tb3+', 'Dy', 'Dy3+', 'Ho', 'Ho3+', 'Er', 'Er3+', 'Tm', 'Tm3+', 'Yb', 'Yb2+', 'Yb3+', 'Lu', 'Lu3+', 'Hf', 'Hf4+', 'Ta', 'Ta5+', 'W', 'W6+', 'Re', 'Os', 'Os4+', 'Ir', 'Ir3+', 'Ir4+', 'Pt', 'Pt2+', 'Pt4+', 'Au', 'Au1+', 'Au3+', 'Hg', 'Hg1+', 'Hg2+', 'Tl', 'Tl1+', 'Tl3+', 'Pb', 'Pb2+', 'Pb4+', 'Bi', 'Bi3+', 'Bi5+', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ra2+', 'Ac', 'Ac3+', 'Th', 'Th4+', 'Pa', 'U', 'U3+', 'U4+', 'U6+', 'Np', 'Np3+', 'Np4+', 'Np6+', 'Pu', 'Pu3+', 'Pu4+', 'Pu6+', 'Am', 'Cm', 'Bk', 'Cf']
atomic_mass
dalton
_atom_type.atomic_number
Atomic number of this atom type.
_atom_type.element_symbol
['H', 'D', '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', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']
atomic_number
_atom_type.description
_atom_type_description
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.
['deuterium', '0.34Fe+0.66Ni']
_atom_type.display_colour
The display colour assigned to this atom type. Note that the possible colours are enumerated in the DISPLAY_COLOUR list category of items.
['white', 'blue_light', 'white', '?', '?', '?', '?', '?', '?', 'grey_steel', 'blue', 'red', 'red', 'green', 'green', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', 'violet_magenta', 'yellow', 'green', 'green', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'yellow', 'green', 'green', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', 'green', 'green', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', '?', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', 'violet_magenta', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?', '?']
['black', 'white', 'grey', 'gray', 'grey_light', 'grey_slate', 'grey_steel', 'blue', 'blue_light', 'blue_medium', 'blue_dark', 'blue_navy', 'blue_royal', 'blue_sky', 'blue_steel', 'turquoise', 'colourless', 'cyan', 'cyan_light', 'green', 'green_light', 'green_dark', 'green_sea', 'green_lime', 'green_olive', 'green_khaki', 'yellow', 'yellow_light', 'yellow_gold', 'brown', 'brown_sienna', 'brown_beige', 'brown_tan', 'salmon', 'salmon_light', 'salmon_dark', 'orange', 'orange_dark', 'red', 'red_coral', 'red_tomato', 'red_orange', 'red_violet', 'red_maroon', 'pink', 'pink_light', 'pink_deep', 'pink_hot', 'violet', 'violet_red', 'violet_magenta', 'violet_dark', 'violet_blue']
display_colour
_atom_type.electron_count
Number of electrons in this atom type.
electron_count
Element symbol for of this atom type. The default value is extracted from the ion-to-element enumeration_default list using the index value of _atom_type.symbol.
['H', 'D', 'H', 'He', 'Li', 'Li', 'Be', 'Be', 'B', 'C', 'N', 'O', 'O', 'F', 'F', 'Ne', 'Na', 'Na', 'Mg', 'Mg', 'Al', 'Al', 'Si', 'Si', 'P', 'S', 'Cl', 'Cl', 'Ar', 'K', 'K', 'Ca', 'Ca', 'Sc', 'Sc', 'Ti', 'Ti', 'Ti', 'Ti', 'V', 'V', 'V', 'V', 'Cr', 'Cr', 'Cr', 'Mn', 'Mn', 'Mn', 'Mn', 'Fe', 'Fe', 'Fe', 'Co', 'Co', 'Co', 'Ni', 'Ni', 'Ni', 'Cu', 'Cu', 'Cu', 'Zn', 'Zn', 'Ga', 'Ga', 'Ge', 'Ge', 'As', 'Se', 'Br', 'Br', 'Kr', 'Rb', 'Rb', 'Sr', 'Sr', 'Y', 'Y', 'Zr', 'Zr', 'Nb', 'Nb', 'Nb', 'Mo', 'Mo', 'Mo', 'Mo', 'Tc', 'Ru', 'Ru', 'Ru', 'Rh', 'Rh', 'Rh', 'Pd', 'Pd', 'Pd', 'Ag', 'Ag', 'Ag', 'Cd', 'Cd', 'In', 'In', 'Sn', 'Sn', 'Sn', 'Sb', 'Sb', 'Sb', 'Te', 'I', 'I', 'Xe', 'Cs', 'Cs', 'Ba', 'Ba', 'La', 'La', 'Ce', 'Ce', 'Ce', 'Pr', 'Pr', 'Pr', 'Nd', 'Nd', 'Pm', 'Sm', 'Sm', 'Eu', 'Eu', 'Eu', 'Gd', 'Gd', 'Tb', 'Tb', 'Dy', 'Dy', 'Ho', 'Ho', 'Er', 'Er', 'Tm', 'Tm', 'Yb', 'Yb', 'Yb', 'Lu', 'Lu', 'Hf', 'Hf', 'Ta', 'Ta', 'W', 'W', 'Re', 'Os', 'Os', 'Ir', 'Ir', 'Ir', 'Pt', 'Pt', 'Pt', 'Au', 'Au', 'Au', 'Hg', 'Hg', 'Hg', 'Tl', 'Tl', 'Tl', 'Pb', 'Pb', 'Pb', 'Bi', 'Bi', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ra', 'Ac', 'Ac', 'Th', 'Th', 'Pa', 'U', 'U', 'U', 'U', 'Np', 'Np', 'Np', 'Np', 'Pu', 'Pu', 'Pu', 'Pu', 'Am', 'Cm', 'Bk', 'Cf']
element_symbol
_atom_type.key
Value is a unique key to a set of ATOM_TYPE items in a looped list.
_atom_type.key = _atom_type.symbol
key
_atom_type.mass_number
Mass number of this atom type. Used to denote a specific isotope. Special value '.' indicates that the element is present in natural isotopic abundance.
mass_number
_atom_type.number_in_cell
_atom_type_number_in_cell
Total number of atoms of this atom type in the unit cell.
With t as atom_type cnt = 0. Loop a as atom_site { if ( a.type_symbol == t.symbol ) { cnt += a.occupancy * a.site_symmetry_multiplicity } } _atom_type.number_in_cell = cnt
number_in_cell
_atom_type.oxidation_number
_atom_type_oxidation_number
Formal oxidation state of this atom type in the structure.
oxidation_number
_atom_type.radius_bond
_atom_type_radius_bond
The effective intra-molecular bonding radius of this atom type.
radius_bond
_atom_type.radius_contact
_atom_type_radius_contact
The effective inter-molecular bonding radius of this atom type.
_enumeration.default = _atom_type.radius_bond + 1.25
radius_contact
_atom_type_symbol
The identity of the atom specie(s) representing this atom type. Normally this code is the element symbol followed by the charge if there is one. The symbol may be composed of any character except an underline or a blank, with the proviso that digits designate an oxidation state and must be followed by a + or - character.
['Mg', 'Cu2+', 'dummy', 'FeNi']
symbol
_atom_type_scat.Cromer_Mann_a1
['_atom_type_scat_Cromer_Mann_a1', '_atom_type.scat_Cromer_Mann_a1']
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
atom_type_scat
Cromer_Mann_a1
_atom_type_scat.Cromer_Mann_a2
['_atom_type_scat_Cromer_Mann_a2', '_atom_type.scat_Cromer_Mann_a2']
Cromer_Mann_a2
_atom_type_scat.Cromer_Mann_a3
['_atom_type_scat_Cromer_Mann_a3', '_atom_type.scat_Cromer_Mann_a3']
Cromer_Mann_a3
_atom_type_scat.Cromer_Mann_a4
['_atom_type_scat_Cromer_Mann_a4', '_atom_type.scat_Cromer_Mann_a4']
Cromer_Mann_a4
_atom_type_scat.Cromer_Mann_b1
['_atom_type_scat_Cromer_Mann_b1', '_atom_type.scat_Cromer_Mann_b1']
Cromer_Mann_b1
_atom_type_scat.Cromer_Mann_b2
['_atom_type_scat_Cromer_Mann_b2', '_atom_type.scat_Cromer_Mann_b2']
Cromer_Mann_b2
_atom_type_scat.Cromer_Mann_b3
['_atom_type_scat_Cromer_Mann_b3', '_atom_type.scat_Cromer_Mann_b3']
Cromer_Mann_b3
_atom_type_scat.Cromer_Mann_b4
['_atom_type_scat_Cromer_Mann_b4', '_atom_type.scat_Cromer_Mann_b4']
Cromer_Mann_b4
_atom_type_scat.Cromer_Mann_c
['_atom_type_scat_Cromer_Mann_c', '_atom_type.scat_Cromer_Mann_c']
Cromer_Mann_c
_atom_type_scat.Cromer_Mann_coeffs
The set of Cromer-Mann coefficients for generating X-ray scattering factors. [ c, a1, b1, a2, b2, a3, b3, a4, b4 ] Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.4
With t as atom_type_scat _atom_type_scat.Cromer_Mann_coeffs = [ t.Cromer_Mann_c, t.Cromer_Mann_a1, t.Cromer_Mann_b1, t.Cromer_Mann_a2, t.Cromer_Mann_b2, t.Cromer_Mann_a3, t.Cromer_Mann_b3, t.Cromer_Mann_a4, t.Cromer_Mann_b4 ]
Cromer_Mann_coeffs
List
unspecified
_atom_type_scat.Gaussian_coefs
The set of Gaussian coefficients for generating X-ray scattering factors: [ c, a_1, b_1, a_2, b_2, ... , a_N, b_N ]. f(s; Z) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:N) where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength of the incident radiation in angstroms.
Gaussian_coefs
_atom_type_scat.Gaussian_coefs_su
Standard uncertainty of _atom_type_scat.Gaussian_coefs.
Gaussian_coefs_su
_atom_type_scat.Gaussian_lower_limit
The inclusive lower limit of s for which the corresponding Gaussian coefficients are valid. See _atom_type_scat.Gaussian_coefs.
Gaussian_lower_limit
_atom_type_scat.Gaussian_upper_limit
The exclusive upper limit of s for which the corresponding Gaussian coefficients are valid. See _atom_type_scat.Gaussian_coefs.
Gaussian_upper_limit
_atom_type_scat.dispersion
The anomalous dispersion scattering factor in its complex form for this atom type and radiation by _diffrn_radiation_wavelength.value
With s as atom_type_scat d = Complex( s.dispersion_real, s.dispersion_imag ) if(_reflns.apply_dispersion_to_Fcalc == 'no') d = 0. _atom_type_scat.dispersion = d
dispersion
Complex
_atom_type_scat.dispersion_imag
['_atom_type_scat_dispersion_imag', '_atom_type.scat_dispersion_imag']
The imaginary component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
With q as atom_type_scat If ( _diffrn_radiation.type[0:2] == 'Cu' ) a = q.dispersion_imag_Cu If ( _diffrn_radiation.type[0:2] == 'Mo' ) a = q.dispersion_imag_Mo _atom_type_scat.dispersion_imag = a
dispersion_imag
_atom_type_scat.dispersion_imag_Cu
The imaginary component of the anomalous dispersion scattering factors for this atom type and Cu Kα radiation.
['H', 'D', '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']
dispersion_imag_Cu
_atom_type_scat.dispersion_imag_Mo
The imaginary component of the anomalous dispersion scattering factors for this atom type and Mo Kα radiation.
dispersion_imag_Mo
_atom_type_scat.dispersion_real
['_atom_type_scat_dispersion_real', '_atom_type.scat_dispersion_real']
The real component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
With q as atom_type_scat If ( _diffrn_radiation.type[0:2] == 'Cu' ) a = q.dispersion_real_Cu If ( _diffrn_radiation.type[0:2] == 'Mo' ) a = q.dispersion_real_Mo _atom_type_scat.dispersion_real = a
dispersion_real
_atom_type_scat.dispersion_real_Cu
The real component of the anomalous dispersion scattering factors for this atom type and Cu Kα radiation.
dispersion_real_Cu
_atom_type_scat.dispersion_real_Mo
The real component of the anomalous dispersion scattering factors for this atom type and Mo Kα radiation.
dispersion_real_Mo
_atom_type_scat.dispersion_source
['_atom_type_scat_dispersion_source', '_atom_type.scat_dispersion_source']
Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type.
International Tables Vol. IV Table 2.3.1
dispersion_source
_atom_type_scat.exponential_polynomial_coefs
The set of polynomial coefficients for generating X-ray scattering factors: [ a_0, a_1, ... , a_N ]. f(s; Z) = exp(Sum(a~i~ * s^i^), i=0:N) where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength of the incident radiation in angstroms.
exponential_polynomial_coefs
_atom_type_scat.exponential_polynomial_coefs_su
Standard uncertainty of _atom_type_scat.exponential_polynomial_coefs.
exponential_polynomial_coefs_su
_atom_type_scat.exponential_polynomial_lower_limit
The inclusive lower limit of s for which the corresponding exponential polynomial coefficients are valid. See _atom_type_scat.exponential_polynomial_coefs.
exponential_polynomial_lower_limit
_atom_type_scat.exponential_polynomial_upper_limit
The exclusive upper limit of s for which the corresponding exponential polynomial coefficients are valid. See _atom_type_scat.exponential_polynomial_coefs.
exponential_polynomial_upper_limit
_atom_type_scat.hi_ang_Fox_c0
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
hi_ang_Fox_c0
_atom_type_scat.hi_ang_Fox_c1
hi_ang_Fox_c1
_atom_type_scat.hi_ang_Fox_c2
hi_ang_Fox_c2
_atom_type_scat.hi_ang_Fox_c3
hi_ang_Fox_c3
angstrom_cubed
_atom_type_scat.hi_ang_Fox_coeffs
The set of Fox et al. coefficients for generating high angle X-ray scattering factors. [ c0, c1, c2, c3 ] Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.5
With t as atom_type_scat _atom_type_scat.hi_ang_Fox_coeffs = [t.hi_ang_Fox_c0,t.hi_ang_Fox_c1,t.hi_ang_Fox_c2,t.hi_ang_Fox_c3]
hi_ang_Fox_coeffs
_atom_type_scat.inv_Mott_Bethe_coefs
The set of Gaussian coefficients for use in the inverse Mott-Bethe relationship for generating X-ray scattering factors: [ e, c_1, d_1, c_2, d_2, ... , c_N, d_N ]. f(s; Z) = Z - 8π * a~0~ * s^2^ * (e + Sum( c~i~ * exp(-d~i~ * s^2^), i=1:N)) where s = sin(θ)/λ, a~0~ is the Bohr radius, and Z is the atomic number. θ is the diffraction angle and λ is the wavelength of the incident radiation in angstroms.
inv_Mott_Bethe_coefs
_atom_type_scat.inv_Mott_Bethe_coefs_su
Standard uncertainty of _atom_type_scat.inv_Mott_Bethe_coefs.
inv_Mott_Bethe_coefs_su
_atom_type_scat.inv_Mott_Bethe_lower_limit
The inclusive lower limit of s for which the corresponding Gaussian coefficients are valid. See _atom_type_scat.inv_Mott_Bethe_coefs.
inv_Mott_Bethe_lower_limit
_atom_type_scat.inv_Mott_Bethe_upper_limit
The exclusive upper limit of s for which the corresponding Gaussian coefficients are valid. See _atom_type_scat.inv_Mott_Bethe_coefs.
inv_Mott_Bethe_upper_limit
_atom_type_scat.length_neutron
['_atom_type_scat_length_neutron', '_atom_type.scat_length_neutron']
The bound coherent scattering length for the atom type at the isotopic composition used for the diffraction experiment.
length_neutron
femtometres
_atom_type_scat.source
['_atom_type_scat_source', '_atom_type.scat_source']
Reference to source of scattering factors used for this atom type.
International Tables Vol. IV Table 2.4.6B
source
_atom_type_scat.symbol
_atom_type_scat_symbol
_atom_type_scat.versus_stol_list
['_atom_type_scat_versus_stol_list', '_atom_type.scat_versus_stol_list']
['_atom_scat_versus_stol.atom_type', '_atom_scat_versus_stol.stol_value', '_atom_scat_versus_stol.scat_value']
Deprecated. Data items from the ATOM_SCAT_VERSUS_STOL category should be used instead of this item. A table of scattering factors as a function of sin(θ)/λ (sin theta over lambda, stol). This table should be well-commented to indicate the items present. Regularly formatted lists are strongly recommended.
versus_stol_list
_audit.block_DOI
_audit_block_DOI
The digital object identifier (DOI) registered to identify the data set publication represented by the current data block. This can be used as a unique identifier for the data block so long as the code used is a valid DOI (i.e. begins with a valid publisher prefix assigned by a Registration Agency and a suffix guaranteed to be unique by the publisher) and has had its metadata deposited with a DOI Registration Agency. A DOI is a unique character string identifying any object of intellectual property. It provides a persistent identifier for an object on a digital network and permits the association of related current data in a structured extensible way. A DOI is an implementation of the Internet concepts of Uniform Resource Name and Universal Resource Locator managed according to the specifications of the International DOI Foundation (see https://www.doi.org/).
audit
block_DOI
_audit.block_code
['_audit_block_code', '_audit.revision_id']
A unique block code identifier for each revision.
block_code
_audit.creation_date
_audit_creation_date
The timestamp of the data revision.
creation_date
DateTime
_audit.creation_method
_audit_creation_method
A description of how the revision was applied to the data.
spawned by the program QBEE
creation_method
_audit.schema
This data item identifies the type of information contained in the data block. Software written for one schema will not, in general, correctly interpret datafiles written against a different schema. Specifically, each value of _audit.schema corresponds to a list of categories that were (potentially implicitly) restricted to a single packet in the default Base schema, but which can contain multiple packets in the specified schema. All categories containing child keys of the listed categories may also contain multiple packets and do not need to be listed. The category list for each schema may instead be determined from examination of the dictionaries that this data block conforms to (see _audit_conform.dict_name).
Base
['\n Original Core CIF schema.', '\n space_group category is looped.', '\n Entry category is defined and looped: information from multiple data\n blocks in one block.', '\n Examine dictionaries listed using data items from the AUDIT_CONFORM\n category.', '\n Locally modified dictionaries. These datafiles should not be\n distributed.']
['Base', 'Space group tables', 'Entry', 'Custom', 'Local']
schema
_audit.update_record
_audit_update_record
A description of the revision applied to the data.
Updated by coeditor
update_record
_audit_author.address
_audit_author_address
The address of an author of this data block. If there are multiple authors, _audit_author.address is looped with _audit_author.name.
Department Institute Street City and postcode COUNTRY
audit_author
address
_audit_author.email
The electronic mail address of an author of the data block, 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.
['name@host.domain.country', 'bm@iucr.org']
email
_audit_author.fax
Facsimile telephone number of an author of the 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.
fax
_audit_author.id
Arbitrary identifier for this author.
_enumeration.default = Unique_id(audit_author.id)
_audit_author.id_ORCID
Identifier in the ORCID Registry of a publication author. ORCID is an open, non-profit, community-driven service to provide a registry of unique researcher identifiers (https://orcid.org/).
id_ORCID
Code
_audit_author.name
_audit_author_name
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). For authors with only one name, provide the full name without abbreviation.
['Bleary, Percival R.', "O'Neil, F.K.", 'Van den Bossche, G.', 'Yang, D.-L.', 'Simonov, Yu.A.', 'Müller, H.A.', 'Ross II, C.R.', 'Chandra']
name
_audit_author.phone
Telephone number of an author of the 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.
phone
_audit_author_role.id
Unique identifier for the author for whom a role is identified. This may be repeated where an author took on multiple roles. The identifier for the author is drawn from the list of authors given in the AUDIT_AUTHOR category.
audit_author_role
_audit_author_role.role
The role taken by the author identified by _audit_author_role.id, drawn from a predefined list. Additional details can be provided in _audit_author_role.special_details
['\n Conceived and/or designed the experiment.', '\n Synthesized the samples.', '\n Prepared the samples for measurement, e.g. crystallized or\n recrystallized the sample.', '\n Performed non-crystallographic measurements on the samples.', '\n Collected and/or reduced diffraction data.', '\n Obtained fitted parameters, such as a structural model, from the data.', '\n Developed bespoke software for specialised data processing and/or\n analysis.', '\n Prepared the final CIF file.', '\n None of the listed roles. See _audit_author_role.special_details.']
['design', 'synthesis', 'preparation', 'characterisation', 'measurement', 'analysis', 'software', 'submission', 'other']
role
_audit_author_role.special_details
Description of the contribution of the author identified by _audit_author_role.id.
_audit_conform.dict_location
_audit_conform_dict_location
File name or uniform resource locator (URL) where the conformant data dictionary resides.
audit_conform
dict_location
_audit_conform.dict_name
_audit_conform_dict_name
Name identifying highest-level data dictionary defining data names used in this file.
dict_name
_audit_conform.dict_version
_audit_conform_dict_version
Code for the version of data dictionary defining data names used in this file.
dict_version
_audit_contact_author.address
_audit_contact_author_address
The mailing address of the author of the data block to whom correspondence should be addressed.
audit_contact_author
_audit_contact_author.email
_audit_contact_author_email
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.
_audit_contact_author.fax
_audit_contact_author_fax
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.
_audit_contact_author.id
with aca as audit_contact_author count = 0 target = '' loop aa as audit_author { if (aca.name == aa.name) { count++ target = aa.id } } if (count == 1) { _enumeration.default = target } else { _enumeration.default = missing }
_audit_contact_author.name
['_audit_contact_author_name', '_audit_contact_author']
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). For authors with only one name, provide the full name without abbreviation.
['Bleary, Percival R.', "O'Neil, F.K.", 'Van den Bossche, G.', 'Chandra']
_audit_contact_author.phone
_audit_contact_author_phone
Telephone number of 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.
_audit_link.block_code
_audit_link_block_code
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.
audit_link
_audit_link.block_description
_audit_link_block_description
Description of the relationship of the referenced data block to the current one.
block_description
_audit_support.award_number
The award number associated with this source of support.
audit_support
award_number
_audit_support.award_recipient
The recipient of the support. May be an individual or institution.
Cardiff University
award_recipient
_audit_support.award_type
Type or kind of award.
['\n Funds were drawn from an unobligated, discretionary source under the\n control of one of the participants in the research program. This\n includes prize money and personal funds.', '\n Funds were provided by an organization or person outside the research\n program for the specific purpose of supporting the research, as\n directed by the primary investigator', '\n Funds were provided as part of a contractual agreement not covered by\n other award types.', '\n Funds were provided specifically to support a student in conducting\n research, whether directly or indirectly. This category includes\n scholarships and bursaries where the student is expected to engage in\n research.', '\n Other type of support, including financial support not explicitly\n directed towards research. This category includes scholarships and\n bursaries for students that cover living expenses while pursuing\n higher education with no requirement to conduct research.']
['gift', 'grant', 'contract', 'studentship', 'other']
award_type
_audit_support.funding_organization
The name of the organization providing funding support for the data collected and analysed in the data block. The recommended source for such names is the Open Funder Registry (https://gitlab.com/crossref/open_funder_registry).
National Center for Complementary and Alternative Medicine
funding_organization
_audit_support.funding_organization_DOI
The Digital Object Identifier (DOI) associated with the Organization providing funding support for the data collected and analysed in the data block. In accordance with CrossRef guidelines, the full URI of the resolved page describing the funding organization should be given (i.e. including the https://doi.org/ component).
funding_organization_DOI
_audit_support.id
An arbitrary unique identifier for each source of support for the data collected and analysed in the data block.
_cell.angle_alpha
_cell_angle_alpha
The angle between the bounding cell axes.
cell
angle_alpha
degrees
_cell.angle_alpha_su
['_cell_angle_alpha_su', '_cell.angle_alpha_esd']
Standard uncertainty of the angle between the bounding cell axes.
angle_alpha_su
_cell.angle_beta
_cell_angle_beta
angle_beta
_cell.angle_beta_su
['_cell_angle.beta_su', '_cell_angle_beta_su', '_cell.angle_beta_esd']
angle_beta_su
_cell.angle_gamma
_cell_angle_gamma
angle_gamma
_cell.angle_gamma_su
['_cell_angle.gamma_su', '_cell_angle_gamma_su', '_cell.angle_gamma_esd']
angle_gamma_su
_cell.atomic_mass
Atomic mass of the contents of the unit cell. This calculated from the atom sites present in the ATOM_TYPE list, rather than the ATOM_SITE lists of atoms in the refined model.
mass = 0. Loop t as atom_type { mass += t.number_in_cell * t.atomic_mass } _cell.atomic_mass = mass
_cell.convert_Uij_to_betaij
The reciprocal space matrix for converting the U(ij) matrix of atomic displacement parameters to a dimensionless beta(IJ) matrix. The ADP factor in a structure factor expression: t = exp - 2π^2^ ( U11 h h a* a* + ...... 2 U23 k l b* c* ) t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* ) = exp - ( β11 h h + ............ 2 β23 k l ) The conversion of the U or B matrices to the β matrix β = C U C = C B C /8π^2^ where C is conversion matrix defined here.
With c as cell _cell.convert_Uij_to_betaij = 1.4142 * Pi * Matrix([[ c.reciprocal_length_a, 0, 0 ], [ 0, c.reciprocal_length_b, 0 ], [ 0, 0, c.reciprocal_length_c ]])
convert_Uij_to_betaij
_cell.convert_Uij_to_betaij_su
Standard uncertainty of _cell.convert_Uij_to_betaij.
convert_Uij_to_betaij_su
_cell.convert_Uiso_to_Uij
The reciprocal space matrix for converting the isotropic Uiso atomic displacement parameter to the anisotropic matrix Uij. | 1 cos(γ*) cos(β*) | U[i,j] = Uiso * | cos(γ*) 1 cos(α*) | | cos(β*) cos(α*) 1 |
With c as cell _cell.convert_Uiso_to_Uij = [[ 1., Cosd(c.reciprocal_angle_gamma), Cosd(c.reciprocal_angle_beta) ], [ Cosd(c.reciprocal_angle_gamma), 1., Cosd(c.reciprocal_angle_alpha) ], [ Cosd(c.reciprocal_angle_beta), Cosd(c.reciprocal_angle_alpha), 1. ]]
convert_Uiso_to_Uij
_cell.convert_Uiso_to_Uij_su
Standard uncertainty of _cell.convert_Uiso_to_Uij.
convert_Uiso_to_Uij_su
_cell.diffrn_id
A pointer to the diffraction conditions to which this cell has been applied, for example, to locate and extract diffraction peaks. These will normally be the same conditions as those under which the cell was measured, but some legacy data sets may have used a cell measured under differing conditions, in which case those conditions should be indicated using the _cell_measurement.condition_id data item.
_diffrn.id
diffrn_id
_cell.formula_units_Z
_cell_formula_units_Z
The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum.
formula_units_Z
_cell.length_a
_cell_length_a
The length of each cell axis.
length_a
_cell.length_a_su
['_cell_length_a_su', '_cell.length_a_esd']
Standard uncertainty of the length of each cell axis.
length_a_su
_cell.length_b
_cell_length_b
length_b
_cell.length_b_su
['_cell_length_b_su', '_cell.length_b_esd']
length_b_su
_cell.length_c
_cell_length_c
length_c
_cell.length_c_su
['_cell_length_c_su', '_cell.length_c_esd']
length_c_su
_cell.metric_tensor
The direct space (covariant) metric tensor used to transform vectors and coordinates from real (direct) to reciprocal space.
with c as cell _cell.metric_tensor = [[ c.vector_a*c.vector_a, c.vector_a*c.vector_b, c.vector_a*c.vector_c ], [ c.vector_b*c.vector_a, c.vector_b*c.vector_b, c.vector_b*c.vector_c ], [ c.vector_c*c.vector_a, c.vector_c*c.vector_b, c.vector_c*c.vector_c ]]
metric_tensor
_cell.orthogonal_matrix
Orthogonal matrix of the crystal unit cell. Definition 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.
With c as cell _cell.orthogonal_matrix = [ [ c.length_a*Sind(c.angle_beta)*Sind(c.reciprocal_angle_gamma), 0, 0 ], [ -c.length_a*Sind(c.angle_beta)*Cosd(c.reciprocal_angle_gamma), c.length_b*Sind(c.angle_alpha), 0 ], [ c.length_a*Cosd(c.angle_beta), c.length_b*Cosd(c.angle_alpha), c.length_c ]]
orthogonal_matrix
_cell.reciprocal_angle_alpha
_cell_reciprocal_angle_alpha
Reciprocal of the angle between _cell.length_b and _cell.length_c. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
With c as cell _cell.reciprocal_angle_alpha = Acosd((Cosd(c.angle_beta)*Cosd(c.angle_gamma)-Cosd(c.angle_alpha))/ (Sind(c.angle_beta)*Sind(c.angle_gamma)))
reciprocal_angle_alpha
_cell.reciprocal_angle_alpha_su
['_cell_reciprocal_angle_alpha_su', '_cell.reciprocal_angle_alpha_esd']
Standard uncertainty of the reciprocal of the angle between _cell.length_b and _cell.length_c.
reciprocal_angle_alpha_su
_cell.reciprocal_angle_beta
_cell_reciprocal_angle_beta
Reciprocal of the angle between _cell.length_a and _cell.length_c. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
With c as cell _cell.reciprocal_angle_beta = Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_gamma)-Cosd(c.angle_beta))/ (Sind(c.angle_alpha)*Sind(c.angle_gamma)))
reciprocal_angle_beta
_cell.reciprocal_angle_beta_su
['_cell_reciprocal_angle_beta_su', '_cell.reciprocal_angle_beta_esd']
Standard uncertainty of the reciprocal of the angle between _cell.length_a and _cell.length_c.
reciprocal_angle_beta_su
_cell.reciprocal_angle_gamma
_cell_reciprocal_angle_gamma
Reciprocal of the angle between _cell.length_a and _cell.length_b. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
With c as cell _cell.reciprocal_angle_gamma = Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_beta)-Cosd(c.angle_gamma))/ (Sind(c.angle_alpha)*Sind(c.angle_beta)))
reciprocal_angle_gamma
_cell.reciprocal_angle_gamma_su
['_cell_reciprocal_angle_gamma_su', '_cell.reciprocal_angle_gamma_esd']
Standard uncertainty of the reciprocal of the angle between _cell.length_a and _cell.length_b.
reciprocal_angle_gamma_su
_cell.reciprocal_length_a
_cell_reciprocal_length_a
Reciprocal of the _cell.length_a.
_cell.reciprocal_length_a = Norm ( _cell.reciprocal_vector_a )
reciprocal_length_a
_cell.reciprocal_length_a_su
['_cell_reciprocal_length_a_su', '_cell.reciprocal_length_a_esd']
Standard uncertainty of the reciprocal of the _cell.length_a.
reciprocal_length_a_su
_cell.reciprocal_length_b
_cell_reciprocal_length_b
Reciprocal of the _cell.length_b.
_cell.reciprocal_length_b = Norm ( _cell.reciprocal_vector_b )
reciprocal_length_b
_cell.reciprocal_length_b_su
['_cell_reciprocal_length_b_su', '_cell.reciprocal_length_b_esd']
Standard uncertainty of the reciprocal of the _cell.length_b.
reciprocal_length_b_su
_cell.reciprocal_length_c
_cell_reciprocal_length_c
Reciprocal of the _cell.length_c.
_cell.reciprocal_length_c = Norm ( _cell.reciprocal_vector_c )
reciprocal_length_c
_cell.reciprocal_length_c_su
['_cell_reciprocal_length_c_su', '_cell.reciprocal_length_c_esd']
Standard uncertainty of the reciprocal of the _cell.length_c.
reciprocal_length_c_su
_cell.reciprocal_metric_tensor
The reciprocal (contravariant) metric tensor used to transform vectors and coordinates from reciprocal space to real (direct) space.
with c as cell _cell.reciprocal_metric_tensor = [ [ c.reciprocal_vector_a*c.reciprocal_vector_a, c.reciprocal_vector_a*c.reciprocal_vector_b, c.reciprocal_vector_a*c.reciprocal_vector_c ], [ c.reciprocal_vector_b*c.reciprocal_vector_a, c.reciprocal_vector_b*c.reciprocal_vector_b, c.reciprocal_vector_b*c.reciprocal_vector_c ], [ c.reciprocal_vector_c*c.reciprocal_vector_a, c.reciprocal_vector_c*c.reciprocal_vector_b, c.reciprocal_vector_c*c.reciprocal_vector_c ]]
reciprocal_metric_tensor
reciprocal_angstrom_squared
_cell.reciprocal_metric_tensor_su
Standard uncertainty of _cell.reciprocal_metric_tensor.
reciprocal_metric_tensor_su
_cell.reciprocal_orthogonal_matrix
Orthogonal matrix of the reciprocal space. The matrix may be used to transform the non-orthogonal vector h = (h,k,l) into the orthogonal indices p = (p,q,r) M h = p
_cell.reciprocal_orthogonal_matrix = Inverse( Transpose( _cell.orthogonal_matrix ))
reciprocal_orthogonal_matrix
_cell.reciprocal_orthogonal_matrix_su
Standard uncertainty of _cell.reciprocal_orthogonal_matrix.
reciprocal_orthogonal_matrix_su
_cell.reciprocal_vector_a
Reciprocal of the _cell.vector_a.
With c as cell _cell.reciprocal_vector_a = c.vector_b ^ c.vector_c / _cell.volume
reciprocal_vector_a
_cell.reciprocal_vector_a_su
Standard uncertainty of _cell.reciprocal_vector_a.
reciprocal_vector_a_su
_cell.reciprocal_vector_b
Reciprocal of the _cell.vector_b.
With c as cell _cell.reciprocal_vector_b = c.vector_c ^ c.vector_a / _cell.volume
reciprocal_vector_b
_cell.reciprocal_vector_b_su
Standard uncertainty of _cell.reciprocal_vector_b.
reciprocal_vector_b_su
_cell.reciprocal_vector_c
Reciprocal of the _cell.vector_c.
With c as cell _cell.reciprocal_vector_c = c.vector_a ^ c.vector_b / _cell.volume
reciprocal_vector_c
_cell.reciprocal_vector_c_su
Standard uncertainty of _cell.reciprocal_vector_c.
reciprocal_vector_c_su
_cell.special_details
['_cell_special_details', '_cell.details']
Description of special aspects of the cell choice, noting possible alternative settings.
_cell.vector_a
The cell vector along the x axis.
_cell.vector_a = _cell.orthogonal_matrix * Matrix([1,0,0])
vector_a
_cell.vector_a_su
Standard uncertainty of _cell.vector_a.
vector_a_su
_cell.vector_b
The cell vector along the y axis.
_cell.vector_b = _cell.orthogonal_matrix * Matrix([0,1,0])
vector_b
_cell.vector_b_su
Standard uncertainty of _cell.vector_b.
vector_b_su
_cell.vector_c
The cell vector along the z axis.
_cell.vector_c = _cell.orthogonal_matrix * Matrix([0,0,1])
vector_c
_cell.vector_c_su
Standard uncertainty of _cell.vector_c.
vector_c_su
_cell.volume
_cell_volume
Volume of the crystal unit cell.
With c as cell _cell.volume = c.vector_a * ( c.vector_b ^ c.vector_c )
volume
_cell.volume_su
['_cell_volume_su', '_cell.volume_esd']
Standard uncertainty of the volume of the crystal unit cell.
volume_su
_cell_measurement.condition_id
A pointer to the diffraction conditions used for cell measurement, where different to the diffraction conditions used for data collection.
_enumeration.default = _cell_measurement.diffrn_id
cell_measurement
condition_id
_cell_measurement.diffrn_id
A pointer to the diffraction experiment to which the measured cell has been applied.
_cell_measurement.pressure
_cell_measurement_pressure
_diffrn.ambient_pressure
**DEPRECATED** The pressure at which the unit-cell parameters were measured (not the pressure used to synthesize the sample). Replaced by '_diffrn.ambient_pressure'
pressure
kilopascals
_cell_measurement.pressure_su
['_cell_measurement_pressure_su', '_cell_measurement.pressure_esd']
_diffrn.ambient_pressure_su
** DEPRECATED ** Standard uncertainty of the pressure at which the unit-cell parameters were measured.
pressure_su
_cell_measurement.radiation
_cell_measurement_radiation
** DEPRECATED ** Description of the radiation used to measure the unit-cell data. Items from the DIFFRN_RADIATION category should be used instead of this item.
['neutron', 'X-ray tube', 'synchrotron']
radiation
_cell_measurement.reflns_used
_cell_measurement_reflns_used
Total number of reflections used to determine the unit cell. The reflections may be specified as cell_measurement_refln items.
reflns_used
_cell_measurement.temperature
['_cell_measurement_temperature', '_cell_measurement_temp', '_cell_measurement.temp']
_diffrn.ambient_temperature
** DEPRECATED ** The temperature at which the unit-cell parameters were measured (not the temperature of synthesis). _diffrn.ambient_temperature should be used instead of this item.
_cell_measurement.temperature_su
['_cell_measurement_temp_su', '_cell_measurement.temp_esd']
_diffrn.ambient_temperature_su
** DEPRECATED ** Standard uncertainty of the temperature of at which the unit-cell parameters were measured.
temperature_su
_cell_measurement.theta_max
_cell_measurement_theta_max
Maximum θ scattering angle of reflections used to measure the crystal unit cell.
theta_max
_cell_measurement.theta_min
_cell_measurement_theta_min
Minimum θ scattering angle of reflections used to measure the crystal unit cell.
theta_min
_cell_measurement.wavelength
_cell_measurement_wavelength
_diffrn_radiation_wavelength.value
** DEPRECATED ** Wavelength of the radiation used to measure the unit cell. Items from the DIFFRN_RADIATION_WAVELENGTH category should be used instead of this item.
wavelength
_cell_measurement_refln.hkl
Miller indices of a reflection used to measure the unit cell.
With c as cell_measurement_refln _cell_measurement_refln.hkl = [c.index_h, c.index_k, c.index_l]
cell_measurement_refln
hkl
_cell_measurement_refln.index_h
_cell_measurement_refln_index_h
The index of a reciprocal space vector.
index_h
_cell_measurement_refln.index_k
_cell_measurement_refln_index_k
index_k
_cell_measurement_refln.index_l
_cell_measurement_refln_index_l
index_l
_cell_measurement_refln.theta
_cell_measurement_refln_theta
Theta angle of reflection used to measure the crystal unit cell.
theta
_cell_measurement_refln.theta_su
Standard uncertainty of _cell_measurement_refln.theta.
theta_su
_chemical.absolute_configuration
_chemical_absolute_configuration
Necessary conditions for this assignment are given by Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. https://doi.org/10.1107/S0108767399004262 https://www.iucr.org/paper?sh0129 Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. https://doi.org/10.1107/S0021889800007184 https://www.iucr.org/paper?ks0021
["\n 'reference molecule' Absolute configuration established by the\n structure determination of a compound containing a chiral reference\n molecule of known absolute configuration.", "\n 'anomalous dispersion' Absolute configuration established by a-d\n effects in diffraction measurements on the crystal.", "\n 'rm + ad' Absolute configuration established by the structure\n determination of a compound containing a chiral reference molecule of\n known absolute configuration and confirmed by a-d effects in\n diffraction measurements on the crystal.", "\n 'synthetic' Absolute configuration has not been established by\n anomalous-dispersion effects in diffraction measurements on the\n crystal. The enantiomer has been assigned by reference to an\n unchanging chiral centre in the synthetic procedure.", "\n 'unknown' No firm chemical or a-d evidence for an assignment is\n available. An arbitrary choice of enantiomer has been made.", '\n Inapplicable.']
['rm', 'ad', 'rmad', 'syn', 'unk', '.']
chemical
absolute_configuration
_chemical.compound_source
_chemical_compound_source
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.
compound_source
_chemical.enantioexcess_bulk
_chemical_enantioexcess_bulk
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. https://doi.org/10.1351/pac199668122193 https://iupac.qmul.ac.uk/stereo/
enantioexcess_bulk
_chemical.enantioexcess_bulk_su
Standard uncertainty of _chemical.enantioexcess_bulk.
enantioexcess_bulk_su
_chemical.enantioexcess_bulk_technique
_chemical_enantioexcess_bulk_technique
Technique used to determine the enantioexcess of the bulk compound.
['\n Enantioexcess determined by measurement of the specific rotation of\n the optical activity of the bulk compound in solution.', '\n Enantioexcess determined by measurement of the visible/near UV\n circular dichroism spectrum of the bulk compound in solution.', '\n Enantioexcess determined by enantioselective chromatography of the\n bulk compound in solution.', '\n Enantioexcess determined by a technique not in this list.']
['OA', 'CD', 'EC', 'other']
enantioexcess_bulk_technique
_chemical.enantioexcess_crystal
_chemical_enantioexcess_crystal
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. https://doi.org/10.1351/pac199668122193 https://iupac.qmul.ac.uk/stereo/
enantioexcess_crystal
_chemical.enantioexcess_crystal_su
Standard uncertainty of _chemical.enantioexcess_crystal.
enantioexcess_crystal_su
_chemical.enantioexcess_crystal_technique
_chemical_enantioexcess_crystal_technique
Technique used to determine the enantioexcess of the crystal.
['\n Enantioexcess determined by measurement of the visible/near UV\n circular dichroism spectrum of the crystal taken into solution.', '\n Enantioexcess determined by enantioselective chromatography of the\n crystal taken into solution.', '\n Enantioexcess determined by a technique not in this list.']
['CD', 'EC', 'other']
enantioexcess_crystal_technique
_chemical.identifier_InChI
_chemical_identifier_InChI
The IUPAC International Chemical Identifier (InChI) is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web. Ref: McNaught, A. (2006). Chem. Int. (IUPAC), 28 (6), 12-14. https://doi.org/10.1515/ci.2006.28.6.12 https://www.iupac.org/inchi/
naphthalene
identifier_InChI
_chemical.identifier_InChI_key
_chemical_identifier_InChI_key
The InChIKey is a compact hashed version of the full InChI (IUPAC International Chemical Identifier), designed to allow for easy web searches of chemical compounds. See https://www.iupac.org/inchi/
OROGSEYTTFOCAN-DNJOTXNNSA-N
codeine
identifier_InChI_key
_chemical.identifier_InChI_version
_chemical_identifier_InChI_version
Version number of the InChI standard to which the associated chemical identifier string applies.
identifier_InChI_version
_chemical.melting_point
_chemical_melting_point
The temperature at which a crystalline solid changes to a liquid.
melting_point
_chemical.melting_point_gt
_chemical_melting_point_gt
A temperature above which the melting point lies. _chemical.melting_point should be used in preference where possible.
melting_point_gt
_chemical.melting_point_lt
_chemical_melting_point_lt
A temperature below which the melting point lies. _chemical.melting_point should be used in preference where possible.
melting_point_lt
_chemical.melting_point_su
Standard uncertainty of _chemical.melting_point.
melting_point_su
_chemical.name_common
_chemical_name_common
Trivial name by which the compound is commonly known.
name_common
_chemical.name_mineral
_chemical_name_mineral
Mineral name accepted by the International Mineralogical Association. Use only for natural minerals.
name_mineral
_chemical.name_structure_type
_chemical_name_structure_type
Commonly used structure-type name. Usually only applied to minerals or inorganic compounds.
name_structure_type
_chemical.name_systematic
_chemical_name_systematic
IUPAC or Chemical Abstracts full name of compound.
name_systematic
_chemical.optical_rotation
_chemical_optical_rotation
The optical rotation in solution of the compound is specified in the following format: '[α]^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 in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.α/(l.c), where α is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC in g, and SOLV is the chemical formula of the solvent.
optical_rotation
_chemical.properties_biological
_chemical_properties_biological
A description of the biological properties of the material.
['\n diverse biological activities including use as a laxative\n and strong antibacterial activity against S. aureus and weak\n activity against cyclooxygenase-1 (COX-1)', '\n antibiotic activity against Bacillus subtilis (ATCC 6051) but no\n significant activity against Candida albicans (ATCC 14053),\n Aspergillus flavus (NRRL 6541) & Fusarium verticillioides (NRRL 25457)', '\n weakly potent lipoxygenase nonredox inhibitor', '\n no influenza A virus sialidase inhibitory & plaque reduction activities', '\n low toxicity against Drosophila melanogaster']
properties_biological
_chemical.properties_physical
_chemical_properties_physical
A description of the physical properties of the material.
['air-sensitive', 'moisture-sensitive', 'hygroscopic', 'deliquescent', 'oxygen-sensitive', 'photo-sensitive', 'pyrophoric', 'semiconductor', 'ferromagnetic at low temperature', 'paramagnetic and thermochromic']
properties_physical
_chemical.temperature_decomposition
_chemical_temperature_decomposition
The temperature at which a crystalline solid decomposes.
temperature_decomposition
_chemical.temperature_decomposition_gt
_chemical_temperature_decomposition_gt
The temperature above which a crystalline solid decomposes. _chemical.temperature_decomposition should be used in preference.
temperature_decomposition_gt
_chemical.temperature_decomposition_lt
_chemical_temperature_decomposition_lt
The temperature below which a crystalline solid decomposes. _chemical.temperature_decomposition should be used in preference.
temperature_decomposition_lt
_chemical.temperature_decomposition_su
['_chemical_temperature_decomposition_su', '_chemical.temperature_decomposition_esd']
Standard uncertainty of the temperature at which a crystalline solid decomposes.
temperature_decomposition_su
_chemical.temperature_sublimation
_chemical_temperature_sublimation
The temperature at which a crystalline solid sublimates.
temperature_sublimation
_chemical.temperature_sublimation_gt
_chemical_temperature_sublimation_gt
The temperature above which a crystalline solid sublimates. _chemical.temperature_sublimation should be used in preference.
temperature_sublimation_gt
_chemical.temperature_sublimation_lt
_chemical_temperature_sublimation_lt
The temperature below which a crystalline solid sublimates. _chemical.temperature_sublimation should be used in preference.
temperature_sublimation_lt
_chemical.temperature_sublimation_su
['_chemical_temperature_sublimation_su', '_chemical.temperature_sublimation_esd']
Standard uncertainty of the temperature at which a crystalline solid sublimates.
temperature_sublimation_su
_chemical_conn_atom.NCA
_chemical_conn_atom_NCA
Total number of connected atoms excluding terminal hydrogen atoms.
chemical_conn_atom
NCA
_chemical_conn_atom.NH
_chemical_conn_atom_NH
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.
_chemical_conn_atom.charge
_chemical_conn_atom_charge
The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
charge
_chemical_conn_atom.display_x
_chemical_conn_atom_display_x
Cartesian coordinate (x) of the atom site in a chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal.
display_x
_chemical_conn_atom.display_y
_chemical_conn_atom_display_y
Cartesian coordinate (y) of the atom site in a chemical diagram. The coordinate origin is at the lower left corner, the y axis is vertical.
display_y
_chemical_conn_atom_number
The chemical sequence number to be associated with this atom.
number
_chemical_conn_atom.type_symbol
_chemical_conn_atom_type_symbol
A code identifying the atom type.
_chemical_conn_bond.atom_1
['_chemical_conn_bond_atom_1', '_chem_comp_bond.atom_id_1']
Index id of first atom in a bond connecting two atom sites.
chemical_conn_bond
atom_1
_chemical_conn_bond.atom_2
['_chemical_conn_bond_atom_2', '_chem_comp_bond.atom_id_2']
Index id of second atom in a bond connecting two atom sites.
atom_2
_chemical_conn_bond.distance
_chem_comp_bond.value_dist
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance.
distance
_chemical_conn_bond.id
Unique identifier for the bond.
_chemical_conn_bond.type
['_chemical_conn_bond_type', '_chem_comp_bond.value_order']
Code for the chemical bond type.
['Single bond.', 'Double bond.', 'Triple bond.', 'Quadruple bond.', 'Aromatic bond.', 'Polymeric bond.', 'Delocalized double bond.', 'Pi bond.']
['sing', 'doub', 'trip', 'quad', 'arom', 'poly', 'delo', 'pi']
type
_chemical_formula.IUPAC
_chemical_formula_IUPAC
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.
[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H
chemical_formula
IUPAC
_chemical_formula.analytical
_chemical_formula_analytical
Formula determined by standard chemical analysis including trace elements. Parentheses are used only for standard uncertainties (su's).
analytical
_chemical_formula.moiety
_chemical_formula_moiety
Formula with each discrete bonded residue or ion shown as a separate moiety. See above CHEMICAL_FORMULA 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 CHEMICAL_FORMULA. 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 Singlege '+' 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.
['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)']
moiety
_chemical_formula.structural
_chemical_formula_structural
This formula should correspond to the structure as reported, i.e. trace elements not included in atom type and atom site lists should not be included. See 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 (see also _chemical_formula.analytical).
['(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2', 'Ca ((Cl O3)2 O)2 (H2 O)6']
structural
_chemical_formula.sum
_chemical_formula_sum
Chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in rule 5 of the CATEGORY description. Parentheses normally not used.
C18 H19 N7 O8 S
sum
_chemical_formula.weight
_chemical_formula_weight
Mass corresponding to the formulae _chemical_formula.structural, *_IUPAC, *_moiety or *_sum and, together with the Z value and cell parameters yield the density given as _exptl_crystal.density_diffrn.
weight
_chemical_formula.weight_meas
_chemical_formula_weight_meas
Formula mass measured by a non-diffraction experiment.
weight_meas
_chemical_formula.weight_meas_su
Standard uncertainty of _chemical_formula.weight_meas.
weight_meas_su
_citation.DOI
_citation_DOI
The Digital Object Identifier (DOI) of the cited work. A DOI is a unique character string identifying any object of intellectual property. It provides a persistent identifier for an object on a digital network and permits the association of related current data in a structured extensible way. A DOI is an implementation of the Internet concepts of Uniform Resource Name and Universal Resource Locator managed according to the specifications of the International DOI Foundation (see https://www.doi.org/).
citation
DOI
_citation.URL
The Uniform Resource Locator (URL) of the cited work. The _citation.DOI data item should be used in preference to this item when possible.
URL
Uri
_citation.abstract
_citation_abstract
Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information.
abstract
_citation.abstract_id_CAS
_citation_abstract_id_CAS
Chemical Abstracts Service (CAS) abstract identifier.
abstract_id_CAS
_citation.book_id_ISBN
_citation_book_id_ISBN
International Standard Book Number (ISBN) for book chapter cited.
book_id_ISBN
_citation.book_publisher
_citation_book_publisher
Publisher of the citation; relevant for book chapters.
book_publisher
_citation.book_publisher_city
_citation_book_publisher_city
Location of publisher of the citation; relevant for book chapters.
book_publisher_city
_citation.book_title
_citation_book_title
Title of the book in which the citation appeared.
book_title
_citation.coordinate_linkage
_citation_coordinate_linkage
Code specifies whether 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'.
['Citation unrelated to current coordinates.', 'Abbreviation for "no".', 'Citation related to current coordinates.', 'Abbreviation for "yes".']
['no', 'n', 'yes', 'y']
coordinate_linkage
_citation.country
_citation_country
Country of publication; for journal articles and book chapters.
country
_citation.database_id_CSD
_citation_database_id_CSD
Identifier ('refcode') of the database record in the Cambridge Structural Database containing details of the cited structure.
database_id_CSD
_citation.database_id_Medline
_citation_database_id_Medline
MEDLINE accession number categorizing a bibliographic entry.
database_id_Medline
_citation.id
_citation_id
Unique identifier to the CITATION list. A value of '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.
['primary', '1', '2', '3']
if (len(citation) == 1) { _enumeration.default = "primary" } else { _enumeration.default = missing }
_citation.journal_abbrev
_citation_journal_abbrev
Abbreviated name of the journal cited as given in the Chemical Abstracts Service Source Index.
J. Mol. Biol.
journal_abbrev
_citation.journal_full
_citation_journal_full
Full name of the journal cited; relevant for journal articles.
Journal of Molecular Biology
journal_full
_citation.journal_id_ASTM
_citation_journal_id_ASTM
American Society for the Testing of Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles.
journal_id_ASTM
_citation.journal_id_CSD
_citation_journal_id_CSD
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).
journal_id_CSD
_citation.journal_id_ISSN
_citation_journal_id_ISSN
The International Standard Serial Number (ISSN) code assigned to the journal cited. Relevant for journal articles.
journal_id_ISSN
_citation.journal_issue
_citation_journal_issue
Issue identifier of the journal cited; relevant for articles.
['2', 'Special Issue']
journal_issue
_citation.journal_volume
_citation_journal_volume
Volume number of the journal cited; relevant for articles.
journal_volume
_citation.language
_citation_language
Language in which the citation appears.
German
language
_citation.page_first
_citation_page_first
First page of citation; relevant for articles and book chapters.
page_first
_citation.page_last
_citation_page_last
Last page of citation; relevant for articles and book chapters.
page_last
_citation.publisher
_citation_publisher
The name of the publisher of the cited work. This should be used for citations of journal articles or datasets (in the latter case the publisher could be a curated database). For books or book chapters use _citation.book_publisher.
Cambridge Crystallographic Data Centre
publisher
_citation.special_details
['_citation_special_details', '_citation.details']
Special aspects of the relationship of the data block contents to the literature item cited.
_citation.title
_citation_title
Title of citation; relevant for articles and book chapters.
title
_citation.year
_citation_year
Year of citation; relevant for articles and book chapters.
year
_citation_author.citation_id
_citation_author_citation_id
Code identifier in the CITATION data list. The value of must match an identifier specified in the CITATION list.
citation_author
citation_id
_citation_author.name
_citation_author_name
Name of citation author; relevant for articles and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). For authors with only one name, provide the full name without abbreviation.
['Bleary, Percival R.', "O'Neil, F.K.", 'Van den Bossche, G.', 'Yang, D.-L.', 'Simonov, Yu.A', 'Müller, H.A.', 'Ross II, C.R.', 'Chandra']
_citation_author.ordinal
_citation_author_ordinal
Ordinal code specifies the order of the author's name in the list of authors of the citation.
ordinal
_citation_editor.citation_id
_citation_editor_citation_id
Code identifier in the CITATION list. The value must match an identifier specified by _citation.id in the CITATION list.
citation_editor
_citation_editor.name
['_citation_editor', '_citation_editor_name']
Name of citation editor; relevant for book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
['Bleary, Percival R.', "O'Neil, F.K.", 'Van den Bossche, G.', 'Yang, D.-L.', 'Simonov, Yu.A', 'Müller, H.A.', 'Ross II, C.R.']
_citation_editor.ordinal
_citation_editor_ordinal
This data item defines the order of the editor's name in the list of editors of a citation.
_computing.cell_refinement
_computing_cell_refinement
Brief description of software used for cell refinement.
CAD-4 (Enraf-Nonius, 1989)
computing
cell_refinement
_computing.diffrn_collection
['_computing_data_collection', '_computing.data_collection']
Description of software used to measure diffraction data.
diffrn_collection
_computing.diffrn_reduction
['_computing_data_reduction', '_computing.data_reduction']
Description of software used to convert diffraction data to measured structure factors.
DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)
diffrn_reduction
_computing.molecular_graphics
_computing_molecular_graphics
Brief description of software used for molecular graphics.
molecular_graphics
_computing.publication_material
_computing_publication_material
Brief description of software used for publication material.
publication_material
_computing.structure_refinement
_computing_structure_refinement
Brief description of software used for structure refinement.
SHELXL93 (Sheldrick, 1993)
structure_refinement
_computing.structure_solution
_computing_structure_solution
Brief description of software used for structure solution.
SHELXS86 (Sheldrick, 1990)
structure_solution
_database.CSD_history
_database_CSD_history
The history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD).
database
CSD_history
_database.dataset_DOI
_database_dataset_DOI
The digital object identifier (DOI) registered to identify a data set publication associated with the structure described in the current data block. This should be used for a dataset obtained from a curated database such as CSD or PDB. A DOI is a unique character string identifying any object of intellectual property. It provides a persistent identifier for an object on a digital network and permits the association of related current data in a structured extensible way. A DOI is an implementation of the Internet concepts of Uniform Resource Name and Universal Resource Locator managed according to the specifications of the International DOI Foundation (see https://www.doi.org/).
dataset_DOI
_database.journal_ASTM
_database_journal_ASTM
ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service.
journal_ASTM
_database.journal_CSD
_database_journal_CSD
The journal code used in the Cambridge Structural Database.
journal_CSD
_database_code.CAS
['_database_code_CAS', '_database.code_CAS']
Code assigned by the Chemical Abstracts Service.
database_code
CAS
_database_code.COD
['_database_code_COD', '_database.code_COD']
Code assigned by the Crystallography Open Database (COD).
COD
_database_code.CSD
['_database_code_CSD', '_database.code_CSD']
Code assigned by the Cambridge Structural Database.
CSD
_database_code.ICSD
['_database_code_ICSD', '_database.code_ICSD']
Code assigned by the Inorganic Crystal Structure Database.
ICSD
_database_code.MDF
['_database_code_MDF', '_database.code_MDF']
Code assigned in the Metals Data File.
MDF
_database_code.NBS
['_database_code_NBS', '_database.code_NBS']
Code assigned by the NBS (NIST) Crystal Data Database.
NBS
_database_code.PDB
['_database_code_PDB', '_database.code_PDB']
Code assigned by the Protein Data Bank.
PDB
['_database_code_PDF', '_database.code_PDF']
Code assigned in the Powder Diffraction File.
PDF
_database_code.depnum_CCDC_archive
['_database_code_depnum_CCDC_archive', '_database.code_depnum_CCDC_archive']
Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC.
depnum_CCDC_archive
_database_code.depnum_CCDC_fiz
['_database_code_depnum_CCDC_fiz', '_database.code_depnum_CCDC_fiz']
Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
depnum_CCDC_fiz
_database_code.depnum_CCDC_journal
['_database_code_depnum_CCDC_journal', '_database.code_depnum_CCDC_journal']
Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
depnum_CCDC_journal
_database_related.database_id
An identifier for the database that contains the related dataset.
['Chemical Abstracts', 'Crystallography Open Database', 'Cambridge Structural Database', 'Inorganic Crystal Structure Database', 'Metals Data File', 'Nucleic Acid Database', 'Protein Data Bank', 'Powder Diffraction File (JCPDS/ICDD)', 'Research Collaboratory for Structural Bioinformatics', 'European Bioinformatics Institute']
['CAS', 'COD', 'CSD', 'ICSD', 'MDF', 'NDB', 'PDB', 'PDF', 'RCSB', 'EBI']
database_related
database_id
_database_related.entry_code
The code used by the database referred to in _database_related.database_id to identify the related dataset.
entry_code
_database_related.id
An identifier for this database reference.
_database_related.relation
The general relationship of the data in the data block to the dataset referred to in the database.
['\n The dataset contents are identical.', '\n The dataset contents are a proper subset of the contents of the data\n block.', '\n The dataset contents include the contents of the data block.', '\n The dataset contents are derivable from the contents of the data block.', '\n The dataset contents share a common source.', '\n The dataset contents are related to the contents of the data block in\n a way not included elsewhere in this list. In case this value is used,\n it is strongly recommended to also provide the specifics of the\n relationship using the _database_related.special_details data item.']
['Identical', 'Subset', 'Superset', 'Derived', 'Common', 'Other']
relation
_database_related.special_details
Information about the external dataset and relationship not encoded elsewhere.
_diffrn.ambient_environment
_diffrn_ambient_environment
The gas or liquid environment of the crystal sample, if not air.
['He', 'vacuum', 'mother liquor']
diffrn
ambient_environment
_diffrn_ambient_pressure
Mean hydrostatic pressure at which intensities were measured.
ambient_pressure
_diffrn.ambient_pressure_gt
_diffrn_ambient_pressure_gt
Mean hydrostatic pressure above which intensities were measured. These items allow for a pressure range to be given. _diffrn.ambient_pressure should be used in preference to this item when possible.
ambient_pressure_gt
_diffrn.ambient_pressure_lt
_diffrn_ambient_pressure_lt
Mean hydrostatic pressure below which intensities were measured. These items allow for a pressure range to be given. _diffrn.ambient_pressure should be used in preference to this item when possible.
ambient_pressure_lt
['_diffrn_ambient_pressure_su', '_diffrn.ambient_pressure_esd']
Standard uncertainty of the mean hydrostatic pressure at which intensities were measured.
ambient_pressure_su
['_diffrn_ambient_temperature', '_diffrn_ambient_temp', '_diffrn.ambient_temp']
Mean temperature at which intensities were measured.
ambient_temperature
_diffrn.ambient_temperature_details
['_diffrn_ambient_temp_details', '_diffrn.ambient_temp_details']
A description of special aspects of temperature control during data collection.
ambient_temperature_details
_diffrn.ambient_temperature_gt
['_diffrn_ambient_temp_gt', '_diffrn_ambient_temperature_gt', '_diffrn.ambient_temp_gt']
Mean temperature above which intensities were measured. These items allow for a temperature range to be given. _diffrn.ambient_temperature should be used in preference to this item when possible.
ambient_temperature_gt
_diffrn.ambient_temperature_lt
['_diffrn_ambient_temp_lt', '_diffrn_ambient_temperature_lt', '_diffrn.ambient_temp_lt']
Mean temperature below which intensities were measured. These items allow for a temperature range to be given. _diffrn.ambient_temperature should be used in preference to this item when possible.
ambient_temperature_lt
['_diffrn_ambient_temperature_su', '_diffrn_ambient_temp_su', '_diffrn.ambient_temp_esd']
Standard uncertainty of the mean temperature at which intensities were measured.
ambient_temperature_su
_diffrn.crystal_id
Identifier for the crystal from which diffraction data were collected. This is a pointer to _exptl_crystal.id.
_exptl_crystal.id
crystal_id
_diffrn.crystal_support
The physical device used to support the crystal during data collection.
['glass capillary', 'quartz capillary', 'fiber', 'metal loop']
crystal_support
_diffrn.crystal_treatment
_diffrn_crystal_treatment
Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature.
['equilibrated in hutch for 24 hours', 'flash frozen in liquid nitrogen', 'slow cooled with direct air stream']
crystal_treatment
Unique identifier for a diffraction data set collected under particular diffraction conditions.
_diffrn.measured_fraction_theta_full
_diffrn_measured_fraction_theta_full
Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns.theta_full.
measured_fraction_theta_full
_diffrn.measured_fraction_theta_max
_diffrn_measured_fraction_theta_max
Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns.theta_max.
measured_fraction_theta_max
_diffrn.special_details
['_diffrn_special_details', '_diffrn.details']
Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation, etc.
The results may not be entirely reliable as the measurement was made during a heat wave when the air-conditioning had failed.
_diffrn.symmetry_description
_diffrn_symmetry_description
Recorded diffraction point symmetry, systematic absences and possible space group(s) or superspace group(s) compatible with these.
symmetry_description
_diffrn_attenuator.code
_diffrn_attenuator_code
Code identifying a particular attenuator setting; referenced by the _diffrn_refln.attenuator_code which is stored with the intensities.
diffrn_attenuator
code
_diffrn_attenuator.material
_diffrn_attenuator_material
Description of the material from which the attenuator is made.
material
_diffrn_attenuator.scale
_diffrn_attenuator_scale
The scale factor applied to a measured intensity if it is reduced by an attenuator identified by _diffrn_attenuator.code.
scale
_diffrn_detector.area_resol_mean
_diffrn_detector_area_resol_mean
The resolution limit of an area diffraction radiation detector.
diffrn_detector
area_resol_mean
pixels_per_millimetre
_diffrn_detector.description
['_diffrn_radiation_detector', '_diffrn_detector', '_diffrn_detector.detector']
Description of the type of diffraction radiation detector.
['photographic film', 'scintillation counter', 'CCD plate', 'BF~3~ counter']
_diffrn_detector.details
_diffrn_detector_details
Description of special aspects of the radiation detector.
details
_diffrn_detector.dtime
['_diffrn_detector_dtime', '_diffrn_radiation.detector_dtime', '_diffrn_radiation_detector_dtime']
The maximum time between two detector signals that cannot be resolved.
dtime
microseconds
_diffrn_detector.make
['_diffrn_detector_type', '_diffrn_detector.type']
The make, model or name of the diffraction radiation detector.
make
_diffrn_measurement.details
['_diffrn_measurement_details', '_diffrn.measurement_details']
Description of special aspects of the diffraction measurement.
440 frames of 0.25°
diffrn_measurement
_diffrn_measurement.device_class
['_diffrn_measurement_device', '_diffrn.measurement_device_class', '_diffrn_measurement.device']
Type of goniometer device used to mount and orient the specimen.
['three-circle diffractometer', 'four-circle diffractometer', 'κ-geometry diffractometer', 'oscillation camera', 'precession camera']
device_class
_diffrn_measurement.device_details
['_diffrn_measurement_device_details', '_diffrn.measurement_device_details']
Details of the goniometer device used in the diffraction experiment.
commercial goniometer modified locally to allow for 90° θ arc
device_details
_diffrn_measurement.device_make
['_diffrn_measurement_device_type', '_diffrn.measurement_device_make', '_diffrn_measurement.device_type']
The make, model or name of the goniometer device used.
['Supper model q', 'Huber model r', 'Enraf-Nonius model s', 'home-made']
device_make
_diffrn_measurement.method
['_diffrn_measurement_method', '_diffrn.measurement_method']
Description of scan method used to measure diffraction intensities.
profile data from θ/2θ scans
method
_diffrn_measurement.specimen_attachment_type
The way in which the sample is attached to the sample holder, including the type of adhesive material used if relevant. The sample holder is usually wholly outside the beam, whereas the attachment method may cause non-sample material to be illuminated. If the attachment method is not included in the list below, 'other' should be chosen and details provided in _diffrn_measurement.specimen_support.
['\n An epoxy glue.', '\n An oil.', '\n A type of grease, for example hydrocarbon or silicone grease.', '\n A frozen liquid, not water or oil.', '\n A method not listed here.', '\n The specimen is frozen in place using water ice.', '\n The specimen is held in place by mechanical forces, e.g. capillary or\n pressure cell.']
['epoxy', 'oil', 'grease', 'frozen_liquid', 'other', 'ice', 'mechanical']
specimen_attachment_type
_diffrn_measurement.specimen_support
['_diffrn_measurement_specimen_support', '_diffrn.measurement_specimen_support']
Mounting method for the crystal specimen during data collection.
specimen_support
_diffrn_orient_matrix.UB_11
['_diffrn_orient_matrix_UB_11', '_diffrn_orient_matrix.UB[1][1]']
The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer.
diffrn_orient_matrix
UB_11
_diffrn_orient_matrix.UB_12
['_diffrn_orient_matrix_UB_12', '_diffrn_orient_matrix.UB[1][2]']
UB_12
_diffrn_orient_matrix.UB_13
['_diffrn_orient_matrix_UB_13', '_diffrn_orient_matrix.UB[1][3]']
UB_13
_diffrn_orient_matrix.UB_21
['_diffrn_orient_matrix_UB_21', '_diffrn_orient_matrix.UB[2][1]']
UB_21
_diffrn_orient_matrix.UB_22
['_diffrn_orient_matrix_UB_22', '_diffrn_orient_matrix.UB[2][2]']
UB_22
_diffrn_orient_matrix.UB_23
['_diffrn_orient_matrix_UB_23', '_diffrn_orient_matrix.UB[2][3]']
UB_23
_diffrn_orient_matrix.UB_31
['_diffrn_orient_matrix_UB_31', '_diffrn_orient_matrix.UB[3][1]']
UB_31
_diffrn_orient_matrix.UB_32
['_diffrn_orient_matrix_UB_32', '_diffrn_orient_matrix.UB[3][2]']
UB_32
_diffrn_orient_matrix.UB_33
['_diffrn_orient_matrix_UB_33', '_diffrn_orient_matrix.UB[3][3]']
UB_33
_diffrn_orient_matrix.UBij
The 3x3 matrix specifying the orientation of the crystal with respect to the diffractometer axes.
With o as diffrn_orient_matrix _diffrn_orient_matrix.UBIJ = [[ o.ub_11, o.ub_12, o.ub_13 ], [ o.ub_21, o.ub_22, o.ub_23 ], [ o.ub_31, o.ub_32, o.ub_33 ]]
UBij
_diffrn_orient_matrix.type
_diffrn_orient_matrix_type
Description of orientation matrix and how it should be applied to define the orientation of the crystal with respect to the diffractometer axes.
_diffrn_orient_refln.angle_chi
_diffrn_orient_refln_angle_chi
Diffractometer angle of a reflection measured at the centre of the diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
diffrn_orient_refln
angle_chi
_diffrn_orient_refln.angle_chi_su
Standard uncertainty of _diffrn_orient_refln.angle_chi.
angle_chi_su
_diffrn_orient_refln.angle_kappa
_diffrn_orient_refln_angle_kappa
angle_kappa
_diffrn_orient_refln.angle_kappa_su
Standard uncertainty of _diffrn_orient_refln.angle_kappa.
angle_kappa_su
_diffrn_orient_refln.angle_omega
_diffrn_orient_refln_angle_omega
angle_omega
_diffrn_orient_refln.angle_omega_su
Standard uncertainty of _diffrn_orient_refln.angle_omega.
angle_omega_su
_diffrn_orient_refln.angle_phi
_diffrn_orient_refln_angle_phi
angle_phi
_diffrn_orient_refln.angle_phi_su
Standard uncertainty of _diffrn_orient_refln.angle_phi.
angle_phi_su
_diffrn_orient_refln.angle_psi
_diffrn_orient_refln_angle_psi
angle_psi
_diffrn_orient_refln.angle_psi_su
Standard uncertainty of _diffrn_orient_refln.angle_psi.
angle_psi_su
_diffrn_orient_refln.angle_theta
_diffrn_orient_refln_angle_theta
angle_theta
_diffrn_orient_refln.angle_theta_su
Standard uncertainty of _diffrn_orient_refln.angle_theta.
angle_theta_su
_diffrn_orient_refln.hkl
Miller indices of a reflection used to define the orientation matrix.
With a as diffrn_orient_refln _diffrn_orient_refln.hkl = [a.index_h, a.index_k, a.index_l]
_diffrn_orient_refln.index_h
_diffrn_orient_refln_index_h
_diffrn_orient_refln.index_k
_diffrn_orient_refln_index_k
_diffrn_orient_refln.index_l
_diffrn_orient_refln_index_l
_diffrn_radiation.collimation
_diffrn_radiation_collimation
Description of the collimation or focusing applied to the radiation.
['0.3 mm double-pinhole', '0.5 mm', 'focusing mirrors']
diffrn_radiation
collimation
_diffrn_radiation.filter_edge
_diffrn_radiation_filter_edge
Absorption edge of the radiation filter used.
filter_edge
_diffrn_radiation.inhomogeneity
_diffrn_radiation_inhomogeneity
Half-width of the incident beam perpendicular to the diffraction plane.
inhomogeneity
millimetres
_diffrn_radiation.monochromator
_diffrn_radiation_monochromator
Description of the method used to obtain monochromatic radiation. If a monochromator crystal is used the material and the indices of the Bragg reflection are specified.
['Zr filter', 'Ge 220', 'none', 'equatorial mounted graphite']
monochromator
_diffrn_radiation.polarisn_norm
_diffrn_radiation_polarisn_norm
The angle, as viewed from the specimen, between the perpendicular component of the polarisation and the diffraction plane.
polarisn_norm
_diffrn_radiation.polarisn_ratio
_diffrn_radiation_polarisn_ratio
Polarisation ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarised to the parallel polarised component 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).
polarisn_ratio
_diffrn_radiation.probe
_diffrn_radiation_probe
Enumerated code for the nature of radiation used (i.e. name of subatomic particle or region of the electromagnetic spectrum).
['x-ray', 'neutron', 'electron', 'gamma']
probe
_diffrn_radiation.type
_diffrn_radiation_type
_diffrn_radiation_wavelength.type
DEPRECATED. Use _diffrn_radiation_wavelength.type. Details of the radiation source or energy spectrum.
['Mo Kα', 'Cu Kα', 'Cu Kα~1~', 'Cu K-L~2,3~', 'white-beam']
_diffrn_radiation.xray_symbol
_diffrn_radiation_xray_symbol
_diffrn_radiation_wavelength.xray_symbol
DEPRECATED. Use _diffrn_radiation_wavelength.xray_symbol. IUPAC symbol for the X-ray wavelength for probe radiation.
['Kα~1~ in older Siegbahn notation.', 'Kα~2~ in older Siegbahn notation.', 'Kβ~1~ in older Siegbahn notation.', 'Use where K-L~3~ and K-L~2~ are not resolved.']
xray_symbol
_diffrn_radiation_wavelength.details
['_diffrn_radiation_wavelength_details', '_diffrn_radiation.wavelength_details']
Information about the determination of the radiation diffrn_radiation_wavelength that is not conveyed completely by an enumerated value of _diffrn_radiation_wavelength.determination.
diffrn_radiation_wavelength
_diffrn_radiation_wavelength.determination
['_diffrn_radiation_wavelength_determination', '_diffrn_radiation.wavelength_determination']
Method by which the radiation wavelength was determined.
['Fundamental property of matter, e.g. MoKα.', 'Estimated, e.g. from monochromator angle or time of flight.', 'Refined using a standard crystal with known cell parameters.']
['fundamental', 'estimated', 'refined']
determination
_diffrn_radiation_wavelength.id
['_diffrn_radiation_wavelength_id', '_diffrn_radiation.wavelength_id']
Code identifying the radiation used in the diffraction measurements. This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id
Details of the radiation source or energy spectrum.
['_diffrn_radiation_wavelength', '_diffrn_radiation_wavelength.wavelength']
Wavelength of radiation used in diffraction measurements.
value
_diffrn_radiation_wavelength.value_su
['_diffrn_radiation_wavelength_su', '_diffrn_radiation_wavelength.wavelength_su']
Standard uncertainty of the wavelength of radiation used in diffraction measurements.
value_su
_diffrn_radiation_wavelength.wt
_diffrn_radiation_wavelength_wt
Relative intensity of a radiation used in the diffraction measurements.
IUPAC symbol for the X-ray wavelength for probe radiation.
_diffrn_refln.angle_chi
_diffrn_refln_angle_chi
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.
diffrn_refln
_diffrn_refln.angle_kappa
_diffrn_refln_angle_kappa
_diffrn_refln.angle_omega
_diffrn_refln_angle_omega
_diffrn_refln.angle_phi
_diffrn_refln_angle_phi
_diffrn_refln.angle_psi
_diffrn_refln_angle_psi
_diffrn_refln.angle_theta
_diffrn_refln_angle_theta
_diffrn_refln.attenuator_code
_diffrn_refln_attenuator_code
Code identifying any attenuator setting for this reflection.
attenuator_code
_diffrn_refln.class_code
_diffrn_refln_class_code
Code for reflection class, if assigned. e.g. modulated structures
_diffrn_reflns_class.code
class_code
_diffrn_refln.counts_bg_1
_diffrn_refln_counts_bg_1
The measured background scattering on one side of a diffraction peak when measuring using a point detector. Note that counts-per-second values should be converted to total counts. Standard uncertainties should not be quoted for these values. If the standard uncertainties differ from the square root of the number of counts, _diffrn_refln.intensity_* should be used.
counts_bg_1
counts
_diffrn_refln.counts_bg_2
_diffrn_refln_counts_bg_2
The measured background counts on the other side of the peak to the measurement of _diffrn_refln.counts_bg_1 when measuring using a point detector. Note that counts-per-second values should be converted to total counts. Standard uncertainties should not be quoted for these values. If the standard uncertainties differ from the square root of the number of counts, _diffrn_refln.intensity_* should be used.
counts_bg_2
_diffrn_refln.counts_net
_diffrn_refln_counts_net
Counts measured in the reflection peak after background subtraction. If background and peak counts were collected for different times, the background counts must be scaled to the peak counts prior to subtraction. Note that counts-per-second values should be converted to total counts. The value for this data item must be derived from count values. If not, _diffrn_refln.intensity_* should be used.
counts_net
_diffrn_refln.counts_net_su
Standard uncertainty of _diffrn_refln.counts_net.
counts_net_su
_diffrn_refln.counts_peak
_diffrn_refln_counts_peak
Counts measured in the reflection peak before background subtraction. That is, the region of interest consists of only the diffraction peak. Note that counts-per-second values should be converted to total counts. Standard uncertainties should not be quoted for these values. If the standard uncertainties differ from the square root of the number of counts, _diffrn_refln.intensity_* should be used.
counts_peak
_diffrn_refln.counts_total
_diffrn_refln_counts_total
Counts measured in the total reflection including background and peak regions. That is, the region of interest consists of the diffraction peak and an area of background immediately surrounding the peak of interest. Note that counts-per-second values should be converted to total counts. Standard uncertainties should not be quoted for these values. If the standard uncertainties differ from the square root of the number of counts, _diffrn_refln.intensity_* should be used.
counts_total
_diffrn_refln.detect_slit_horiz
_diffrn_refln_detect_slit_horiz
Total slit aperture angle in the diffraction plane.
detect_slit_horiz
_diffrn_refln.detect_slit_vert
_diffrn_refln_detect_slit_vert
Total slit aperture angle perpendicular to the diffraction plane.
detect_slit_vert
_diffrn_refln.elapsed_time
_diffrn_refln_elapsed_time
Elapsed time from the start to the end of the intensity measurement.
elapsed_time
minutes
_diffrn_refln.hkl
Miller indices of a measured reflection. These need not match the _refln.hkl values if a transformation of the original measured cell has taken place.
With a as diffrn_refln _diffrn_refln.hkl = [a.index_h, a.index_h, a.index_l]
_diffrn_refln.index_h
_diffrn_refln_index_h
_diffrn_refln.index_k
_diffrn_refln_index_k
_diffrn_refln.index_l
_diffrn_refln_index_l
_diffrn_refln.intensity_bg_1
The measured background intensity on one side of a diffraction peak when measuring using a point detector. Use these entries for measurements where intensity values are not counts (use _diffrn_refln.counts_* for event-counting measurements where the standard uncertainty is estimated as the square root of the number of counts).
intensity_bg_1
_diffrn_refln.intensity_bg_1_su
Standard uncertainty of _diffrn_refln.intensity_bg_1.
intensity_bg_1_su
_diffrn_refln.intensity_bg_2
The measured background counts on the other side of the peak to the measurement of _diffrn_refln.intensity_bg_1 when measuring using a point detector. Use these entries for measurements where intensity values are not counts (use _diffrn_refln.counts_* for event-counting measurements where the standard uncertainty is estimated as the square root of the number of counts).
intensity_bg_2
_diffrn_refln.intensity_bg_2_su
Standard uncertainty of _diffrn_refln.intensity_bg_2.
intensity_bg_2_su
_diffrn_refln.intensity_net
_diffrn_refln_intensity_net
Net intensity in the reflection peak calculated from the diffraction counts after the attenuator and standard scales have been applied.
intensity_net
_diffrn_refln.intensity_net_su
['_diffrn_refln_intensity_u', '_diffrn_refln_intensity_sigma', '_diffrn_refln.intensity_sigma', '_diffrn_refln.intensity_u']
Standard uncertainty of _diffrn_refln.intensity_net.
intensity_net_su
_diffrn_refln.intensity_peak
Intensity measured in the reflection peak before background subtraction. That is, the region of interest consists of only the diffraction peak. Use these entries for measurements where intensity values are not counts (use _diffrn_refln.counts_* for event-counting measurements where the standard uncertainty is estimated as the square root of the number of counts).
intensity_peak
_diffrn_refln.intensity_peak_su
Standard uncertainty of _diffrn_refln.intensity_peak.
intensity_peak_su
_diffrn_refln.intensity_total
Intensity measured in the total reflection including background and peak regions. That is, the region of interest consists of the diffraction peak and an area of background immediately surrounding the peak of interest. Use these entries for measurements where intensity values are not counts (use _diffrn_refln.counts_* for event-counting measurements where the standard uncertainty is estimated as the square root of the number of counts).
intensity_total
_diffrn_refln.intensity_total_su
Standard uncertainty of _diffrn_refln.intensity_total.
intensity_total_su
_diffrn_refln.scale_group_code
_diffrn_refln_scale_group_code
Code identifying the scale applying to this reflection.
_diffrn_scale_group.code
scale_group_code
_diffrn_refln.scan_mode
_diffrn_refln_scan_mode
Code identifying the mode of scanning with a diffractometer. See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
['ω-scan.', 'ω/2θ-scan.', 'Q-scans (arbitrary reciprocal directions).']
['om', 'ot', 'q']
scan_mode
_diffrn_refln.scan_mode_backgd
_diffrn_refln_scan_mode_backgd
Code identifying mode of scanning to measure the background intensity.
['Stationary counter background.', 'Moving counter background.']
['st', 'mo']
scan_mode_backgd
_diffrn_refln.scan_rate
_diffrn_refln_scan_rate
Angular rate of scanning a reflection to measure the intensity.
scan_rate
degree_per_minute
_diffrn_refln.scan_time_backgd
_diffrn_refln_scan_time_backgd
Time spent measuring background counts.
scan_time_backgd
seconds
_diffrn_refln.scan_width
_diffrn_refln_scan_width
Angular scan width when measuring the peak intensity.
scan_width
_diffrn_refln.sin_theta_over_lambda
['_diffrn_refln_sint/lambda', '_diffrn_refln_sint_over_lambda', '_diffrn_refln.sint_over_lambda']
sin(θ)/λ value for this reflection.
sin_theta_over_lambda
_diffrn_refln.standard_code
_diffrn_refln_standard_code
Code identifying reflections measured repeated as standard intensity. Must match a _diffrn_standard_refln.code values OR set to '.' if it was not used as an intensity standard.
_diffrn_standard_refln.code
standard_code
_diffrn_refln.wavelength
_diffrn_refln_wavelength
Mean wavelength of radiation used to measure this intensity.
_diffrn_refln.wavelength_id
_diffrn_refln_wavelength_id
Code identifying the wavelength in the diffrn_radiation_wavelength list.
wavelength_id
_diffrn_reflns.Laue_measured_fraction_full
_diffrn_reflns_Laue_measured_fraction_full
Fraction of Laue group 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.
diffrn_reflns
Laue_measured_fraction_full
_diffrn_reflns.Laue_measured_fraction_max
_diffrn_reflns_Laue_measured_fraction_max
Fraction of Laue group 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.
Laue_measured_fraction_max
_diffrn_reflns.av_R_equivalents
_diffrn_reflns_av_R_equivalents
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.
av_R_equivalents
_diffrn_reflns.av_sunetI_over_netI
['_diffrn_reflns_av_sigmaI_over_netI', '_diffrn_reflns_av_sigmaI/netI', '_diffrn_reflns.av_unetI/netI', '_diffrn_reflns_av_unetI/netI', '_diffrn_reflns.av_sigmaI_over_netI']
Recorded [sum |su(netI)| / sum |netI|] for all measured reflections.
av_sunetI_over_netI
_diffrn_reflns.limit_h_max
_diffrn_reflns_limit_h_max
limit_h_max
_diffrn_reflns.limit_h_min
_diffrn_reflns_limit_h_min
limit_h_min
_diffrn_reflns.limit_k_max
_diffrn_reflns_limit_k_max
limit_k_max
_diffrn_reflns.limit_k_min
_diffrn_reflns_limit_k_min
limit_k_min
_diffrn_reflns.limit_l_max
_diffrn_reflns_limit_l_max
limit_l_max
_diffrn_reflns.limit_l_min
_diffrn_reflns_limit_l_min
limit_l_min
_diffrn_reflns.limit_max
Maximum Miller indices of measured diffraction reflections.
With t as diffrn_reflns _diffrn_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max]
limit_max
_diffrn_reflns.limit_min
Minimum Miller indices of measured diffraction reflections.
With t as diffrn_reflns _diffrn_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min]
limit_min
_diffrn_reflns.number
_diffrn_reflns_number
Total number of measured intensities, excluding reflections that are classed as systematically absent arising from translational symmetry in the crystal unit cell.
_diffrn_reflns.point_measured_fraction_full
_diffrn_reflns_point_group_measured_fraction_full
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.
point_measured_fraction_full
_diffrn_reflns.point_measured_fraction_max
_diffrn_reflns_point_group_measured_fraction_max
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.
point_measured_fraction_max
_diffrn_reflns.reduction_process
_diffrn_reflns_reduction_process
How intensities were reduced to structure-factor magnitudes.
data averaged using Fisher test
reduction_process
_diffrn_reflns.resolution_full
_diffrn_reflns_resolution_full
The resolution 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.
resolution_full
_diffrn_reflns.resolution_max
_diffrn_reflns_resolution_max
Maximum resolution of the measured diffraction pattern. The fraction of unique reflections measured out to this angle is given by _diffrn.measured_fraction_theta_max.
resolution_max
_diffrn_reflns.theta_full
_diffrn_reflns_theta_full
Theta angle at which the count of measured reflections is almost complete. The fraction of unique reflections measured out to this angle is given by _diffrn.measured_fraction_theta_full.
theta_full
_diffrn_reflns.theta_max
_diffrn_reflns_theta_max
Maximum θ angle of the measured reflections.
_diffrn_reflns.theta_min
_diffrn_reflns_theta_min
Minimum θ angle of the measured reflections.
_diffrn_reflns_class.av_R_eq
_diffrn_reflns_class_av_R_eq
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.
diffrn_reflns_class
av_R_eq
_diffrn_reflns_class.av_suI_over_I
['_diffrn_reflns_class_av_uI_over_I', '_diffrn_reflns_class.av_uI/I', '_diffrn_reflns_class_av_uI/I', '_diffrn_reflns_class.av_sgI/I', '_diffrn_reflns_class_av_sgI/I']
Recorded [sum|su(net I)|/sum|net I|] in a reflection class.
av_suI_over_I
_diffrn_reflns_class_code
Code identifying a reflection class.
_diffrn_reflns_class.d_res_high
_diffrn_reflns_class_d_res_high
Highest resolution in reflection class i.e. smallest d value in class.
d_res_high
_diffrn_reflns_class.d_res_low
_diffrn_reflns_class_d_res_low
Lowest resolution in reflection class i.e. largest d value in class.
d_res_low
_diffrn_reflns_class.description
_diffrn_reflns_class_description
Description of a reflection class.
m=1 first order satellites
_diffrn_reflns_class.number
_diffrn_reflns_class_number
Number of measured intensities for a reflection class, excluding the systematic absences arising from centring translations.
_diffrn_reflns_transf_matrix.11
['_diffrn_reflns_transf_matrix_11', '_diffrn_reflns.transf_matrix[1][1]']
The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl.
diffrn_reflns_transf_matrix
_diffrn_reflns_transf_matrix.12
['_diffrn_reflns_transf_matrix_12', '_diffrn_reflns.transf_matrix[1][2]']
_diffrn_reflns_transf_matrix.13
['_diffrn_reflns_transf_matrix_13', '_diffrn_reflns.transf_matrix[1][3]']
_diffrn_reflns_transf_matrix.21
['_diffrn_reflns_transf_matrix_21', '_diffrn_reflns.transf_matrix[2][1]']
_diffrn_reflns_transf_matrix.22
['_diffrn_reflns_transf_matrix_22', '_diffrn_reflns.transf_matrix[2][2]']
_diffrn_reflns_transf_matrix.23
['_diffrn_reflns_transf_matrix_23', '_diffrn_reflns.transf_matrix[2][3]']
_diffrn_reflns_transf_matrix.31
['_diffrn_reflns_transf_matrix_31', '_diffrn_reflns.transf_matrix[3][1]']
_diffrn_reflns_transf_matrix.32
['_diffrn_reflns_transf_matrix_32', '_diffrn_reflns.transf_matrix[3][2]']
_diffrn_reflns_transf_matrix.33
['_diffrn_reflns_transf_matrix_33', '_diffrn_reflns.transf_matrix[3][3]']
_diffrn_reflns_transf_matrix.TIJ
Elements of the matrix used to transform the diffraction reflection indices _diffrn_refln.hkl into the _refln.hkl indices. |11 12 13| (h k l) diffraction |21 22 23| = (h' k' l') |31 32 33|
With t as diffrn_reflns_transf_matrix _diffrn_reflns_transf_matrix.TIJ = [[t.11, t.12, t.13], [t.21, t.22, t.23], [t.31, t.32, t.33]]
TIJ
_diffrn_scale_group.I_net
_diffrn_scale_group_I_net
Scale for a specific measurement group of reflections. Is multiplied with the net intensity to place all intensities on a common scale.
diffrn_scale_group
I_net
_diffrn_scale_group.I_net_su
Standard uncertainty of _diffrn_scale_group.I_net.
I_net_su
_diffrn_scale_group_code
Code identifying a specific scale group of reflections (e.g. for multi-film or multi-crystal data). The code must match a _diffrn_refln.scale_group_code in the DIFFRN_REFLN list.
_diffrn_source.beamline
The name of the beamline at the synchrotron or other large-scale experimental facility at which the experiment was conducted.
I19
diffrn_source
beamline
_diffrn_source.current
_diffrn_source_current
Generator current at which the radiation source device was operated.
current
milliamperes
_diffrn_source.description
['_diffrn_source', '_diffrn_radiation_source', '_diffrn_source.source']
['_diffrn_source.device', '_diffrn_source.details']
The general class of the source of radiation. This is deprecated. Use _diffrn_source.device and _diffrn_source.details.
_diffrn_source.details
_diffrn_source_details
A description of special aspects of the source not covered by other data items.
_diffrn_source.device
Enumerated code for the device providing the source of radiation.
['Sealed X-ray tube.', 'Nuclear reactor.', 'Spallation source.', 'Electron microscope.', 'Rotating-anode X-ray tube.', 'Synchrotron.']
['tube', 'nuclear', 'spallation', 'elect-micro', 'rot_anode', 'synch']
device
_diffrn_source.facility
The name of the synchrotron or other large-scale experimental facility at which the experiment was conducted. Names should conform to the spelling and format used in the 'Light Sources of the World' listing of lightsources.org (https://lightsources.org/lightsources-of-the-world/)
Diamond Light Source
facility
_diffrn_source.make
['_diffrn_source_make', '_diffrn_source.type', '_diffrn_source_type']
Description of the make, model or name of the source device. Large scale facilities should use _diffrn_source.facility and _diffrn_source.beamline to identify the source of radiation.
Rigaku RU2012-05-07
_diffrn_source.power
_diffrn_source_power
Generator power at which the radiation source device was operated.
power
kilowatts
_diffrn_source.size
_diffrn_source_size
Description of the collimated source beam as viewed from the sample.
['8 mm x 0.4 mm fine-focus', 'broad focus']
size
_diffrn_source.take_off_angle
['_diffrn_source_take-off_angle', '_diffrn_source.take-off_angle']
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.
take_off_angle
_diffrn_source.target
_diffrn_source_target
Chemical element symbol for the radiation source target (usually the anode). This can be used also for spallation sources.
target
_diffrn_source.voltage
_diffrn_source_voltage
Generator voltage at which the radiation source device was operated.
voltage
kilovolts
['_diffrn_standard_refln_code', '_diffrn_standard_refln.diffrn_id']
Code identifying a standard reflection used to monitor source intensity variations or crystal degradation or movement during data collection.
diffrn_standard_refln
_diffrn_standard_refln.hkl
Miller indices of a standard reflection.
With d as diffrn_standard_refln _diffrn_standard_refln.hkl = [d.index_h, d.index_h, d.index_l]
_diffrn_standard_refln.index_h
_diffrn_standard_refln_index_h
_diffrn_standard_refln.index_k
_diffrn_standard_refln_index_k
_diffrn_standard_refln.index_l
_diffrn_standard_refln_index_l
_diffrn_standards.decay_percent
['_diffrn_standards_decay_%', '_diffrn_standards.decay_%', '_diffrn_standards_decay_percent']
The percentage decrease in the mean of the intensities for the standard reflections at the start to the finish of the measurement process. This value affords a measure of the overall decay in crystal quality during measurement. Negative values only occur in exceptional instances where the final intensities are greater than the initial ones. If no measurable decay has occurred, the standard uncertainty should be quoted to indicate the maximum possible value the decay might have. A range of 3 standard uncertainties is considered possible. Thus 0.0(1) would indicate a decay of less than 0.3% or an enhancement of less than 0.3%.
['Represents a decay between 0.2% and 0.8%.', 'Change in standards between 2% decay and 4% rise.', 'Change in standards between 0.6% decay and 0.6% rise.']
diffrn_standards
decay_percent
_diffrn_standards.decay_percent_su
Standard uncertainty of _diffrn_standards.decay_percent.
decay_percent_su
_diffrn_standards.interval_count
_diffrn_standards_interval_count
Reflection count between the standard reflection measurements.
interval_count
_diffrn_standards.interval_time
_diffrn_standards_interval_time
Time between the standard reflection measurements.
interval_time
_diffrn_standards.number
_diffrn_standards_number
Number of unique standard reflections used in measurements.
_diffrn_standards.scale_su_average
['_diffrn_standards_scale_sigma', '_diffrn_standards.scale_sigma', '_diffrn_standards.scale_u', '_diffrn_standards_scale_u']
The average standard uncertainty of the individual standard scales applied to the intensity data.
scale_su_average
_diffrn_standards.scale_su_average_su
Standard uncertainty of _diffrn_standards.scale_su_average.
scale_su_average_su
_display_colour.RGB
The red-green-blue intensities, bases 256, for each colour code.
With c as display_colour _display_colour.RGB = [ c.red, c.green, c.blue ]
RGB
_display_colour.blue
Integer value between 0 and 255 giving the intensity of a specific colour component (red, green or blue) for the RGB display colour code.
blue
_display_colour.green
green
_display_colour.hue
Colour hue as an enumerated code.
hue
_display_colour.red
red
_exptl.crystals_number
_exptl_crystals_number
Total number of crystals used in the measurement of intensities.
exptl
crystals_number
_exptl.method
The method used in the experiment.
['single-crystal x-ray diffraction', 'single-crystal neutron diffraction', 'single-crystal electron diffraction', 'fiber x-ray diffraction', 'fiber neutron diffraction', 'fiber electron diffraction', 'single-crystal joint x-ray and neutron diffraction', 'single-crystal joint x-ray and electron diffraction', 'solution nmr', 'solid-state nmr', 'theoretical model', 'other']
_exptl.method_details
A description of special aspects of the experimental method.
['29 structures', 'minimized average structure']
method_details
_exptl.special_details
['_exptl_special_details', '_exptl.details']
Details of the experiment prior to intensity measurement. See also _exptl_crystal.preparation
_exptl.transmission_factor_max
_exptl_transmission_factor_max
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. For the applied correction see _exptl_absorpt.correction_T_max.
transmission_factor_max
_exptl.transmission_factor_max_su
Standard uncertainty of _exptl.transmission_factor_max.
transmission_factor_max_su
_exptl.transmission_factor_min
_exptl_transmission_factor_min
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. For the applied correction see _exptl_absorpt.correction_T_min.
transmission_factor_min
_exptl.transmission_factor_min_su
Standard uncertainty of _exptl.transmission_factor_min.
transmission_factor_min_su
_exptl_absorpt.coefficient_mu
['_exptl_absorpt_coefficient_mu', '_exptl.absorpt_coefficient_mu']
Linear absorption coefficient, μ, calculated from the atomic content of the cell, the density and the radiation wavelength.
exptl_absorpt
coefficient_mu
reciprocal_millimetres
_exptl_absorpt.coefficient_mu_su
Standard uncertainty of _exptl_absorpt.coefficient_mu.
coefficient_mu_su
_exptl_absorpt.correction_T_max
['_exptl_absorpt_correction_T_max', '_exptl.absorpt_correction_T_max']
Maximum transmission factor for the crystal and radiation applied to the measured intensities, it includes the correction for absorption by the specimen mount and diffractometer as well as by the specimen itself. These values give the transmission (T) factor by which measured intensities have been REDUCED due to absorption. Sometimes referred to as absorption correction A or 1/A* (see "Crystal Structure Analysis for Chemists and Biologists" by J.P. Glusker et al., Wiley)
correction_T_max
_exptl_absorpt.correction_T_min
['_exptl_absorpt_correction_T_min', '_exptl.absorpt_correction_T_min']
Minimum transmission factor for the crystal and radiation applied to the measured intensities, it includes the correction for absorption by the specimen mount and diffractometer as well as by the specimen itself. These values give the transmission (T) factor by which measured intensities have been REDUCED due to absorption. Sometimes referred to as absorption correction A or 1/A* (see "Crystal Structure Analysis for Chemists and Biologists" by J.P. Glusker et al., Wiley)
correction_T_min
_exptl_absorpt.correction_type
['_exptl_absorpt_correction_type', '_exptl.absorpt_correction_type']
Code identifying the absorption correction type and method. The 'empirical' approach should NOT be used if more detailed information on the crystal shape is available.
['Analytical from crystal shape.', 'Cylindrical.', 'Empirical from intensities.', 'Gaussian from crystal shape.', 'Integration from crystal shape.', 'Symmetry-related measurements.', 'No absorption correction applied.', 'Numerical from crystal shape.', 'Psi-scan corrections.', 'Refined from delta-F.', 'Spherical.']
['analytical', 'cylinder', 'empirical', 'gaussian', 'integration', 'multi-scan', 'none', 'numerical', 'psi-scan', 'refdelf', 'sphere']
correction_type
_exptl_absorpt.process_details
['_exptl_absorpt_process_details', '_exptl.absorpt_process_details']
Description of the absorption correction process applied to the measured intensities. A literature reference should be supplied for psi-scan or multi-scan techniques.
['Tompa analytical', 'MolEN (Fair, 1990)', '(North, Phillips & Mathews, 1968)']
process_details
_exptl_absorpt.special_details
_exptl_absorpt_special_details
Details of the absorption correction process applied to the measured intensities that cannot otherwise be given using other data items from the EXPTL_ABSORPT category.
['\n X-ray beam inhomogeneity and goniometer imperfection account for much\n of the difference between estimated values of Tmin and Tmax and the\n _exptl_absorpt_correction_ values.', '\n Neutron linear absorption coefficient is wavelength dependent. The\n value of 0.2216 (mm^-1^) shown in _exptl_absorpt_coefficient_mu is the\n sample absorption coefficient for a neutron wavelength at 1.0 Å.']
['\n Text modified from:\n Petty, Anthony J. et al. Computationally aided design of a high-\n performance organic semiconductor: the development of a universal\n crystal engineering core. Chemical Science, 2019\n https://doi.org/10.1039/C9SC02930C\n COD 1552381', '\n Text modified from:\n Lengyel, Jeff et al. Antiferroelectric Phase Transition in a\n Proton-Transfer Salt of Squaric Acid and 2,3-Dimethylpyrazine.\n Journal of the American Chemical Society, 2019, 141, 16279-16287\n https://doi.org/10.1021/jacs.9b04473\n COD 4127699']
_exptl_crystal.F_000
_exptl_crystal_F_000
Number of electrons in the crystal unit cell contributing to F(000). It may contain dispersion contributions, and is calculated as F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ f~r~ = real part of the scattering factors at θ = 0 f~i~ = imaginary part of the scattering factors at θ = 0 the sum is taken over each atom in the unit cell For X-rays, non-dispersive F(000) is a positive number and counts the effective number of electrons in the unit cell; for neutrons, non-dispersive F(000) (which may be negative) counts the total nuclear scattering power in the unit cell. See https://dictionary.iucr.org/F(000)
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" Else _units.code = "electrons"
exptl_crystal
_exptl_crystal.colour
_exptl_crystal_colour
Colour description of the crystal. Data items from EXPTL_CRYSTAL_APPEARANCE category should be used in preference to this item when possible.
['translucent pale green', 'dark yellow', 'metallic blue', 'red', 'colourless', 'dichroic dark purple/pale blue']
default_value = "" With c as exptl_crystal_appearance { if (not Is_missing(c.general)) default_value = c.general if (not Is_missing(c.intensity)) { if (len(default_value) > 0) default_value = default_value + " " default_value = default_value + c.intensity } if (not Is_missing(c.hue)) { if (len(default_value) > 0) default_value = default_value + " " default_value = default_value + c.hue } } if (len(default_value) > 0) _enumeration.default = default_value
colour
Composite
_exptl_crystal.density_diffrn
_exptl_crystal_density_diffrn
Crystal density calculated from crystal unit cell and atomic content.
_exptl_crystal.density_diffrn = 1.6605 * _cell.atomic_mass / _cell.volume
density_diffrn
megagrams_per_metre_cubed
_exptl_crystal.density_diffrn_su
Standard uncertainty of _exptl_crystal.density_diffrn.
density_diffrn_su
_exptl_crystal.density_meas
_exptl_crystal_density_meas
Crystal density measured using standard chemical and physical methods.
density_meas
_exptl_crystal.density_meas_gt
_exptl_crystal_density_meas_gt
The value above which the density measured using standard chemical and physical methods lies. This item is used only when _exptl_crystal.density_meas cannot be employed. It is intended for use in reporting information in databases and archives which would be misleading if reported otherwise.
density_meas_gt
_exptl_crystal.density_meas_lt
_exptl_crystal_density_meas_lt
The value below which the density measured using standard chemical and physical methods lies. This item is used only when _exptl_crystal.density_meas cannot be employed. It is intended for use in reporting information in databases and archives which would be misleading if reported otherwise.
density_meas_lt
_exptl_crystal.density_meas_su
['_exptl_crystal_density_meas_su', '_exptl_crystal.density_meas_esd']
Standard uncertainty of the crystal density measured using standard chemical and physical methods.
density_meas_su
_exptl_crystal.density_meas_temp
_exptl_crystal_density_meas_temp
Temperature at which _exptl_crystal.density_meas was determined.
density_meas_temp
_exptl_crystal.density_meas_temp_gt
_exptl_crystal_density_meas_temp_gt
Temperature above which the measured density was determined. This item is used only when _exptl_crystal.density_meas_temp cannot be employed. It is intended for use in reporting values from databases which would be misleading if reported otherwise.
density_meas_temp_gt
_exptl_crystal.density_meas_temp_lt
_exptl_crystal_density_meas_temp_lt
Temperature below which the measured density was determined. This item is used only when _exptl_crystal.density_meas_temp cannot be employed. It is intended for use in reporting values from databases which would be misleading if reported otherwise.
density_meas_temp_lt
_exptl_crystal.density_meas_temp_su
['_exptl_crystal_density_meas_temp_su', '_exptl_crystal.density_meas_temp_esd']
Standard uncertainty of the temperature at which _exptl_crystal.density_meas was determined.
density_meas_temp_su
_exptl_crystal.density_method
_exptl_crystal_density_method
Description of method used to measure _exptl_crystal.density_meas.
flotation in aqueous KI
density_method
_exptl_crystal.description
_exptl_crystal_description
Description of the quality and habit of the crystal. The crystal dimensions should be provided using the exptl_crystal.size_* data items.
_exptl_crystal_id
Code identifying a crystal.
_exptl_crystal.preparation
_exptl_crystal_preparation
Details of crystal growth and preparation of the crystals (e.g. mounting) prior to the intensity measurements.
mounted in an argon-filled quartz capillary
preparation
_exptl_crystal.pressure_history
_exptl_crystal_pressure_history
Details concerning the pressure history of the crystals.
pressure_history
_exptl_crystal.recrystallization_method
_exptl_crystal_recrystallization_method
Method used to recrystallize the sample. Sufficient details should be given for the procedure to be repeated. Temperatures, solvents, flux or carrier gases with concentrations or pressures and ambient atmosphere details should be given.
recrystallization_method
_exptl_crystal.size_length
_exptl_crystal_size_length
The length of needle/cylindrical crystals.
size_length
_exptl_crystal.size_length_su
Standard uncertainty of _exptl_crystal.size_length.
size_length_su
_exptl_crystal.size_max
_exptl_crystal_size_max
The maximum dimension of a crystal.
size_max
_exptl_crystal.size_max_su
Standard uncertainty of _exptl_crystal.size_max.
size_max_su
_exptl_crystal.size_mid
_exptl_crystal_size_mid
The medial dimension of a crystal.
size_mid
_exptl_crystal.size_mid_su
Standard uncertainty of _exptl_crystal.size_mid.
size_mid_su
_exptl_crystal.size_min
_exptl_crystal_size_min
The minimum dimension of a crystal.
size_min
_exptl_crystal.size_min_su
Standard uncertainty of _exptl_crystal.size_min.
size_min_su
_exptl_crystal.size_rad
_exptl_crystal_size_rad
The radius of a spherical or cylindrical crystal.
size_rad
_exptl_crystal.size_rad_su
Standard uncertainty of _exptl_crystal.size_rad.
size_rad_su
_exptl_crystal.thermal_history
_exptl_crystal_thermal_history
Details concerning the thermal history of the crystals.
thermal_history
_exptl_crystal_appearance.general
['_exptl_crystal_colour_lustre', '_exptl_crystal.colour_lustre']
Appearance of the crystal as prescribed state codes. Note that 'dull' and 'clear' should no longer be used.
['metallic', 'lustrous', 'transparent', 'translucent', 'opaque', 'dull', 'clear', '.']
exptl_crystal_appearance
general
_exptl_crystal_appearance.hue
['_exptl_crystal_colour_primary', '_exptl_crystal.colour_primary']
Colour hue of the crystals as prescribed state codes.
_exptl_crystal_appearance.intensity
['_exptl_crystal_colour_modifier', '_exptl_crystal.colour_modifier']
Colour intensity of the crystal as prescribed state codes.
['dark', 'light', 'intense', 'pale', 'whitish', 'blackish', 'greyish', 'grayish', 'brownish', 'reddish', 'pinkish', 'orangish', 'yellowish', 'greenish', 'bluish', '.']
intensity
_exptl_crystal_face.diffr_chi
_exptl_crystal_face_diffr_chi
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.
exptl_crystal_face
diffr_chi
_exptl_crystal_face.diffr_chi_su
Standard uncertainty of _exptl_crystal_face.diffr_chi.
diffr_chi_su
_exptl_crystal_face.diffr_kappa
_exptl_crystal_face_diffr_kappa
diffr_kappa
_exptl_crystal_face.diffr_kappa_su
Standard uncertainty of _exptl_crystal_face.diffr_kappa.
diffr_kappa_su
_exptl_crystal_face.diffr_phi
_exptl_crystal_face_diffr_phi
diffr_phi
_exptl_crystal_face.diffr_phi_su
Standard uncertainty of _exptl_crystal_face.diffr_phi.
diffr_phi_su
_exptl_crystal_face.diffr_psi
_exptl_crystal_face_diffr_psi
diffr_psi
_exptl_crystal_face.diffr_psi_su
Standard uncertainty of _exptl_crystal_face.diffr_psi.
diffr_psi_su
_exptl_crystal_face.hkl
Miller indices of the crystal face.
With f as exptl_crystal_face _exptl_crystal_face.hkl = [f.index_h, f.index_h, f.index_l]
_exptl_crystal_face.index_h
_exptl_crystal_face_index_h
_exptl_crystal_face.index_k
_exptl_crystal_face_index_k
_exptl_crystal_face.index_l
_exptl_crystal_face_index_l
_exptl_crystal_face.perp_dist
_exptl_crystal_face_perp_dist
Perpendicular distance of face to the centre of rotation of the crystal.
perp_dist
_exptl_crystal_face.perp_dist_su
Standard uncertainty of _exptl_crystal_face.perp_dist.
perp_dist_su
_function.AtomType
The function r = AtomType( s ) returns an atom type symbol (element name) from the atom site label.
Function AtomType( s :[Single, Word]) { # atom label m = Len(s) n = 1 If (m > 1 and s[1] not in '0123456789') n = 2 If (m > 2 and s[2] in '+-' ) n = 3 If (m > 3 and s[3] in '+-' ) n = 4 AtomType = s[0:n] }
function
AtomType
_function.Closest
The function d = Closest( v, w ) returns the cell translation vector required to obtain the closest cell-translated occurrence of the vector V to the vector W.
Function Closest( v :[Matrix, Real], # coord vector to be cell translated w :[Matrix, Real]) { # target vector d = v - w Closest = Int( Mod( 99.5 + d, 1.0 ) - d ) }
Closest
_function.SeitzFromJones
The function s = SeitzFromJones( j ) returns a 4x4 Seitz matrix from the Jones faithful representation of the equivalent position which is a character string e.g. 1/2+x,-x,z.
Function SeitzFromJones( j :[Single, Text]) { # Jones symmetry notation joneschrs = "123456xyz/,+- " s = Matrix([[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]]) axis = 0 sign = 1 inum = 0 do i=0,Len(j)-1 { c = j[i] If (c not in joneschrs) dummy = print('illegal char in symmetry xyz') If (c == ' ') Next If (c == ',') { axis += 1 inum = 0 sign = 1 } Else If (c == '+') sign = +1 Else If (c == '-') sign = -1 Else If (c == 'x') s[axis,0] = sign Else If (c == 'y') s[axis,1] = sign Else If (c == 'z') s[axis,2] = sign Else { If (inum == 0) m = AtoI(c) If (inum == 1 and c != '/') dummy = print('illegal num in symmetry xyz') If (inum == 2) { n = AtoI(c) If(n == 5) dummy = print('illegal translation in symmetry xyz') s[axis,3] = Mod(10.+ Float(sign*m)/Float(n), 1.) sign = 1 } inum += 1 } } SeitzFromJones = s }
SeitzFromJones
_function.SymEquiv
The function xyz' = SymEquiv( symop, xyz ) returns a fractional coordinate vector xyz' which is input vector xyz transformed by the input symop 'n_pqr' applied to the symmetry equivalent matrix extracted from the category SPACE_GROUP_SYMOP.
Function SymEquiv( c :[Single, Symop], # symop string n_pqr x :[Matrix, Real] ){ # fract coordinate vector s = space_group_symop [ SymKey( c ) ] SymEquiv = s.R * x + s.T + SymLat( c ) }
SymEquiv
_function.SymKey
The function m = SymKey( s ) returns an integer index to the Seitz matrices from the character string of the form 'n_pqr'.
Function SymKey( s :[Single, Symop]) { # symop string If (s == '.') n = 1 Else n = AtoI(s[0]) SymKey = n # index from 1 }
SymKey
_function.SymLat
The function v = SymLat( s ) returns a vector of the cell translations applied to the coordinates from the character string of the form 'n_pqr'. i.e. p-5, q-5, r-5.
Function SymLat( s :[Single, Symop]) { # symop string If (s[0] == ' ') v = [ 5, 5, 5 ] Else v = [ AtoI(s[2]), AtoI(s[3]), AtoI(s[4]) ] SymLat = v - 5 }
SymLat
_function.Symop
The function s = Symop( n, t ) returns a character string of the form 'n_pqr' where n is the symmetry equivalent site number and [p,q,r] is the cell translation vector PLUS [5,5,5].
Function Symop( n :[Single, Integer], # symmetry equivalent site number t :[List , Integer]) { # cell translation vector d = t + 5 Symop = repr(n) + '_' + repr(d[0]) + repr(d[1]) + repr(d[2]) }
Symop
_geom.bond_distance_incr
Increment added to the bond radii for the atomic species to specify the maximum permitted "bonded" distance between two atom sites.
geom
bond_distance_incr
_geom.bond_distance_min
Minimum permitted "bonded" distance between two atom sites.
bond_distance_min
_geom.contact_distance_incr
Increment added to the bond radii for the atomic species to specify the maximum permitted "contact" distance between two "non-bonded" atom sites.
contact_distance_incr
_geom.contact_distance_min
Minimum permitted "contact" distance between two "non-bonded" atom sites.
contact_distance_min
_geom.special_details
['_geom_special_details', '_geom.details']
Description of geometry information not covered by the existing data names in the geometry categories, such as least-squares planes.
_geom_angle.atom_site_label_1
['_geom_angle_atom_site_label_1', '_geom_angle.atom_site_id_1']
This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell.
geom_angle
atom_site_label_1
_geom_angle.atom_site_label_2
['_geom_angle_atom_site_label_2', '_geom_angle.atom_site_id_2']
The unique identifier for the vertex atom of the angle.
atom_site_label_2
_geom_angle.atom_site_label_3
['_geom_angle_atom_site_label_3', '_geom_angle.atom_site_id_3']
atom_site_label_3
_geom_angle.distances
The pair of distances between sites 1 - 2 and 2 - 3.
distances
_geom_angle.distances_su
Standard uncertainty of _geom_angle.distances.
distances_su
_geom_angle.id
An arbitrary, unique identifier for the angle formed by the three atoms.
_geom_angle.publ_flag
_geom_angle_publ_flag
Code signals if the angle is referred to in a publication or should be placed in a table of significant angles.
['Do not include angle in special list.', 'Abbreviation for "no".', 'Do include angle in special list.', 'Abbreviation for "yes".']
publ_flag
_geom_angle.site_symmetry_1
_geom_angle_site_symmetry_1
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
['4th symmetry operation applied.', '7th symm. posn.; +a on x; -b on y.', 'No symmetry or translation to site.']
site_symmetry_1
_geom_angle.site_symmetry_2
_geom_angle_site_symmetry_2
site_symmetry_2
_geom_angle.site_symmetry_3
_geom_angle_site_symmetry_3
site_symmetry_3
_geom_angle.value
_geom_angle
Angle defined by the atoms located at atom_site_x/site_symmetry_x for x = 1,2,3. The vertex atom is at site x = 2.
With a as geom_angle xc = List() bundle = [[a.site_symmetry_1,a.atom_site_label_1], [a.site_symmetry_2,a.atom_site_label_2], [a.site_symmetry_3.a.atom_site_label_3]] for symop,label in bundle { xf = SymEquiv(symop, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } v1,v2 = xc[0]-xc[1], xc[2]-xc[1] _geom_angle.value = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) )
_geom_angle.value_su
['_geom_angle_su', '_geom_angle.value_esd']
Standard uncertainty of the angle defined by the sites identified by _geom_angle.id.
_geom_bond.atom_site_label_1
['_geom_bond_atom_site_label_1', '_geom_bond.atom_site_id_1']
geom_bond
_geom_bond.atom_site_label_2
['_geom_bond_atom_site_label_2', '_geom_bond.atom_site_id_2']
_geom_bond.distance
['_geom_bond_distance', '_geom_bond.dist']
Intramolecular bond distance between the sites identified by _geom_bond.id
With b as geom_bond xc = List() For [label,symop] in [[b.atom_site_label_1,b.site_symmetry_1], [b.atom_site_label_2,b.site_symmetry_2]] { xf = SymEquiv(symop, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_bond.distance = Norm ( xc[0] - xc[1] )
_geom_bond.distance_su
['_geom_bond_distance_su', '_geom_bond.dist_esd']
Standard uncertainty of the intramolecular bond distance between the sites identified by _geom_bond.id.
distance_su
_geom_bond.id
_geom_bond.multiplicity
_geom_bond_multiplicity
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.
multiplicity
_geom_bond.publ_flag
_geom_bond_publ_flag
This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles.
['Do not include bond in special list.', 'Abbreviation for "no".', 'Do include bond in special list.', 'Abbreviation for "yes".']
_geom_bond.site_symmetry_1
_geom_bond_site_symmetry_1
_geom_bond.site_symmetry_2
_geom_bond_site_symmetry_2
_geom_bond.valence
_geom_bond_valence
Bond valence calculated from the bond distance.
valence
_geom_bond.valence_su
Standard uncertainty of _geom_bond.valence.
valence_su
_geom_contact.atom_site_label_1
['_geom_contact_atom_site_label_1', '_geom_contact.atom_site_id_1']
geom_contact
_geom_contact.atom_site_label_2
['_geom_contact_atom_site_label_2', '_geom_contact.atom_site_id_2']
_geom_contact.distance
['_geom_contact_distance', '_geom_contact.dist']
Intermolecular distance between the atomic sites identified by _geom_contact.id
With c as geom_contact xc = List() For [label,symop] in c.atom_site_label_1,c.site_symmetry_1, c.atom_site_label_2,c.site_symmetry_2 { xf = SymEquiv(symop, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_contact.distance = Norm ( xc[0] - xc[1] )
_geom_contact.distance_su
['_geom_contact_distance_su', '_geom_contact.dist_esd']
Standard uncertainty of the intermolecular distance between the atomic sites identified by _geom_contact.id.
_geom_contact.id
An identifier for the contact that is unique within the loop.
_geom_contact.publ_flag
_geom_contact_publ_flag
This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances.
['Do not include distance in special list.', 'Abbreviation for "no".', 'Do include distance in special list.', 'Abbreviation for "yes".']
_geom_contact.site_symmetry_1
_geom_contact_site_symmetry_1
_geom_contact.site_symmetry_2
_geom_contact_site_symmetry_2
_geom_hbond.angle_DHA
_geom_hbond_angle_DHA
Angle subtended by the sites identified by _geom_hbond.id. The hydrogen at site H is at the apex of the angle.
With a as geom_hbond xc = List() bundle = [[ a.atom_site_label_D, a.site_symmetry_D ], [ a.atom_site_label_H, a.site_symmetry_H ], [ a.atom_site_label_A, a.site_symmetry_A ]] For [label,symop] in bundle { xf = SymEquiv(symop, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } v1,v2 = xc[0]-xc[1], xc[2]-xc[1] _geom_hbond.angle_DHA = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) )
geom_hbond
angle_DHA
_geom_hbond.angle_DHA_su
['_geom_hbond_angle_DHA_su', '_geom_hbond.angle_DHA_esd']
Standard uncertainty of the angle subtended by the sites identified by _geom_hbond.id. The hydrogen at site H is at the apex of the angle.
angle_DHA_su
_geom_hbond.atom_site_label_A
['_geom_hbond_atom_site_label_A', '_geom_hbond.atom_site_id_A']
atom_site_label_A
_geom_hbond.atom_site_label_D
['_geom_hbond_atom_site_label_D', '_geom_hbond.atom_site_id_D']
atom_site_label_D
_geom_hbond.atom_site_label_H
['_geom_hbond_atom_site_label_H', '_geom_hbond.atom_site_id_H']
atom_site_label_H
_geom_hbond.distance_DA
['_geom_hbond_distance_DA', '_geom_hbond.dist_DA']
The set of data items which specify the distance between the three atom sites identified by _geom_hbond.id.
with g as geom_hbond l,s = g.atom_site_label_D, g.site_symmetry_D d_pos = SymEquiv(s, _atom_site[l].fract_xyz) d_pos = _atom_sites_Cartn_transform.matrix * d_pos l,s = g.atom_site_label_A,g.site_symmetry_A a_pos = SymEquiv(s, _atom_site[l].fract_xyz) a_pos = _atom_sites_Cartn_transform.matrix * a_pos _geom_hbond.distance_DA = Norm ( a_pos - d_pos )
distance_DA
_geom_hbond.distance_DA_su
['_geom_hbond_distance_DA_su', '_geom_hbond.dist_DA_esd']
Standard uncertainty of the set of data items which specify the distance between the three atom sites identified by _geom_hbond.id.
distance_DA_su
_geom_hbond.distance_DH
['_geom_hbond_distance_DH', '_geom_hbond.dist_DH']
with g as geom_hbond l,s = g.atom_site_label_D, g.site_symmetry_D d_pos = SymEquiv(s, _atom_site[l].fract_xyz) d_pos = _atom_sites_Cartn_transform.matrix * d_pos l,s = g.atom_site_label_H,g.site_symmetry_H h_pos = SymEquiv(s, _atom_site[l].fract_xyz) h_pos = _atom_sites_Cartn_transform.matrix * h_pos _geom_hbond.distance_DH = Norm ( h_pos - d_pos )
distance_DH
_geom_hbond.distance_DH_su
['_geom_hbond_distance_DH_su', '_geom_hbond.dist_DH_esd']
distance_DH_su
_geom_hbond.distance_HA
['_geom_hbond_distance_HA', '_geom_hbond.dist_HA']
with g as geom_hbond l,s = g.atom_site_label_A, g.site_symmetry_A a_pos = SymEquiv(s, _atom_site[l].fract_xyz) a_pos = _atom_sites_Cartn_transform.matrix * a_pos l,s = g.atom_site_label_H,g.site_symmetry_H h_pos = SymEquiv(s, _atom_site[l].fract_xyz) h_pos = _atom_sites_Cartn_transform.matrix * h_pos _geom_hbond.distance_HA = Norm ( h_pos - a_pos )
distance_HA
_geom_hbond.distance_HA_su
['_geom_hbond_distance_HA_su', '_geom_hbond.dist_HA_esd']
distance_HA_su
_geom_hbond.id
An identifier for the hydrogen bond that is unique within the loop.
_geom_hbond.publ_flag
_geom_hbond_publ_flag
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.
_geom_hbond.site_symmetry_A
_geom_hbond_site_symmetry_A
site_symmetry_A
_geom_hbond.site_symmetry_D
_geom_hbond_site_symmetry_D
site_symmetry_D
_geom_hbond.site_symmetry_H
_geom_hbond_site_symmetry_H
site_symmetry_H
_geom_torsion.angle
['_geom_torsion', '_geom_torsion.value']
Angle defined by the sites identified by _geom_torsion.id. 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.
geom_torsion
angle
_geom_torsion.angle_su
['_geom_torsion_su', '_geom_torsion.value_esd']
Standard uncertainty of the torsion angle.
angle_su
_geom_torsion.atom_site_label_1
['_geom_torsion_atom_site_label_1', '_geom_torsion.atom_site_id_1']
_geom_torsion.atom_site_label_2
['_geom_torsion_atom_site_label_2', '_geom_torsion.atom_site_id_2']
_geom_torsion.atom_site_label_3
['_geom_torsion_atom_site_label_3', '_geom_torsion.atom_site_id_3']
_geom_torsion.atom_site_label_4
['_geom_torsion_atom_site_label_4', '_geom_torsion.atom_site_id_4']
atom_site_label_4
_geom_torsion.distances
Distances between sites 1 - 2, 2 - 3 and 3 - 4.
_geom_torsion.distances_su
Standard uncertainty of _geom_torsion.distances.
_geom_torsion.id
An identifier for the torsion angle that is unique within its loop.
_geom_torsion.publ_flag
_geom_torsion_publ_flag
Code signals if the torsion angle is required for publication.
['Publish.', 'Abbreviation for "yes".', 'Do not publish.', 'Abbreviation for "no".']
['yes', 'y', 'no', 'n']
_geom_torsion.site_symmetry_1
_geom_torsion_site_symmetry_1
_geom_torsion.site_symmetry_2
_geom_torsion_site_symmetry_2
_geom_torsion.site_symmetry_3
_geom_torsion_site_symmetry_3
_geom_torsion.site_symmetry_4
_geom_torsion_site_symmetry_4
site_symmetry_4
_journal.coden_ASTM
_journal_coden_ASTM
ASTM code assigned to journal.
journal
coden_ASTM
_journal.coden_Cambridge
_journal_coden_Cambridge
Cambridge Cryst. Data Centre code assigned to journal.
coden_Cambridge
_journal.data_validation_number
_journal_data_validation_number
Journal data items are defined by the journal staff.
data_validation_number
_journal.issue
_journal_issue
Issue identifier within the journal.
issue
_journal.language
_journal_language
Language of the publication.
_journal.name_full
_journal_name_full
Full name of the journal.
name_full
_journal.page_first
_journal_page_first
First page of the publication in the journal.
_journal.page_last
_journal_page_last
Last page of the publication in the journal.
_journal.paper_DOI
_journal_paper_DOI
DOI of the publication in the journal.
paper_DOI
_journal.paper_URL
The Uniform Resource Locator (URL) of the publication. The _journal.paper_DOI data item should be used in preference to this item when possible.
paper_URL
_journal.paper_category
_journal_paper_category
Category of the publication in the journal.
paper_category
_journal.paper_number
Article number that is used by some journals instead of a page range. Usually applies to electronic-only journals.
paper_number
_journal.paper_pages
Number of pages in the journal article.
paper_pages
_journal.suppl_publ_number
_journal_suppl_publ_number
Number of the supplementary publication.
suppl_publ_number
_journal.suppl_publ_pages
_journal_suppl_publ_pages
Number of pages in the supplementary publication.
suppl_publ_pages
_journal.validation_number
Data validation number assigned to journal.
validation_number
_journal.volume
_journal_volume
Volume number of the publication.
_journal.year
_journal_year
Year of the publication.
_journal_coeditor.address
['_journal_coeditor_address', '_journal.coeditor_address']
The postal address of the coeditor.
journal_coeditor
_journal_coeditor.code
['_journal_coeditor_code', '_journal.coeditor_code']
The coeditor identifier.
_journal_coeditor.email
['_journal_coeditor_email', '_journal.coeditor_email']
The email address of the coeditor.
_journal_coeditor.fax
['_journal_coeditor_fax', '_journal.coeditor_fax']
The fax number of the coeditor.
_journal_coeditor.name
['_journal_coeditor_name', '_journal.coeditor_name']
The name of the coeditor.
_journal_coeditor.notes
['_journal_coeditor_notes', '_journal.coeditor_notes']
Notes on coeditor interaction wrt this publication.
notes
_journal_coeditor.phone
['_journal_coeditor_phone', '_journal.coeditor_phone']
The phone number of the coeditor.
_journal_date.accepted
['_journal_date_accepted', '_journal.date_accepted']
Date when the publication was accepted.
journal_date
accepted
Date
_journal_date.from_coeditor
['_journal_date_from_coeditor', '_journal.date_from_coeditor']
Date when the publication was received from the coeditor.
from_coeditor
_journal_date.printers_final
['_journal_date_printers_final', '_journal.date_printers_final']
Date when the publication was last sent to the printers.
printers_final
_journal_date.printers_first
['_journal_date_printers_first', '_journal.date_printers_first']
Date when the publication was first sent to the printers.
printers_first
_journal_date.proofs_in
['_journal_date_proofs_in', '_journal.date_proofs_in']
Date when the publication proofs were received.
proofs_in
_journal_date.proofs_out
['_journal_date_proofs_out', '_journal.date_proofs_out']
Date when the publication proofs were sent out.
proofs_out
_journal_date.recd_copyright
['_journal_date_recd_copyright', '_journal.date_recd_copyright']
Date when the completed copyright was received.
recd_copyright
_journal_date.recd_electronic
['_journal_date_recd_electronic', '_journal.date_recd_electronic']
Date when the publication was received electronically.
recd_electronic
_journal_date.recd_hard_copy
['_journal_date_recd_hard_copy', '_journal.date_recd_hard_copy']
Date when the publication was received as hard copy.
recd_hard_copy
_journal_date.to_coeditor
['_journal_date_to_coeditor', '_journal.date_to_coeditor']
Date when the publication was sent to the coeditor.
to_coeditor
_journal_index.id
Unique identifier for a journal index entry.
journal_index
_journal_index.subterm
_journal_index_subterm
Sub-term index assigned for the publication.
subterm
_journal_index.term
_journal_index_term
Term index assigned for the publication.
term
_journal_index.type
_journal_index_type
Type of index assigned for the publication.
['Organic formula index.', 'Inorganic formula index.', 'Metal-organic formula index.', 'Subject index.']
_journal_techeditor.address
['_journal_techeditor_address', '_journal.techeditor_address']
Postal address of the technical editor for this publication.
journal_techeditor
_journal_techeditor.code
['_journal_techeditor_code', '_journal.techeditor_code']
Code of the technical editor for this publication.
_journal_techeditor.email
['_journal_techeditor_email', '_journal.techeditor_email']
Email address of the technical editor for this publication.
_journal_techeditor.fax
['_journal_techeditor_fax', '_journal.techeditor_fax']
Fax number of the technical editor for this publication.
_journal_techeditor.name
['_journal_techeditor_name', '_journal.techeditor_name']
Name of the technical editor for this publication.
_journal_techeditor.notes
['_journal_techeditor_notes', '_journal.techeditor_notes']
Notes of the technical editor for this publication.
_journal_techeditor.phone
['_journal_techeditor_phone', '_journal.techeditor_phone']
Phone number of the technical editor for this publication.
_model_site.ADP_eigenvalues
The set of three ADP eigenvalues for the associated eigenvectors given by _model_site.ADP_eigenvectors. The eigenvalues are sorted in order of magnitude with the largest first.
A = _cell.orthogonal_matrix U = A * _model_site.ADP_matrix_beta * Transpose(A) /(2*Pi**2) _model_site.ADP_eigenvalues = Eigen( U )[:,0]
model_site
ADP_eigenvalues
Array
_model_site.ADP_eigenvalues_su
Standard uncertainty of _model_site.ADP_eigenvalues.
ADP_eigenvalues_su
_model_site.ADP_eigenvectors
The set of three ADP eigenvectors corresponding to the values given in _model_site.ADP_eigenvalues. The eigenvectors are contained in the rows of a matrix ordered from top to bottom in order largest to smallest corresponding eigenvalue. The eigenvector elements are direction cosines to the orthogonal axes X,Y,Z.
A = _cell.orthogonal_matrix U = A * _model_site.ADP_matrix_beta * Transpose(A) /(2*Pi**2) _model_site.ADP_eigenvectors = Eigen( U )[:,1:4]
ADP_eigenvectors
_model_site.ADP_eigenvectors_su
Standard uncertainty of _model_site.ADP_eigenvectors.
ADP_eigenvectors_su
_model_site.ADP_matrix_beta
Matrix of dimensionless anisotropic atomic displacement parameters.
with m as model_site a = atom_site[m.label] s = space_group_symop[SymKey(m.symop)] _model_site.ADP_matrix_beta = s.R * a.matrix_beta * s.RT
ADP_matrix_beta
_model_site.ADP_matrix_beta_su
Standard uncertainty of _model_site.ADP_matrix_beta.
ADP_matrix_beta_su
_model_site.Cartn_xyz
With m as model_site _model_site.Cartn_xyz = _atom_sites_Cartn_transform.matrix * m.fract_xyz
_model_site.Cartn_xyz_su
Standard uncertainty of _model_site.Cartn_xyz.
_model_site.display_colour
Display colour code assigned to this atom site. Note that the possible colours are enumerated in the colour_RGB list, and the default code is enumerated in the colour_hue list.
_model_site.type_symbol
_model_site.fract_xyz
Vector of fractional atom site coordinates.
With m as model_site xyz = _atom_site[m.label].fract_xyz _model_site.fract_xyz = SymEquiv(m.symop, xyz)
_model_site.fract_xyz_su
Standard uncertainty of _model_site.fract_xyz.
_model_site.id
An identifier for the model site that is unique within its loop.
_model_site.index
Index number of an atomic site in the connected molecule.
index
_model_site.label
Code identifies a site in the ATOM_SITE category of data.
_model_site.mole_index
Index number of distinct molecules in the cell, not related by symmetry.
mole_index
_model_site.radius_bond
Atomic radius of atom located at this site.
With m as model_site _model_site.radius_bond = _atom_type[m.type_symbol].radius_bond
_model_site.radius_contact
Atomic contact radius of atom specie located at this site.
With m as model_site _model_site.radius_contact = _atom_type[m.type_symbol].radius_contact
_model_site.symop
symop
Code to identify the atom specie(s) occupying this site.
_model_site.type_symbol = AtomType ( _model_site.label )
_publ.contact_letter
_publ_contact_letter
A letter submitted to the journal editor by the contact author.
publ
contact_letter
_publ_author.address
_publ_author_address
The address of a publication author. If there is more than one author, this will be looped with _publ_author.name.
publ_author
_publ_author.email
_publ_author_email
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.
_publ_author.footnote
_publ_author_footnote
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.
footnote
_publ_author.id
_enumeration.default = Unique_id(publ_author.id)
_publ_author.id_IUCr
_publ_author_id_IUCr
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).
id_IUCr
_publ_author.id_ORCID
_publ_author_id_ORCID
_publ_author.id_audit
Identifier corresponding to this author in the AUDIT_AUTHOR category list, if present.
id_audit
_publ_author.name
_publ_author_name
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. For authors with only one name, provide the full name without abbreviation.
_publ_author.phone
_publ_author_phone
Telephone number of the author submitting the manuscript and data block. 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. The earlier convention of including the international dialing prefix in parentheses is no longer recommended.
_publ_body.contents
_publ_body_contents
A text section of a submitted paper.
publ_body
contents
_publ_body.element
_publ_body_element
The functional role of the associated text section.
section
['section', 'subsection', 'subsubsection', 'appendix', 'footnote']
element
_publ_body.format
_publ_body_format
Enumerated state indicating the appropriate typesetting conventions for accented characters and special symbols in the text section.
cif
['No coding for special symbols.', 'CIF convention.', 'LaTeX.', 'Rich Text Format.', 'SGML (ISO 8879).', 'TeX.', 'troff or nroff.']
['ascii', 'cif', 'latex', 'rtf', 'sgml', 'tex', 'troff']
format
_publ_body.label
_publ_body_label
Unique identifier for each part of the body of the paper.
_publ_body.title
_publ_body_title
Title of the associated section of text.
_publ_contact_author.address
['_publ_contact_author_address', '_publ.contact_author_address']
The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff.
Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1
publ_contact_author
_publ_contact_author.email
['_publ_contact_author_email', '_publ.contact_author_email']
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.
['name@host.domain.country', 'banjo.patterson@gulgong.edu.au']
_publ_contact_author.fax
['_publ_contact_author_fax', '_publ.contact_author_fax']
_publ_contact_author.id
with pca as publ_contact_author count = 0 target = '' loop pa as publ_author { if (pca.name == pa.name) { count++ target = pa.id } } if (count == 1) { _enumeration.default = target } else { _enumeration.default = missing }
_publ_contact_author.id_IUCr
_publ_contact_author_id_IUCr
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 (https://wdc.iucr.org/).
_publ_contact_author.id_ORCID
_publ_contact_author_id_ORCID
Identifier in the ORCID Registry of the author submitting the manuscript and data block. ORCID is an open, non-profit, community-driven service to provide a registry of unique researcher identifiers (https://orcid.org/).
_publ_contact_author.name
['_publ_contact_author_name', '_publ.contact_author', '_publ_contact_author', '_publ.contact_author_name']
The name of the author(s) submitting the manuscript and data block. This is the person contacted by the journal editorial staff.
Professor George Ferguson
_publ_contact_author.phone
['_publ_contact_author_phone', '_publ.contact_author_phone']
_publ_manuscript.creation
['_publ_manuscript_creation', '_publ.manuscript_creation']
A description of the word processor package and computer used to create the manuscript stored as _publ_manuscript.processed.
publ_manuscript
creation
_publ_manuscript.processed
['_publ_manuscript_processed', '_publ.manuscript_processed']
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.
processed
_publ_manuscript.text
['_publ_manuscript_text', '_publ.manuscript_text']
The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text.
text
_publ_manuscript_incl_extra.defn
['_publ_manuscript_incl_extra_defn', '_publ_manuscript_incl.extra_defn']
Yes/No flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not.
yes
['Include item in journal request list.', 'Include item in journal request list.', 'Exclude item in journal request list.', 'Exclude item in journal request list.']
publ_manuscript_incl_extra
defn
_publ_manuscript_incl_extra.info
['_publ_manuscript_incl_extra_info', '_publ_manuscript_incl.extra_info']
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.
info
_publ_manuscript_incl_extra.item
['_publ_manuscript_incl_extra_item', '_publ_manuscript_incl.extra_item']
The data name (i.e. Tag) of a specific data item included in the manuscript which is not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list.
item
Tag
_publ_requested.category
['_publ_requested_category', '_publ.requested_category']
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.
['Addenda and Errata (Acta C, Acta E).', 'CIF-access paper - inorganic (Acta C) (no longer in use).', 'CIF-access paper - metal-organic (Acta C) (no longer in use).', 'CIF-access paper - organic (Acta C) (no longer in use).', 'Electronic submission - inorganic (Acta E).', 'Electronic submission - metal-organic (Acta E).', 'Electronic submission - organic (Acta E).', 'Full article.', 'Full submission - inorganic (Acta C).', 'Full submission - metal-organic (Acta C).', 'Full submission - organic (Acta C).', 'Research communications - inorganic compounds (Acta E).', 'Research communications - metal-organic compounds (Acta E).', 'Research communications - organic compounds (Acta E).', 'Data reports - inorganic compounds (Acta E).', 'Data reports - metal-organic compounds (Acta E).', 'Data reports - organic compounds (Acta E).', 'Inorganic compounds (Acta E).', 'Metal-organic compounds (Acta E).', 'Organic compounds (Acta E).', 'Short communication.']
['AD', 'CI', 'CM', 'CO', 'EI', 'EM', 'EO', 'FA', 'FI', 'FM', 'FO', 'GI', 'GM', 'GO', 'HI', 'HM', 'HO', 'QI', 'QM', 'QO', 'SC']
publ_requested
category
_publ_requested.coeditor_name
['_publ_requested_coeditor_name', '_publ.requested_coeditor_name']
The name of the coeditor whom the authors would like to process the submitted manuscript.
coeditor_name
_publ_requested.journal
['_publ_requested_journal', '_publ.requested_journal']
Name of the journal to which the manuscript is being submitted.
_publ_section.abstract
['_publ_section_abstract', '_publ.section_abstract']
The abstract of the submitted paper.
publ_section
_publ_section.acknowledgements
['_publ_section_acknowledgements', '_publ.section_acknowledgements']
The acknowledgements section of the submitted paper.
acknowledgements
_publ_section.comment
['_publ_section_comment', '_publ.section_comment']
The comment section of the submitted paper.
comment
_publ_section.discussion
['_publ_section_discussion', '_publ.section_discussion']
The discussion section of the submitted paper.
discussion
_publ_section.experimental
['_publ_section_experimental', '_publ.section_experimental']
The experimental section of the submitted paper.
experimental
_publ_section.exptl_prep
['_publ_section_exptl_prep', '_publ.section_exptl_prep']
The experimental preparation section of the submitted paper.
exptl_prep
_publ_section.exptl_refinement
['_publ_section_exptl_refinement', '_publ.section_exptl_refinement']
The experimental refinement section of the submitted paper.
exptl_refinement
_publ_section.exptl_solution
['_publ_section_exptl_solution', '_publ.section_exptl_solution']
The experimental solution section of the submitted paper.
exptl_solution
_publ_section.figure_captions
['_publ_section_figure_captions', '_publ.section_figure_captions']
The figure captions of the submitted paper.
figure_captions
_publ_section.introduction
['_publ_section_introduction', '_publ.section_introduction']
The introduction section of the submitted paper.
introduction
_publ_section.keywords
['_publ_section_keywords', '_publ.section_keywords']
The keywords of the submitted paper.
keywords
_publ_section.references
['_publ_section_references', '_publ.section_references']
The references section of the submitted paper.
references
_publ_section.related_literature
['_publ_section_related_literature', '_publ.section_related_literature']
The related literature section of the submitted paper.
related_literature
_publ_section.synopsis
['_publ_section_synopsis', '_publ.section_synopsis']
The synopsis of the submitted paper.
synopsis
_publ_section.table_legends
['_publ_section_table_legends', '_publ.section_table_legends']
The table legends of the submitted paper.
table_legends
_publ_section.title
['_publ_section_title', '_publ.section_title']
The full title of the submitted paper.
_publ_section.title_footnote
['_publ_section_title_footnote', '_publ.section_title_footnote']
Footnote (if any) to the title of the submitted paper.
title_footnote
_refine.special_details
['_refine_special_details', '_refine.details']
Details of the refinement not specified by other data items.
refine
_refine_diff.density_RMS
['_refine_diff_density_RMS', '_refine.diff_density_RMS']
Root mean square density value in a difference Fourier map. This 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.
# Default units. Applicable to x-ray, electron and gamma radiation. _units.code = "electrons_per_angstrom_cubed" If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres_per_angstrom_cubed"
refine_diff
density_RMS
_refine_diff.density_RMS_su
['_refine_diff_density_RMS_su', '_refine.diff_density_RMS_esd']
Standard uncertainty of the root mean square density value in a difference Fourier map.
density_RMS_su
_refine_diff.density_max
['_refine_diff_density_max', '_refine.diff_density_max']
Maximum density value in a difference Fourier map.
density_max
_refine_diff.density_max_su
['_refine_diff_density_max_su', '_refine.diff_density_max_esd']
Standard uncertainty of the maximum density value in a difference Fourier map.
density_max_su
_refine_diff.density_min
['_refine_diff_density_min', '_refine.diff_density_min']
Minimum density value in a difference Fourier map.
density_min
_refine_diff.density_min_su
['_refine_diff_density_min_su', '_refine.diff_density_min_esd']
Standard uncertainty of the minimum density value in a difference Fourier map.
density_min_su
_refine_ls.F_calc_details
_refine_ls_F_calc_details
Details concerning the evaluation of the structure factors using the expression given in _refine_ls.F_calc_formula.
['\n Gaussian integration using 16 points', '\n Bessel functions expansion up to 5th order. Estimated accuracy of\n Bessel function better than 0.001 electrons']
refine_ls
F_calc_details
_refine_ls.F_calc_formula
_refine_ls_F_calc_formula
Analytical expression used to calculate the structure factors.
F_calc_formula
_refine_ls.F_calc_precision
_refine_ls_F_calc_precision
Estimate of the precision resulting from the numerical approximations made during the evaluation of the structure factors using the expression _refine_ls.F_calc_formula following the method outlined in _refine_ls.F_calc_details.
F_calc_precision
_refine_ls.F_calc_precision_su
Standard uncertainty of _refine_ls.F_calc_precision.
F_calc_precision_su
_refine_ls.R_Fsqd_factor
['_refine_ls_R_Fsqd_factor', '_refine.ls_R_Fsqd_factor_obs']
Residual factor R(Fsqd), calculated on the squared amplitudes of the measured and calculated structure factors, for significantly intense reflections (satisfying _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. sum | F(meas_gt)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------------ sum F(meas_gt)^2^ F(meas_gt)^2^ = squares of the 'observed' structure-factor F(calc)^2^ = squares of the calculated structure-factor and the sum is taken over the specified reflections
R_Fsqd_factor
_refine_ls.R_I_factor
['_refine_ls_R_I_factor', '_refine.ls_R_I_factor_obs']
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 of powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(meas_gt) - I(calc) | R(I) = ----------------------------- sum | I(meas_gt) | I(meas_gt) = the net 'observed' intensities I(calc) = the net calculated intensities and the sum is taken over the specified reflections
R_I_factor
_refine_ls.R_factor_all
['_refine_ls_R_factor_all', '_refine.ls_R_factor_all']
Residual factor for all reflections satisfying the resolution limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is the conventional R factor. See also wR factor definitions. sum | F(meas) - F(calc) | R = ------------------------ sum | F(meas) | F(meas) = the measured structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections
sumFdiff = 0. sumFmeas = 0. Loop r as refln { sumFdiff += Abs(r.F_calc - r.F_meas) sumFmeas += Abs(r.F_meas) } _refine_ls.R_factor_all = sumFdiff / sumFmeas
R_factor_all
_refine_ls.R_factor_gt
['_refine_ls_R_factor_obs', '_refine_ls_R_factor_gt', '_refine.ls_R_factor_obs', '_refine.ls_R_factor_gt']
Residual factor for the reflections judged significantly intense (see _reflns.number_gt and _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is the conventional R factor. sum | F(meas_gt) - F(calc) | R = ----------------------------- sum | F(meas_gt) | F(meas_gt) = the 'observed' structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections
R_factor_gt
_refine_ls.abs_structure_Flack
['_refine_ls_abs_structure_Flack', '_refine.ls_abs_structure_Flack']
The measure of absolute structure as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data item 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.
abs_structure_Flack
_refine_ls.abs_structure_Flack_su
['_refine_ls_abs_structure_Flack_su', '_refine.ls_abs_structure_Flack_esd']
Standard uncertainty of the measure of absolute structure as defined by Flack (1983).
abs_structure_Flack_su
_refine_ls.abs_structure_Rogers
['_refine_ls_abs_structure_Rogers', '_refine.ls_abs_structure_Rogers']
The measure of absolute structure as defined by Rogers (1981). The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< η =< 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) =< η =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
abs_structure_Rogers
_refine_ls.abs_structure_Rogers_su
['_refine_ls_abs_structure_Rogers_su', '_refine.ls_abs_structure_Rogers_esd']
Standard uncertainty of the measure of absolute structure as defined by Rogers (1981).
abs_structure_Rogers_su
_refine_ls.abs_structure_details
['_refine_ls_abs_structure_details', '_refine.ls_abs_structure_details']
Details on the absolute structure and how it was determined.
abs_structure_details
_refine_ls.d_res_high
['_refine_ls_d_res_high', '_refine.ls_d_res_high']
Highest resolution for the reflections used in refinement. This corresponds to the smallest interplanar d value.
_refine_ls.d_res_low
['_refine_ls_d_res_low', '_refine.ls_d_res_low']
Lowest resolution for the reflections used in refinement. This corresponds to the largest interplanar d value.
_refine_ls.extinction_coef
['_refine_ls_extinction_coef', '_refine.ls_extinction_coef']
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. 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.
Zachariasen coefficient r* = 0.347(5)e+04.
extinction_coef
_refine_ls.extinction_coef_su
['_refine_ls_extinction_coef_su', '_refine.ls_extinction_coef_esd']
Standard uncertainty of the extinction coefficient.
extinction_coef_su
_refine_ls.extinction_expression
['_refine_ls_extinction_expression', '_refine.ls_extinction_expression']
Description of or reference to the extinction-correction equation used to apply the data item _refine_ls.extinction_coef. This information should be sufficient to reproduce the extinction-correction factors applied to the structure factors.
Larson approach
Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
extinction_expression
_refine_ls.extinction_method
['_refine_ls_extinction_method', '_refine.ls_extinction_method']
Description of the extinction correction method applied with the data item _refine_ls.extinction_coef. 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 are 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 the _refine_ls.extinction_coef and must be listed in _refine.special_details. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665.
['Zachariasen', 'B-C type 2 Gaussian isotropic']
extinction_method
_refine_ls.goodness_of_fit_all
['_refine_ls_goodness_of_fit_all', '_refine.ls_goodness_of_fit_all']
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. { sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ S = { ------------------------------------ } { Nref - Nparam } Y(meas) = the measured 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
goodness_of_fit_all
_refine_ls.goodness_of_fit_all_su
['_refine_ls_goodness_of_fit_all_su', '_refine.ls_goodness_of_fit_all_esd']
Standard uncertainty of the least-squares goodness-of-fit parameter S for all reflections after the final cycle of refinement.
goodness_of_fit_all_su
_refine_ls.goodness_of_fit_gt
['_refine_ls_goodness_of_fit_gt', '_refine_ls_goodness_of_fit_obs', '_refine.ls_goodness_of_fit_obs', '_refine.ls_goodness_of_fit_gt']
Least-squares goodness-of-fit parameter S for significantly intense reflections, (i.e. 'observed' reflections with values greater-than the threshold set in _reflns.threshold_expression), after the final cycle. Ideally, account should be taken of parameters restrained in the least-squares refinement. { sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^ S = { --------------------------------------- } { Nref - Nparam } Y(meas_gt) = 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
goodness_of_fit_gt
_refine_ls.goodness_of_fit_gt_su
['_refine_ls_goodness_of_fit_gt_su', '_refine.ls_goodness_of_fit_gt_esd', '_refine.ls_goodness_of_fit_obs_esd']
Standard uncertainty of the least-squares goodness-of-fit parameter S for gt reflections after the final cycle of refinement.
goodness_of_fit_gt_su
_refine_ls.goodness_of_fit_ref
['_refine_ls_goodness_of_fit_ref', '_refine.ls_goodness_of_fit_ref']
Least-squares goodness-of-fit parameter S for those reflections included in the final cycle of refinement. Account should be taken of restrained parameters. { sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ S = { ------------------------------------ } { Nref - Nparam } Y(meas) = the measured 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
goodness_of_fit_ref
_refine_ls.goodness_of_fit_ref_su
Standard uncertainty of _refine_ls.goodness_of_fit_ref.
goodness_of_fit_ref_su
_refine_ls.hydrogen_treatment
['_refine_ls_hydrogen_treatment', '_refine.ls_hydrogen_treatment']
Code identifying how hydrogen atoms were treated in the refinement.
['\n Refined all H-atom parameters.', '\n Refined H-atom coordinates only.', '\n Refined H-atom Us only.', '\n No refinement of H-atom parameters.', '\n H-atom parameters constrained.', '\n H-atom parameters constrained for H on C, all H-atom parameters\n refined for H on heteroatoms.', '\n H-atom parameters constrained for H on C, refined H-atom coordinates\n only for H on heteroatoms.', "\n H-atom parameters constrained for H on C, refined H-atom U's only for\n H on heteroatoms.", '\n H-atom parameters constrained for H on C, no refinement of H-atom\n parameters for H on heteroatoms.', '\n H-atom parameters constrained for H on C and some heteroatoms, all\n H-atom parameters refined for H on remaining heteroatoms.', '\n H-atom parameters constrained for H on C and some heteroatoms, refined\n H-atom coordinates only for H on remaining heteroatoms.', "\n H-atom parameters constrained for H on C and some heteroatoms, refined\n H-atom U's only for H on remaining heteroatoms.", '\n H-atom parameters constrained for H on C and some heteroatoms, no\n refinement of H-atom parameters for H on remaining heteroatoms.', '\n Some constrained, some independent.', '\n H-atom parameters not defined.']
['refall', 'refxyz', 'refU', 'noref', 'constr', 'hetero', 'heteroxyz', 'heteroU', 'heteronoref', 'hetero-mixed', 'heteroxyz-mixed', 'heteroU-mixed', 'heteronoref-mixed', 'mixed', 'undef']
hydrogen_treatment
_refine_ls.matrix_type
['_refine_ls_matrix_type', '_refine.ls_matrix_type']
Code identifying the matrix type used for least-squares derivatives.
['Full.', 'Full with fixed elements per cycle.', 'Block diagonal per atom.', 'User-defined blocks.', 'Diagonal elements only.', 'Selected elements only.']
['full', 'fullcycle', 'atomblock', 'userblock', 'diagonal', 'sparse']
matrix_type
_refine_ls.number_constraints
['_refine_ls_number_constraints', '_refine.ls_number_constraints']
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.
number_constraints
_refine_ls.number_parameters
['_refine_ls_number_parameters', '_refine.ls_number_parameters']
Number of parameters refined in the least-squares process. If possible this number should include 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.
number_parameters
_refine_ls.number_reflns
['_refine_ls_number_reflns', '_refine.ls_number_reflns_all']
Number of unique reflections used in the least-squares refinement.
number_reflns
_refine_ls.number_reflns_gt
['_refine_ls_number_reflns_gt', '_refine.ls_number_reflns_obs']
The number of reflections that satisfy the resolution limits established by _refine_ls.d_res_high and _refine_ls.d_res_low and the observation limit established by _reflns.observed_criterion.
number_reflns_gt
_refine_ls.number_restraints
['_refine_ls_number_restraints', '_refine.ls_number_restraints']
Number of restrained parameters in the least-squares refinement. These parameters do not directly dependent on another refined parameter. Often restrained parameters involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags_*. A description of refinement constraints may appear in _refine.special_details.
number_restraints
_refine_ls.restrained_S_all
['_refine_ls_restrained_S_all', '_refine.ls_restrained_S_all']
Least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least squares. This parameter explicitly includes the restraints applied in the least-squares process. See also _refine_ls.goodness_of_fit_all definition. {sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^ { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(meas) = the measured 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
restrained_S_all
_refine_ls.restrained_S_all_su
Standard uncertainty of _refine_ls.restrained_S_all.
restrained_S_all_su
_refine_ls.restrained_S_gt
['_refine_ls_restrained_S_obs', '_refine_ls_restrained_S_gt', '_refine.ls_restrained_S_obs']
Least-squares goodness-of-fit parameter S' for significantly intense reflections (satisfying _reflns.threshold_expression) after the final cycle of least squares. This parameter explicitly includes the restraints applied. The expression for S' is given in _refine_ls.restrained_S_all. {sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^ { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(meas_gt) = 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
restrained_S_gt
_refine_ls.restrained_S_gt_su
Standard uncertainty of _refine_ls.restrained_S_gt.
restrained_S_gt_su
_refine_ls.shift_over_su_max
['_refine_ls_shift_over_su_max', '_refine.ls_shift_over_esd_max', '_refine.ls_shift_over_su_max', '_refine_ls_shift/su_max', '_refine_ls_shift/esd_max']
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.).
shift_over_su_max
_refine_ls.shift_over_su_max_lt
['_refine_ls_shift/su_max_lt', '_refine.ls_shift_over_su_max_lt']
Upper limit for the largest ratio of the final l-s 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.
shift_over_su_max_lt
_refine_ls.shift_over_su_mean
['_refine_ls_shift_over_su_mean', '_refine.ls_shift_over_esd_mean', '_refine.ls_shift_over_su_mean', '_refine_ls_shift/su_mean', '_refine_ls_shift/esd_mean']
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.).
shift_over_su_mean
_refine_ls.shift_over_su_mean_lt
['_refine_ls_shift/su_mean_lt', '_refine.ls_shift_over_su_mean_lt']
Upper limit for the average ratio of the final l-s 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.
shift_over_su_mean_lt
_refine_ls.structure_factor_coef
['_refine_ls_structure_factor_coef', '_refine.ls_structure_factor_coef']
Structure-factor coefficient used in the least-squares process.
['Structure factor magnitude.', 'Structure factor squared.', 'Net intensity.']
['F', 'Fsqd', 'Inet']
structure_factor_coef
_refine_ls.wR_factor_all
['_refine_ls_wR_factor_all', '_refine.ls_wR_factor_all']
Weighted residual factors for all reflections satisfying the resolution limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. See also the _refine_ls.R_factor_all definition. ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(meas)^2^ ) Y(meas) = the measured amplitude _refine_ls.structure_factor_coef Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections
wR_factor_all
_refine_ls.wR_factor_gt
['_refine_ls_wR_factor_obs', '_refine.ls_wR_factor_obs', '_refine_ls_wR_factor_gt']
Weighted residual factors for significantly intense reflections (satisfying _reflns.threshold_expression) included in the refinement. The reflections must also satisfy the resolution limits established by _refine_ls.d_res_high and _refine_ls.d_res_low. ( sum w [ Y(meas_gt) - Y(calc) ]^2^ )^1/2^ wR = ( ---------------------------------- ) ( sum w Y(meas_gt)^2^ ) Y(meas_gt) = the 'observed' amplitude _refine_ls.structure_factor_coef Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections
wR_factor_gt
_refine_ls.wR_factor_ref
_refine_ls_wR_factor_ref
Weighted residual factors for reflections included in the refinement which satisfy the limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low. ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(meas)^2^ ) Y(meas) = the measured amplitude _refine_ls.structure_factor_coef Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections
wR_factor_ref
_refine_ls.weighting_details
['_refine_ls_weighting_details', '_refine.ls_weighting_details']
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'.
Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(θ)/λ - 1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement.
weighting_details
_refine_ls.weighting_scheme
['_refine_ls_weighting_scheme', '_refine.ls_weighting_scheme']
General description of the weighting scheme used in the least-squares. An enumerated code should be contained in this description.
["Based on measured s.u.'s.", 'Unit or no weights applied.', 'Calculated weights applied.']
['sigma', 'unit', 'calc']
weighting_scheme
_refine_ls_class.R_Fsqd_factor
_refine_ls_class_R_Fsqd_factor
Residual factor R(F^2^) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in refinement. See _refine_ls.R_Fsqd_factor for details.
refine_ls_class
_refine_ls_class.R_I_factor
_refine_ls_class_R_I_factor
Residual factor R(I) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in refinement. See _refine_ls.R_I_factor for details.
_refine_ls_class.R_factor_all
_refine_ls_class_R_factor_all
Residual factor for reflections in this class included in the refinement. See _refine_ls.R_factor_all definition for details.
_refine_ls_class.R_factor_gt
['_refine_ls_class_R_factor_gt', '_refine_ls_class_R_factor_obs']
Residual factor for the reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in refinement. See _refine_ls.R_factor_gt for details.
_refine_ls_class.code
_refine_ls_class_code
Code identifying a certain reflection class.
_reflns_class.code
_refine_ls_class.d_res_high
_refine_ls_class_d_res_high
Highest resolution for the reflections in this class. This corresponds to the smallest interplanar d value.
_refine_ls_class.d_res_low
_refine_ls_class_d_res_low
Lowest resolution for the reflections in this class. This corresponds to the largest interplanar d value.
_refine_ls_class.wR_factor_all
_refine_ls_class_wR_factor_all
Weight residual for all reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in refinement. See _refine_ls.wR_factor_all for details.
_refln.A_calc
_refln_A_calc
The calculated real structure-factor component A =|Fcalc|cos(phase)
['\n If (_diffrn_radiation.probe == "neutron") _units.code =\n "femtometres" Else If (_diffrn_radiation.probe == "electron")\n _units.code = "volts" Else\n _units.code = "electrons"', '\n _refln.A_calc = Real ( _refln.F_complex )']
['Definition', 'Evaluation']
refln
A_calc
_refln.A_calc_su
Standard uncertainty of _refln.A_calc.
A_calc_su
_refln.A_meas
_refln_A_meas
The measured real structure-factor component A =|Fmeas|cos(phase)
A_meas
_refln.A_meas_su
Standard uncertainty of _refln.A_meas.
A_meas_su
_refln.B_calc
_refln_B_calc
The calculated imaginary structure-factor component B =|Fcalc|sin(phase)
['\n If (_diffrn_radiation.probe == "neutron") _units.code =\n "femtometres" Else If (_diffrn_radiation.probe == "electron")\n _units.code = "volts" Else\n _units.code = "electrons"', '\n _refln.B_calc = Imag ( _refln.F_complex )']
B_calc
_refln.B_calc_su
Standard uncertainty of _refln.B_calc.
B_calc_su
_refln.B_meas
_refln_B_meas
The measured imaginary structure-factor component B =|Fmeas|sin(phase)
B_meas
_refln.B_meas_su
Standard uncertainty of _refln.B_meas.
B_meas_su
_refln.F_calc
_refln_F_calc
The structure factor amplitude for the reflection calculated from the atom site data.
['\n If (_diffrn_radiation.probe == "neutron") _units.code =\n "femtometres" Else If (_diffrn_radiation.probe == "electron")\n _units.code = "volts" Else\n _units.code = "electrons"', '\n _refln.F_calc = Magn ( _refln.F_complex )']
F_calc
_refln.F_calc_su
Standard uncertainty of _refln.F_calc.
F_calc_su
_refln.F_complex
_refln_F_complex
The structure factor vector for the reflection calculated from the atom site data.
['\n If (_diffrn_radiation.probe == "neutron") _units.code =\n "femtometres" Else If (_diffrn_radiation.probe == "electron")\n _units.code = "volts" Else\n _units.code = "electrons"', '\n With r as refln\n\n fc = Complex (0., 0.)\n h = r.hkl\n\n Loop a as atom_site {\n\n f = a.site_symmetry_multiplicity * a.occupancy * (\n r.form_factor_table [a.type_symbol] +\n _atom_type_scat[a.type_symbol].dispersion )\n\n Loop s as space_group_symop {\n\n t = Exp(-h * s.R * a.matrix_beta * s.RT * h)\n\n fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T)))\n } }\n _refln.F_complex = fc / _space_group.multiplicity']
F_complex
_refln.F_complex_su
Standard uncertainty of _refln.F_complex.
F_complex_su
_refln.F_meas
_refln_F_meas
The structure factor amplitude for the reflection derived from the measured intensities.
F_meas
_refln.F_meas_su
['_refln_F_sigma', '_refln.F_meas_sigma', '_refln_F_meas_su']
Standard uncertainty of the measured structure factor amplitude.
F_meas_su
_refln.F_squared_calc
_refln_F_squared_calc
The structure factor amplitude squared for the reflection calculated from the atom site data.
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometre_squared" Else If (_diffrn_radiation.probe == "electron") _units.code = "volt_squared" Else _units.code = "electron_squared"
F_squared_calc
_refln.F_squared_calc_su
Standard uncertainty of _refln.F_squared_calc.
F_squared_calc_su
_refln.F_squared_meas
_refln_F_squared_meas
F_squared_meas
_refln.F_squared_meas_su
['_refln_F_squared_sigma', '_refln.F_squared_sigma', '_refln_F_squared_meas_su']
Standard uncertainty of the measured structure factor squared.
F_squared_meas_su
_refln.Lp_factor
_refln_Lp_factor
The Lorentz-polarization factor appropriate for the instrument used to measure the diffraction intensity. This is applied to convert the net intensity into the measured F squared.
Lp_factor
_refln.class_code
_refln_class_code
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.
_refln.d_spacing
_refln_d_spacing
The distance in angstroms between lattice planes in the crystal with the indices _refln.hkl for this reflection.
_refln.d_spacing = 1 / (2 * _refln.sin_theta_over_lambda)
d_spacing
_refln.fom
The figure of merit m for this reflection. int P~α~ exp(i*α) dα m = -------------------- int P~α~ dα P~α~ = the probability that the phase angle α is correct int is taken over the range α = 0 to 2 π.
fom
_refln.form_factor_table
Atomic scattering factor table for the scattering angle of this diffraction vector and atom types in structure.
['\n _units.code = "none"\n\n If (_diffrn_radiation.probe == "neutron")\n _units.code = "femtometres"', "\n With r as refln\n\n table = Table ()\n s = r.sin_theta_over_lambda\n\n Loop t as atom_type {\n\n If (_diffrn_radiation.probe == 'neutron') {\n\n f = t.length_neutron\n\n } Else If (s < 2.0 ) {\n\n c = t.Cromer_Mann_coeffs\n\n f = (c[0] + c[1] * Exp (-c[2] * s*s)\n + c[3] * Exp (-c[4] * s*s)\n + c[5] * Exp (-c[6] * s*s)\n + c[7] * Exp (-c[8] * s*s))\n } Else {\n\n c = t.hi_ang_Fox_coeffs\n\n f = Exp ( c[0] + c[1]*s + c[2]*s*s + c[3]*s*s*s )\n }\n\n table [ t.symbol ] = f\n\n }\n _refln.form_factor_table = table"]
form_factor_table
Table
_refln.hkl
The Miller indices as a reciprocal space vector.
With r as refln _refln.hkl = [r.index_h, r.index_k, r.index_l]
_refln.include_status
['_refln_include_status', '_refln_observed_status', '_refln.observed_status', '_refln.status']
Code indicating how the reflection was included in the refinement and R-factor calculations.
['ob : within _reflns.threshold_expression; within d-res limits.', 'lt : without _reflns.threshold_expression; within d-res limits.', 'sa : systematically absent reflection due to symmetry.', 'du : deemed unreliable measurement -- not used.', 'hd : above _refine_ls.d_res_high.', 'ld : below _refine_ls.d_res_low.']
include_status
_refln.index_h
_refln_index_h
_refln.index_k
_refln_index_k
_refln.index_l
_refln_index_l
_refln.intensity_calc
_refln_intensity_calc
The intensity of the reflection calculated from the atom site data.
_refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor
intensity_calc
_refln.intensity_calc_su
Standard uncertainty of _refln.intensity_calc.
intensity_calc_su
_refln.intensity_meas
_refln_intensity_meas
The intensity of the reflection derived from the diffraction measurements.
intensity_meas
_refln.intensity_meas_su
['_refln_intensity_meas_su', '_refln.intensity_sigma', '_refln_intensity_sigma']
Standard uncertainty of the measured intensity.
intensity_meas_su
_refln.mean_path_length_tbar
_refln_mean_path_length_tbar
Mean path length through the crystal for this diffraction vector.
mean_path_length_tbar
_refln.phase_calc
_refln_phase_calc
The phase of the calculated structure-factor.
phase = Atan2d ( _refln.B_calc, _refln.A_calc ) If(phase < 0.) _refln.phase_calc = phase + 360. Else _refln.phase_calc = phase
phase_calc
_refln.phase_calc_su
Standard uncertainty of _refln.phase_calc.
phase_calc_su
_refln.phase_meas
_refln_phase_meas
The phase of the measured structure-factor. This may be derived from the atom site data if available or from the phase solution process prior to determination of the structure.
phase_meas
_refln.phase_meas_su
Standard uncertainty of _refln.phase_meas.
phase_meas_su
_refln.refinement_status
_refln_refinement_status
Status code of reflection in the structure refinement process.
['Included in ls process.', 'Excluded from ls process.', 'Excluded due to extinction.']
['incl', 'excl', 'extn']
refinement_status
_refln.scale_group_code
_refln_scale_group_code
Code identifying the scale (if there is more than one scale) used convert the measured structure factor to a common absolute value.
_reflns_scale.group_code
_refln.sin_theta_over_lambda
['_refln_sint/lambda', '_refln_sin_theta_over_lambda', '_refln.sint_over_lambda']
The sin(θ)/λ value for this reflection.
With r as refln h = r.hkl G = _cell.reciprocal_metric_tensor r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2.
_refln.symmetry_epsilon
_refln_symmetry_epsilon
The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations.
symmetry_epsilon
_refln.symmetry_multiplicity
_refln_symmetry_multiplicity
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 (1987), section 10.2.
symmetry_multiplicity
_refln.wavelength
_refln_wavelength
The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method.
_refln.wavelength_id
_refln_wavelength_id
Code identifying the wavelength in DIFFRN_RADIATION_WAVELENGTH list.
_reflns.Friedel_coverage
_reflns_Friedel_coverage
The proportion of Friedel related reflections present in the number of the '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. (a) For centrosymmetric structures its value 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, the value will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are non-zero, they are when l=0. (d) For a crystal in the 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 zero value for _reflns.Friedel_coverage.
reflns
Friedel_coverage
_reflns.Friedel_fraction_full
_reflns_Friedel_fraction_full
The ratio of Friedel pairs measured to _diffrn_reflns.theta_full to the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns.Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be given as not-applicable '.'
Friedel_fraction_full
_reflns.Friedel_fraction_max
_reflns_Friedel_fraction_max
The ratio of Friedel pairs measured to _diffrn_reflns.theta_max to the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns.Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be given as not-applicable '.'
Friedel_fraction_max
_reflns.apply_dispersion_to_Fcalc
Yes or No flag on whether the anomalous dispersion scattering components will be applied in the F complex calculation. See _refln.F_complex
['Apply dispersion.', 'Abbreviation for "yes".', 'Do not apply dispersion.', 'Abbreviation for "no".']
apply_dispersion_to_Fcalc
_reflns.d_resolution_high
_reflns_d_resolution_high
Highest resolution for the final REFLN data set. This corresponds to the smallest interplanar d value.
d_resolution_high
_reflns.d_resolution_low
_reflns_d_resolution_low
Lowest resolution for the final REFLN data set. This corresponds to the largest interplanar d value.
d_resolution_low
_reflns.limit_h_max
_reflns_limit_h_max
_reflns.limit_h_min
_reflns_limit_h_min
_reflns.limit_k_max
_reflns_limit_k_max
_reflns.limit_k_min
_reflns_limit_k_min
_reflns.limit_l_max
_reflns_limit_l_max
_reflns.limit_l_min
_reflns_limit_l_min
_reflns.limit_max
Maximum Miller indices of refined diffraction reflections.
With t as reflns _reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max]
_reflns.limit_min
Minimum Miller indices of refined diffraction reflections.
With t as reflns _reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min]
_reflns.number_gt
['_reflns_number_gt', '_reflns_number_observed', '_reflns_number_obs', '_reflns.number_obs']
Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which are significantly intense (see _reflns.threshold_expression). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending on the nature of the structure and the procedures used.
number_gt
_reflns.number_total
['_reflns_number_total', '_reflns_number_all', '_reflns.number_all']
Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending on the nature of the structure and the procedures used.
number_total
_reflns.special_details
['_reflns_special_details', '_reflns.details']
Description of the properties of the REFLN reflection list that is not given in other data items. Should include details about the averaging of symmetry-equivalent reflections including Friedel pairs.
_reflns.threshold_expression
['_reflns_threshold_expression', '_reflns_observed_criterion', '_reflns.observed_criterion']
Description of the criterion used to classify a reflection as having a "significant intensity". This criterion is usually expressed in terms of a u(I) or u(F) threshold. "u" is the standard uncertainty.
I>2u(I)
threshold_expression
_reflns_class.R_Fsqd_factor
_reflns_class_R_Fsqd_factor
Residual factor R(F^2^) for reflections in this class judged significantly intense (i.e. greater than required by the _reflns.threshold_expression) and included in the refinement. sum | F(meas_gt)^2^ - F(calc)^2^ | R(Fsqd gt) = ------------------------------------ sum F(meas_gt)^2^ F(meas_gt)^2^ = square of the 'observed' structure-factor F(calc )^2^ = square of the calculated structure-factor and the sum is taken over the specified reflections
reflns_class
_reflns_class.R_I_factor
_reflns_class_R_I_factor
Residual factor R(I) for reflections in this class judged significantly intense (i.e. greater than required by the _reflns.threshold_expression) and included in the refinement. sum | I(meas_gt) - I(calc) | R(I gt) = ---------------------------- sum | I(meas_gt) | I(meas_gt) = the net 'observed' intensity I(calc ) = the net calculated intensity and the sum is taken over the specified reflections
_reflns_class.R_factor_all
_reflns_class_R_factor_all
Residual factor for reflections in this class used in refinement. sum | F(meas) - F(calc) | R(F all) = ------------------------ sum | F(meas) | F(meas) = the measured structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections
_reflns_class.R_factor_gt
['_reflns_class_R_factor_gt', '_reflns_class_R_factor_observed']
Residual factor for the reflections in this class judged significantly intense (i.e. greater than required by the _reflns.threshold_expression) and included in the refinement. sum | F(meas_gt) - F(calc) | R(F gt) = -------------------------------- sum | F(meas_gt) | F(meas) = the measured structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections
_reflns_class_code
_reflns_class.d_res_high
_reflns_class_d_res_high
_reflns_class.d_res_low
_reflns_class_d_res_low
_reflns_class.description
_reflns_class_description
H0L0 common projection reflections
_reflns_class.number_gt
['_reflns_class_number_observed', '_reflns_class_number_gt']
Count of reflections in this REFLN class (not the DIFFRN_REFLN set) which are significantly intense (see _reflns.threshold_expression). It may include Friedel equivalent reflections (i.e. those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending on the nature of the structure and the procedures used.
_reflns_class.number_total
_reflns_class_number_total
Count of reflections in this REFLN class (not the DIFFRN_REFLN set). It may include Friedel equivalent reflections (those which are equivalent under the Laue symmetry but inequivalent under the crystal class), depending on the nature of the structure and the procedures used.
_reflns_class.wR_factor_all
_reflns_class_wR_factor_all
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(meas) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------- ) ( sum w Y(meas)^2^ ) Y(meas) = the measured 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.
_reflns_scale_group_code
Code identifying a reflection scale group. These names need not correspond to _diffrn_scale_group.code names.
reflns_scale
group_code
_reflns_scale.meas_F
_reflns_scale_meas_F
Structure factor scale for this scale group.
meas_F
_reflns_scale.meas_F_squared
_reflns_scale_meas_F_squared
Structure factor squared scale for this scale group.
meas_F_squared
_reflns_scale.meas_F_squared_su
Standard uncertainty of _reflns_scale.meas_F_squared.
meas_F_squared_su
_reflns_scale.meas_F_su
Standard uncertainty of _reflns_scale.meas_F.
meas_F_su
_reflns_scale.meas_intensity
_reflns_scale_meas_intensity
Net intensity scale for this scale group.
meas_intensity
_reflns_scale.meas_intensity_su
Standard uncertainty of _reflns_scale.meas_intensity.
meas_intensity_su
_reflns_shell.Rmerge_F_all
_reflns_shell_Rmerge_F_all
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.
reflns_shell
Rmerge_F_all
_reflns_shell.Rmerge_F_gt
['_reflns_shell_Rmerge_F_obs', '_reflns_shell.Rmerge_F_obs', '_reflns_shell_Rmerge_F_gt']
Rmerge(F) for reflections in a shell which are significantly intense (see _reflns.threshold_expression). The residual merge expression is shown in the _reflns_shell.Rmerge_F_all definition.
Rmerge_F_gt
_reflns_shell.Rmerge_I_all
_reflns_shell_Rmerge_I_all
Rmerge(I) for all reflections in a given shell. sum~i~ ( sum~j~ | I~j~ - | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ ) I~j~ = the intensity of the jth observation of reflection 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.
Rmerge_I_all
_reflns_shell.Rmerge_I_gt
['_reflns_shell_Rmerge_I_obs', '_reflns_shell.Rmerge_I_obs', '_reflns_shell_Rmerge_I_gt']
Rmerge(I) for reflections in a shell which are significantly intense (see _reflns.threshold_expression). The residual merge expression is shown in the _reflns_shell.Rmerge_I_all definition.
Rmerge_I_gt
_reflns_shell.d_res_high
_reflns_shell_d_res_high
Highest resolution for the reflections in this shell. This corresponds to the smallest interplanar d value.
_reflns_shell.d_res_limits
Resolution for the reflections in this shell stored as the list of lowest and highest values. This is the category key.
With s as reflns_shell _reflns_shell.d_res_limits = [ s.d_res_low, s.d_res_high ]
d_res_limits
_reflns_shell.d_res_low
_reflns_shell_d_res_low
Lowest resolution for the reflections in this shell. This corresponds to the largest interplanar d value.
_reflns_shell.meanI_over_suI_all
['_reflns_shell_meanI_over_uI_all', '_reflns_shell_meanI_over_sigI_all', '_reflns_shell.meanI_over_sigI_all', '_reflns_shell.meanI_over_uI_all']
Ratio of the mean intensity in a shell to the mean standard uncertainty of the intensities in the shell.
meanI_over_suI_all
_reflns_shell.meanI_over_suI_gt
['_reflns_shell_meanI_over_sigI_obs', '_reflns_shell.meanI_over_sigI_obs', '_reflns_shell.meanI_over_sigI_gt', '_reflns_shell_meanI_over_sigI_gt', '_reflns_shell.meanI_over_uI_gt', '_reflns_shell_meanI_over_uI_gt']
Ratio of the mean intensity of significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean standard uncertainty of the intensities in the shell.
meanI_over_suI_gt
_reflns_shell.number_measured_all
_reflns_shell_number_measured_all
Total count of reflections measured for this resolution shell.
number_measured_all
_reflns_shell.number_measured_gt
['_reflns_shell_number_measured_obs', '_reflns_shell.number_measured_obs', '_reflns_shell_number_measured_gt']
Number of reflections measured for this resolution shell which are significantly intense (see _reflns.threshold_expression).
number_measured_gt
_reflns_shell.number_possible
['_reflns_shell_number_possible', '_reflns_shell.number_possible_all']
Count of symmetry-unique reflections possible in this reflection shell.
number_possible
_reflns_shell.number_unique_all
_reflns_shell_number_unique_all
Count of symmetry-unique reflections present in this reflection shell.
number_unique_all
_reflns_shell.number_unique_gt
['_reflns_shell_number_unique_gt', '_reflns_shell_number_unique_obs', '_reflns_shell.number_unique_obs']
Number of symmetry-unique reflections present in this reflection shell which are significantly intense (see _reflns.threshold_expression).
number_unique_gt
_reflns_shell.percent_possible_all
_reflns_shell_percent_possible_all
Percentage of reflections present in this shell over that possible.
percent_possible_all
_reflns_shell.percent_possible_gt
['_reflns_shell_percent_possible_gt', '_reflns_shell_percent_possible_obs', '_reflns_shell.percent_possible_obs']
Percentage of reflections present in this shell which are significantly intense (see _reflns.threshold_expression), over that possible.
percent_possible_gt
_space_group.Bravais_type
The symbol denoting the lattice type (Bravais type) to which the translational subgroup (vector lattice) of the space group belongs. It consists of a lower-case letter indicating the crystal system followed by an upper-case letter indicating the lattice centring. The setting-independent symbol mS replaces the setting-dependent symbols mB and mC, and the setting-independent symbol oS replaces the setting-dependent symbols oA, oB and oC. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed., p. 15. Dordrecht: Kluwer Academic Publishers.
Triclinic (anorthic) primitive lattice.
['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'hR', 'cP', 'cI', 'cF']
space_group
Bravais_type
_space_group.IT_coordinate_system_code
A qualifier taken from the enumeration list identifying which setting in International Tables for Crystallography Volume A (2002) (IT) is used. See IT Table 4.3.2.1, Section 2.2.16, Table 2.2.16.1, Section 2.2.16.1 and Fig. 2.2.6.4. This item is not computer-interpretable and cannot be used to define the coordinate system. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
['monoclinic unique axis b, cell choice 1, abc', 'monoclinic unique axis b, cell choice 2, abc', 'monoclinic unique axis b, cell choice 3, abc', 'monoclinic unique axis b, cell choice 1, c-ba', 'monoclinic unique axis b, cell choice 2, c-ba', 'monoclinic unique axis b, cell choice 3, c-ba', 'monoclinic unique axis c, cell choice 1, abc', 'monoclinic unique axis c, cell choice 2, abc', 'monoclinic unique axis c, cell choice 3, abc', 'monoclinic unique axis c, cell choice 1, ba-c', 'monoclinic unique axis c, cell choice 2, ba-c', 'monoclinic unique axis c, cell choice 3, ba-c', 'monoclinic unique axis a, cell choice 1, abc', 'monoclinic unique axis a, cell choice 2, abc', 'monoclinic unique axis a, cell choice 3, abc', 'monoclinic unique axis a, cell choice 1, -acb', 'monoclinic unique axis a, cell choice 2, -acb', 'monoclinic unique axis a, cell choice 3, -acb', 'orthorhombic', 'orthorhombic', 'orthorhombic', 'orthorhombic', 'orthorhombic', 'orthorhombic', 'orthorhombic origin choice 1', 'orthorhombic origin choice 1', 'orthorhombic origin choice 1', 'orthorhombic origin choice 1', 'orthorhombic origin choice 1', 'orthorhombic origin choice 1', 'orthorhombic origin choice 2', 'orthorhombic origin choice 2', 'orthorhombic origin choice 2', 'orthorhombic origin choice 2', 'orthorhombic origin choice 2', 'orthorhombic origin choice 2', 'tetragonal or cubic origin choice 1', 'tetragonal or cubic origin choice 2', 'trigonal using hexagonal axes', 'trigonal using rhombohedral axes']
['b1', 'b2', 'b3', '-b1', '-b2', '-b3', 'c1', 'c2', 'c3', '-c1', '-c2', '-c3', 'a1', 'a2', 'a3', '-a1', '-a2', '-a3', 'abc', 'ba-c', 'cab', '-cba', 'bca', 'a-cb', '1abc', '1ba-c', '1cab', '1-cba', '1bca', '1a-cb', '2abc', '2ba-c', '2cab', '2-cba', '2bca', '2a-cb', '1', '2', 'h', 'r']
IT_coordinate_system_code
_space_group.IT_number
['_space_group_IT_number', '_symmetry.Int_Tables_number', '_symmetry_Int_Tables_number']
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 expressed.
IT_number
_space_group.Laue_class
The Hermann-Mauguin symbol of the geometric crystal class of the point group of the space group where a centre of inversion is added if not already present.
Laue_class
_space_group.Patterson_name_H-M
The Hermann-Mauguin symbol of the type of that centrosymmetric symmorphic space group to which the Patterson function belongs; see Table 2.2.5.1 in International Tables for Crystallography Volume A (2002). A space separates each symbol referring to different axes. Underscores may replace the spaces, but this use is discouraged. Subscripts should appear without special symbols. Bars should be given as negative signs before the number to which they apply. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed., Table 2.2.5.1. Dordrecht: Kluwer Academic Publishers.
['P -1', 'P 2/m', 'C 2/m', 'P m m m', 'C m m m', 'I m m m', 'F m m m', 'P 4/m', 'I 4/m', 'P 4/m m m', 'I 4/m m m', 'P -3', 'R -3', 'P -3 m 1', 'R -3 m', 'P -3 1 m', 'P 6/m', 'P 6/m m m', 'P m -3', 'I m -3', 'F m -3', 'P m -3 m', 'I m -3 m', 'F m -3 m']
Patterson_name_H_M
_space_group.centring_type
Symbol for the lattice centring. This symbol may be dependent on the coordinate system chosen.
['Primitive no centring', 'A-face centred (0,1/2,1/2)', 'B-face centred (1/2,0,1/2)', 'C-face centred (1/2,1/2,0)', 'All faces centred (0,1/2,1/2), (1/2,0,1/2), (1/2,1/2,0)', 'Body centred (1/2,1/2,1/2)', 'Rhombohedral obverse centred (2/3,1/3,1/3), (1/3,2/3,2/3)', 'Rhombohedral reverse centred (1/3,2/3,1/3), (2/3,1/3,2/3)', 'Hexagonal centred (2/3,1/3,0), (1/3,2/3,0)']
['P', 'A', 'B', 'C', 'F', 'I', 'R', 'Rrev', 'H']
centring_type
_space_group.crystal_system
_space_group_crystal_system
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.
['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'trigonal', 'hexagonal', 'cubic']
crystal_system
_space_group.multiplicity
Number of unique symmetry elements in the space group.
n = 0 Loop s as space_group_symop n += 1 _space_group.multiplicity = n
_space_group.name_H-M_alt
_space_group_name_H-M_alt
_space_group.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 _space_group.IT_number. 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 _space_group.name_Hall or list the symmetry operations.
['P 1 21/m 1', 'P 2/n 2/n 2/n (origin at -1)', 'R -3 2/m']
['Space group No. 10.', 'Space group No. 48 origin 2.', 'Space group No. 166 rhomb.']
name_H_M_alt
_space_group.name_H-M_alt_description
A free-text description of the code appearing in _space_group.name_H-M_alt.
name_H_M_alt_description
_space_group.name_H-M_full
['_symmetry.space_group_name_H-M', '_symmetry_space_group_name_H-M']
The full international Hermann-Mauguin space-group symbol as defined in Section 2.2.3 and given as the second item of the second line of each of the space-group tables of Part 7 of International Tables for Crystallography Volume A (2002). Each component of the space-group name is separated by a space or an underscore character. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. 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 or _space_group.name_Schoenflies. The full international Hermann-Mauguin symbol contains information about the choice of basis for monoclinic and orthorhombic space groups, but does not give information about the choice of origin. To define the setting uniquely use _space_group.name_Hall, or list the symmetry operations or generators. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
P 21/n 21/m 21/a
Full symbol for Pnma.
name_H_M_full
_space_group.name_H-M_ref
The short international Hermann-Mauguin space-group symbol as defined in Section 2.2.3 and given as the first item of each space-group table in Part 7 of International Tables for Crystallography Volume A (2002). Each component of the space-group name is separated by a space character. Subscripts appear without special symbols. Bars are given as negative signs before the numbers to which they apply. The short international Hermann-Mauguin symbol determines the space-group type uniquely. However, the space-group type is better described using _space_group.IT_number or _space_group.name_Schoenflies. The short international Hermann-Mauguin symbol contains no information on the choice of basis or origin. To define the setting uniquely use _space_group.name_Hall, or list the symmetry operations or generators. _space_group.name_H-M_alt may be used to give the Hermann-Mauguin symbol corresponding to the setting used. In the enumeration list, each possible value is identified by space-group number and Schoenflies symbol. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
['P 1', 'P -1', 'P 2', 'P 21', 'C 2', 'P m', 'P c', 'C m', 'C c', 'P 2/m', 'P 21/m', 'C 2/m', 'P 2/c', 'P 21/c', 'C 2/c', 'P 2 2 2', 'P 2 2 21', 'P 21 21 2', 'P 21 21 21', 'C 2 2 21', 'C 2 2 2', 'F 2 2 2', 'I 2 2 2', 'I 21 21 21', 'P m m 2', 'P m c 21', 'P c c 2', 'P m a 2', 'P c a 21', 'P n c 2', 'P m n 21', 'P b a 2', 'P n a 21', 'P n n 2', 'C m m 2', 'C m c 21', 'C c c 2', 'A m m 2', 'A e m 2', 'A m a 2', 'A e a 2', 'F m m 2', 'F d d 2', 'I m m 2', 'I b a 2', 'I m a 2', 'P m m m', 'P n n n', 'P c c m', 'P b a n', 'P m m a', 'P n n a', 'P m n a', 'P c c a', 'P b a m', 'P c c n', 'P b c m', 'P n n m', 'P m m n', 'P b c n', 'P b c a', 'P n m a', 'C m c m', 'C m c e', 'C m m m', 'C c c m', 'C m m e', 'C c c e', 'F m m m', 'F d d d', 'I m m m', 'I b a m', 'I b c a', 'I m m a', 'P 4', 'P 41', 'P 42', 'P 43', 'I 4', 'I 41', 'P -4', 'I -4', 'P 4/m', 'P 42/m', 'P 4/n', 'P 42/n', 'I 4/m', 'I 41/a', 'P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2', 'I 4 2 2', 'I 41 2 2', 'P 4 m m', 'P 4 b m', 'P 42 c m', 'P 42 n m', 'P 4 c c', 'P 4 n c', 'P 42 m c', 'P 42 b c', 'I 4 m m', 'I 4 c m', 'I 41 m d', 'I 41 c d', 'P -4 2 m', 'P -4 2 c', 'P -4 21 m', 'P -4 21 c', 'P -4 m 2', 'P -4 c 2', 'P -4 b 2', 'P -4 n 2', 'I -4 m 2', 'I -4 c 2', 'I -4 2 m', 'I -4 2 d', 'P 4/m m m', 'P 4/m c c', 'P 4/n b m', 'P 4/n n c', 'P 4/m b m', 'P 4/m n c', 'P 4/n m m', 'P 4/n c c', 'P 42/m m c', 'P 42/m c m', 'P 42/n b c', 'P 42/n n m', 'P 42/m b c', 'P 42/m n m', 'P 42/n m c', 'P 42/n c m', 'I 4/m m m', 'I 4/m c m', 'I 41/a m d', 'I 41/a c d', 'P 3', 'P 31', 'P 32', 'R 3', 'P -3', 'R -3', 'P 3 1 2', 'P 3 2 1', 'P 31 1 2', 'P 31 2 1', 'P 32 1 2', 'P 32 2 1', 'R 3 2', 'P 3 m 1', 'P 3 1 m', 'P 3 c 1', 'P 3 1 c', 'R 3 m', 'R 3 c', 'P -3 1 m', 'P -3 1 c', 'P -3 m 1', 'P -3 c 1', 'R -3 m', 'R -3 c', 'P 6', 'P 61', 'P 65', 'P 62', 'P 64', 'P 63', 'P -6', 'P 6/m ', 'P 63/m', 'P 6 2 2', 'P 61 2 2', 'P 65 2 2', 'P 62 2 2', 'P 64 2 2', 'P 63 2 2', 'P 6 m m', 'P 6 c c', 'P 63 c m', 'P 63 m c', 'P -6 m 2', 'P -6 c 2', 'P -6 2 m', 'P -6 2 c', 'P 6/m m m', 'P 6/m c c', 'P 63/m c m', 'P 63/m m c', 'P 2 3', 'F 2 3', 'I 2 3', 'P 21 3', 'I 21 3', 'P m -3', 'P n -3', 'F m -3', 'F d -3', 'I m -3', 'P a -3', 'I a -3', 'P 4 3 2', 'P 42 3 2', 'F 4 3 2', 'F 41 3 2', 'I 4 3 2', 'P 43 3 2', 'P 41 3 2', 'I 41 3 2', 'P -4 3 m', 'F -4 3 m', 'I -4 3 m', 'P -4 3 n', 'F -4 3 c', 'I -4 3 d', 'P m -3 m', 'P n -3 n', 'P m -3 n', 'P n -3 m', 'F m -3 m', 'F m -3 c', 'F d -3 m', 'F d -3 c', 'I m -3 m', 'I a -3 d']
name_H_M_ref
_space_group.name_Hall
['_space_group_name_Hall', '_symmetry_space_group_name_Hall', '_symmetry.space_group_name_Hall']
Space group symbol defined by Hall. Each component of the space group name is separated by a space or an underscore. The use of space is strongly recommended because it specifies the coordinate system. The underscore in the name is only retained because it was used in earlier archived files. It should not be used in new CIFs. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525 [See also International Tables for Crystallography, Vol. B (1993) 1.4 Appendix B]
name_Hall
_space_group.name_Schoenflies
The Schoenflies symbol as listed in International Tables for Crystallography Volume A denoting the proper affine class (i.e. orientation-preserving affine class) of space groups (space-group type) to which the space group belongs. This symbol defines the space-group type independently of the coordinate system in which the space group is expressed. The symbol is given with a period, '.', separating the Schoenflies point group and the superscript. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
C2h.5
Schoenflies symbol for space group No. 14.
name_Schoenflies
_space_group.point_group_H-M
The Hermann-Mauguin symbol denoting the geometric crystal class of space groups to which the space group belongs, and the geometric crystal class of point groups to which the point group of the space group belongs.
point_group_H_M
_space_group_Wyckoff.coords_xyz
Coordinates of one site of a Wyckoff position expressed in terms of its fractional coordinates (x,y,z) in the unit cell. To generate the coordinates of all sites of this Wyckoff position, it is necessary to multiply these coordinates by the symmetry operations stored in _space_group_symop.operation_xyz.
Coordinates of Wyckoff site with 2.. symmetry.
space_group_Wyckoff
coords_xyz
_space_group_Wyckoff.id
An arbitrary code that is unique to a particular Wyckoff position.
_space_group_Wyckoff.letter
The Wyckoff letter associated with this position, as given in International Tables for Crystallography Volume A. The enumeration values '\a' and α are equivalent, and correspond to the Greek letter 'alpha' used in International Tables. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
letter
_space_group_Wyckoff.multiplicity
The multiplicity of this Wyckoff position as given in International Tables Volume A. It is the number of equivalent sites per conventional unit cell. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
_space_group_Wyckoff.site_symmetry
The subgroup of the space group that leaves the point fixed. It is isomorphic to a subgroup of the point group of the space group. The site-symmetry symbol indicates the symmetry in the symmetry direction determined by the Hermann-Mauguin symbol of the space group (see International Tables for Crystallography Volume A, Section 2.2.12). Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
['\n Position 2b in space group No. 94, P 42 21 2.', '\n Position 6b in space group No. 222, P n -3 n.', '\n Site symmetry for the Wyckoff position 96f in space group\n No. 228, F d -3 c. The site-symmetry group is isomorphic to\n the point group 2 with the twofold axis along one of the {100}\n directions.']
site_symmetry
_space_group_generator.key
Arbitrary identifier for each entry in the _space_group_generator.xyz list.
space_group_generator
_space_group_generator.xyz
A parsable string giving one of the symmetry generators of the space group in algebraic form. If W is a matrix representation of the rotational part of the generator 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 X' = WX + w. (Note: X is used to represent the bold italic x in International Tables for Crystallography Volume A, Section 5.) When a list of symmetry generators is given, it is assumed that the complete list of symmetry operations of the space group (including the identity operation) can be generated through repeated multiplication of the generators, that is, (W3, w3) is an operation of the space group if (W2,w2) and (W1,w1) [where (W1,w1) is applied first] are either operations or generators and: W3 = W2 x W1 w3 = W2 x w1 + w2. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
C glide reflection through the plane (x,1/4,z) chosen as one of the generators of the space group.
xyz
_space_group_symop.R
A matrix containing the symmetry rotation operations of a space group | r11 r12 r13 | R = | r21 r22 r23 | | r31 r32 r33 |
sm = _space_group_symop.Seitz_matrix _space_group_symop.R = [[sm[0,0],sm[0,1],sm[0,2]], [sm[1,0],sm[1,1],sm[1,2]], [sm[2,0],sm[2,1],sm[2,2]]]
space_group_symop
_space_group_symop.RT
The TRANSPOSE of the symmetry rotation matrix representing the point group operations of the space group | r11 r21 r31 | RT = | r12 r22 r32 | | r13 r23 r33 |
_space_group_symop.RT = Transpose (_space_group_symop.R)
_space_group_symop.Seitz_matrix
A matrix containing the symmetry operations of a space group in 4x4 Seitz format. | r11 r12 r13 t1 | | R T | | r21 r22 r23 t2 | | 0 1 | | r31 r32 r33 t3 | | 0 0 0 1 |
_space_group_symop.Seitz_matrix = SeitzFromJones (_space_group_symop.operation_xyz)
Seitz_matrix
_space_group_symop.T
A vector containing the symmetry translation operations of a space group.
sm = _space_group_symop.Seitz_matrix _space_group_symop.T = [sm[0,3],sm[1,3],sm[2,3]]
_space_group_symop.id
['_space_group_symop_id', '_symmetry_equiv.pos_site_id', '_symmetry_equiv_pos_site_id']
Index identifying each entry in the _space_group_symop.operation_xyz list. It is normally the sequence number of the entry in that list, and should be identified with the code 'n' in the geometry symmetry codes of the form 'n_pqr'. The identity operation (i.e. _space_group_symop.operation_xyz set to 'x,y,z') should be set to 1.
_space_group_symop.id = Current_row(space_group_symop.id) + 1
_space_group_symop.operation_description
An optional text description of a particular symmetry operation of the space group.
operation_description
_space_group_symop.operation_xyz
['_space_group_symop_operation_xyz', '_symmetry_equiv.pos_as_xyz', '_symmetry_equiv_pos_as_xyz']
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.
Glide reflection through the plane (x,1/4,z) with glide vector (1/2)c.
operation_xyz
_symmetry.cell_setting
_symmetry_cell_setting
This data item should not be used and is DEPRECATED as it is ambiguous. The original definition is as follows: The cell settings for this space-group symmetry.
['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'rhombohedral', 'trigonal', 'hexagonal', 'cubic']
deprecated_setting
_valence_param.B
_valence_param_B
The bond valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of bond length R.
valence_param
_valence_param.Ro
_valence_param_Ro
The bond valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of bond length R.
_valence_param.atom_1
_valence_param_atom_1
Atom type symbol for atom 1 forming a bond whose valence parameters are given in this category.
_valence_param.atom_1_valence
_valence_param_atom_1_valence
The formal charge of the atom 1 whose bond valence parameters are given in this category.
atom_1_valence
_valence_param.atom_2
_valence_param_atom_2
Atom type symbol for atom 2 forming a bond whose valence parameters are given in this category.
_valence_param.atom_2_valence
_valence_param_atom_2_valence
The formal charge of the atom 2 whose bond valence parameters are given in this category.
atom_2_valence
_valence_param.details
_valence_param_details
Details of valence parameters of stated bond.
_valence_param.id
_valence_param_id
Unique index loop number of the valence parameter loop.
_valence_param.ref_id
_valence_param_ref_id
Code linking parameters to the key _valence_ref.id key in the reference list in category VALENCE_REF.
_valence_ref.id
ref_id
_valence_ref_id
Unique loop code of the valence references.
valence_ref
_valence_ref.reference
_valence_ref_reference
Literature reference from which the valence parameters identified by _valence_param.id were taken.
reference
prefLabel
CORE_DIC
The CIF_CORE dictionary records all the CORE data items defined and used within the Crystallographic Information Framework (CIF).
Instance
CifCore
['\n Merged in most symmetry dictionary definitions (James Hester)', '\n Adjusted and removed keys for changes in dREL operation.\n _citation_id added to key list of citation_author (James Hester).\n _diffrn.crystal_id removed as diffrn is Set category. Changed\n EXPTL_CRYSTAL to Set type in keeping with current use patterns.\n Removed all child keys of exptl_crystal_id.', '\n Added and deprecated symmetry.cell_setting. Removed rhombohedral\n option from dREL method for space_group.crystal_system. (James Hester)', '\n Added missing items from DDL1 version: _citation.doi, _audit.block_doi\n _citation.publisher, _database.dataset_doi,\n _publ_contact_author.id_orcid, _publ_author.id_orcid (James Hester)', '\n Rewrote CITATION category description to cover all relevant uses rather\n than only publication-related uses (James Hester).', '\n Added DATABASE_RELATED category (James Hester).', "\n Removed the _chemical_conn_bond.distance_su data item.\n Changed the purpose of the diffrn_radiation_wavelength.value data item\n from 'Number' to 'Measurand'. Added the\n diffrn_radiation_wavelength.value_su data item.\n\n Replaced all instances of the _definition.replaced_by data item with\n data items from the DEFINITION_REPLACED category.\n\n Marked the _atom_site.refinement_flags data item as deprecated and\n replaced by the _atom_site.refinement_flags_posn,\n _atom_site.refinement_flags_adp and _atom_site.refinement_flags_occupancy\n data items.\n\n Changed the _type.purpose from 'Encode' to 'Link' in the definitions of\n the _geom_angle.atom_site_label_2, _valence_param_atom_1,\n _valence_param_atom_2, _valence_param_ref_id, _atom_site_aniso.label\n and _atom_type_scat.symbol data items. Removed the _name.linked_item_id\n data item from the definitions of the _diffrn_scale_group.code and\n diffrn_standard_refln.code data items.\n\n Updated the definitions of the _geom_hbond.angle_DHA and\n _geom_hbond.angle_DHA_su data items.\n\n Corrected the definitions of the _cell_measurement.temperature_su and\n _cell_measurement.pressure_su data items.\n\n Corrected a typo in the definitions of the _geom_contact.distance and\n _geom_torsion.angle and data items.\n\n Changed the content type of multiple data items from 'Index' or 'Count'\n to 'Integer' and assigned the appropriate enumeration range if needed.", '\n Adjusted the ranges of _geom_bond.angle and _geom_hbond.angle_DHA to\n be 0:180 degrees.\n\n Changed dREL methods for Cartesian transformation matrix elements\n to calculate default values rather than required values.', '\n Changed all synthetic identifiers (\'id\') to be Text, and removed dREL.\n Validation method for _space_group.crystal_system removed as it contained\n undefined dREL functions "throw" and "alert".', '\n Added opaque author identifiers to AUDIT_AUTHOR and PUBL_AUTHOR as well\n as relevant linking identifiers to AUDIT_CONTACT_AUTHOR and\n PUBL_CONTACT_AUTHOR.\n\n Added _diffrn_measurement.specimen_attachment_type.\n\n Changed to DDL version 4.\n\n Removed all instances of the _category.key_id attribute since it is no\n longer defined in the DDLm reference dictionary.\n\n Miscellaneous corrections to dREL and fixing typos.', '\n Replaced _model_site.adp_eigen_system with _model_site.adp_eigenvectors\n and _model_site.adp_eigenvalues.\n\n Added additional enumeration values to the _journal_index.type data item\n definition.\n\n Numerous corrections to measurement units.\n\n Numerous improvements to types and harmonisation of spelling.', "\n Added data names to allow multi-data-block expression of data sets.\n\n Deprecated and replaced _diffrn_radiation.type and\n _diffrn_radiation.xray_symbol.\n\n Added _diffrn_refln.intensity* data items.\n\n Added the _exptl_absorpt.special_details data item.\n\n Added categories and data names to allow for the elemental composition\n of specimens to be recorded.\n\n Corrections and additions for conformance with DDL1.\n\n Explicitly added _diffrn_source.details to the list items that replaced\n _diffrn_source.description.\n\n Added the _citation.URL and _journal.paper_URL data items.\n\n Added the _journal.paper_number and _journal.paper_pages data items.\n\n Reparented CELL to DIFFRN category and added key data names to allow\n multiple cells for different diffraction conditions. Deprecated\n _cell_measurement.temperature,pressure data names.\n\n Changed the purpose of the _diffrn_radiation_wavelength.id data item\n from 'Encode' to 'Key'.", "\n # Please update the date above and describe the change below until\n # ready for the next release\n\n Added _atom_type_scat.exponential_polynomial_coefs, Gaussian_coefs, and\n inv_Mott_Bethe_coefs to allow for an arbitrary number of coefficients in\n the definition of form factors.\n\n Added a dREL definition method for the _citation.id data item.\n\n Rewrote the _atom_type.radius_contact evaluation method as a definition\n method.\n\n Added _atom_type.mass_number to record specific isotope identities.\n\n Changed enumeration of _atom_type.atomic_number,\n _atom_type_scat.dispersion_real_Cu, _atom_type_scat.dispersion_imag_Cu,\n _atom_type_scat.dispersion_real_Mo, _atom_type_scat.dispersion_imag_Mo\n to be defaulted on _atom_type.element_symbol.\n\n Expanded AUDIT_AUTHOR to include email, phone, and fax contact details.\n\n Corrected the content type of the _refln.F_complex_su attribute.\n\n Updated description of _space_group_wyckoff.letter.\n\n Added a dREL definition method that determines the units of measure to\n the definition of the _refln.form_factor_table data item. Changed the\n units of several data items to 'unspecified'.\n\n Added the default value of '1_555' to the site symmetry data items.\n\n Redefined _exptl_absorpt.coefficient_mu as a derived measurand item.\n\n Added the _exptl_absorpt.coefficient_mu_su data item.\n\n Renamed _atom_site.tensor_beta to _atom_site_aniso.matrix_beta and\n updated the associated dREL evaluation methods. The old data name was\n retained as an alias. Added the _atom_site_aniso.beta_* data items.\n\n Reverted _atom_type_scat.versus_stol_list to a text-type to regain\n compatibility with DDL1 dictionary.\n\n Added ATOM_SCAT_VERSUS_STOL to allow for the explicit listing of\n scattering factor values with respect to sin theta over lambda.\n Deprecated the _atom_type_scat.versus_stol_list data item.\n\n Changed the _type.source attribute of all SU data items to 'Related'.\n\n Updated dREL evaluation method of the ATOM_TYPE category.\n\n Changed the purpose of _space_group_Wyckoff.id and _valence_ref.id\n from 'Encode' to 'Key'.\n\n Corrected examples of the _chemical.identifier_InChI and\n _chemical.identifier_InChI_key data items.\n\n Updated description of DIFFRN_RADIATION to remove looping reference."]
DISPLAY
Set
Category
The CATEGORY of data items used to enumerate the display parameters used in the discipline.
PUBLICATION
AUDIT_LINK
Loop
The CATEGORY of data items used to record details about the relationships between data blocks in the current CIF.
AUDIT
DIFFRN_ORIENT
The CATEGORY of data items which specify the orientation of the crystal axes to the diffractometer goniometer.
DIFFRN
SPACE_GROUP_GENERATOR
The CATEGORY of data items used to list generators for the space group
SPACE_GROUP
STRUCTURE
The DICTIONARY group encompassing the CORE STRUCTURE data items defined and used within the Crystallographic Information Framework (CIF).
CIF_CORE
VALENCE
The CATEGORY of items used to specify bond valence parameters used to calculate bond valences from bond lengths.
MODEL
VALENCE_REF
The CATEGORY of items for listing valence references.
AUDIT_AUTHOR_ROLE
['_audit_author_role.id', '_audit_author_role.role']
The CATEGORY of data items used to describe the role that authors took in the production of the dataset.
AUDIT_CONFORM
The CATEGORY of data items used describe dictionary versions by which data names in the current data block are conformant.
CITATION_AUTHOR
['_citation_author.citation_id', '_citation_author.ordinal']
Category of items describing citation author(s) details.
CITATION_EDITOR
['_citation_editor.citation_id', '_citation_editor.ordinal']
Category of items describing citation editor(s) details.
DIFFRACTION
The DICTIONARY group encompassing the CORE DIFFRACTION data items defined and used within the Crystallographic Information Framework (CIF).
DIFFRN_ATTENUATOR
The CATEGORY of data items which specify the attenuators used in the diffraction source.
DIFFRN_SCALE_GROUP
The CATEGORY of data items which specify the groups of reflections in the raw measured diffraction data with different relative scales.
EXPTL_CRYSTAL_APPEARANCE
The CATEGORY of ENUMERATION items used to specify information about the crystal colour and appearance.
EXPTL_CRYSTAL
Items in the MODEL Category specify data for the crystal structure postulated and modelled from the atomic coordinates derived and refined from the diffraction information. The structural model is described principally in terms of the geometry of the 'connected' atom sites and the crystal symmetry in which they reside.
PUBL_MANUSCRIPT_INCL_EXTRA
Category of data items that allow the authors of a manuscript to submit for publication data names that should be added to the standard request list employed by journal printing software. Although these fields are primarily intended to identify CIF data items that the author wishes to include in a published paper, they can also be used to identify data names created so that non-CIF items can be included in the publication. Note that *.item names MUST be enclosed in single quotes.
PUBL_MANUSCRIPT
PUBL_REQUESTED
CATEGORY of data items that enable the author to make specific requests to the journal office for processing.
PUBL
REFINE
The CATEGORY of data items used to specify information about the refinement of the structural model.
ATOM_ANALYTICAL_SOURCE
The CATEGORY of data items used to describe the source of elemental composition information used in crystallographic structure studies.
loop_ _atom_analytical_source.id _atom_analytical_source.technique _atom_analytical_source.equipment_make a XRF 'Hitachi Lab-X5000' b 'X-ray fluorescence EDS' 'Hitachi Lab-X5000' c ICP . d EDS .
Four different measurements of elemental composition are enumerated.
ATOM
ATOM_SCAT_VERSUS_STOL
['_atom_scat_versus_stol.atom_type', '_atom_scat_versus_stol.stol_value']
The CATEGORY of data items used to list atomic scattering factor values for use in crystallographic structure studies.
loop_ _atom_scat_versus_stol.atom_type _atom_scat_versus_stol.stol_value _atom_scat_versus_stol.scat_value Ac 0.00 89.00000 Ac 0.01 88.91457 Ac 0.02 88.66288 #... Ac 4.00 8.24987 Ac 5.00 5.98858 Ac 6.00 4.90623 O 0.00 8.00000 O 0.01 7.99171 O 0.02 7.96693 #... O 4.00 0.13431 O 5.00 0.06740 O 6.00 0.03670
A listing of the scattering factors for Ac and O in the range (0, 6.00) reciprocal angstroms.
JOURNAL_INDEX
Category of items describing publication indices.
JOURNAL
Category of items describing the publication manuscript.
CHEMICAL_CONN_BOND
['_chemical_conn_bond.atom_1', '_chemical_conn_bond.atom_2']
The CATEGORY of data items which specify the connections between the atoms sites in the chemical_conn_atom list and the nature of the chemical bond between these atoms. These are 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.
CHEMICAL
DATABASE
The CATEGORY of data items recording database deposition.
DATABASE_RELATED
A category of items recording entries in databases that describe the same or related data. Databases wishing to insert their own canonical codes when archiving and delivering data blocks should use items from the DATABASE category.
loop_ _database_related.id _database_related.database_id _database_related.entry_code _database_related.relation _database_related.special_details 1 CAS 58-55-9 Other 'Describes the same compound.' 2 COD 2006182 Identical . 3 CSD BAPLOT01 Identical .
The loop relates a specific instance of a theophylline crystal structure to corresponding entries in the COD and CSD crystallographic databases as well as to the general description of the theophyline compound in the CAS registry. This example loop could potentially be added to the CIF file that is provided as supplementary material for the following publication: Ebisuzaki, Y. et al. (1997). Acta Crystallographica, Section C: Crystal Structure Communications, 53(6), 777-779. https://doi.org/10.1107/S0108270197001960
DIFFRN_DETECTOR
The CATEGORY of data items which specify the detectors used in the measurement of diffraction intensities.
DIFFRN_STANDARD_REFLN
['_diffrn_standard_refln.index_h', '_diffrn_standard_refln.index_k', '_diffrn_standard_refln.index_l']
The CATEGORY of data items which specify the "standard" reflections measured repeatedly to monitor variations in intensity due to source flux, environment conditions or crystal quality.
DIFFRN_STANDARDS
DISPLAY_COLOUR
The CATEGORY of data items used to enumerate the display colour codes used in the discipline.
PUBL_BODY
Data items in the PUBL_BODY category permit labelling of different text sections within the body of a submitted paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.
SPACE_GROUP_WYCKOFF
Contains information about Wyckoff positions of a space group. Only one site can be given for each special position, but the remainder can be generated by applying the symmetry operations stored in _space_group_symop.operation_xyz.
ATOM_SITES
The CATEGORY of data items used to describe information which applies to all atom sites in a crystal structure.
AUDIT_CONTACT_AUTHOR
The CATEGORY of data items used for contact author(s) details.
AUDIT_SUPPORT
Data items in the AUDIT_SUPPORT category record details about the funding support for the data collected and analysed in the data set.
loop_ _audit_support.id _audit_support.funding_organization _audit_support.funding_organization_doi _audit_support.award_type _audit_support.award_number _audit_support.award_recipient 1 'Engineering and Physical Sciences Research Council' 'https://doi.org/10.13039/501100000266' studentship 'EP-M506515-1' 'E. T. Broadhurst' 2 'Swedish Funding Council' ? grant '2017-05333' 'M. Lightowler' 3 'Wellcome Trust' 'https://doi.org/10.13039/100004440' grant 'WT087658' 'University of Edinburgh EM facility' 4 'Scottish Universities Life Sciences Alliance (SULSA)' ? other ? 'University of Edinburgh EM facility' 5 'Harvard Medical School' 'https://doi.org/10.13039/100006691' ? ? ?
Example prepared from funding data published in https://doi.org/10.1107/S2052252519016105.
CELL_MEASUREMENT_REFLN
['_cell_measurement_refln.index_h', '_cell_measurement_refln.index_k', '_cell_measurement_refln.index_l']
The CATEGORY of data items used to describe the reflection data used in the measurement of the crystal unit cell.
CELL_MEASUREMENT
Head
The CIF_CORE group contains the definitions of data items that are common to all domains of crystallographic studies.
REFINE_DIFF
The CATEGORY of data items which specify the scattering density limits in a difference Fourier map after the structure has been refined. The RMS value is with respect to the arithmetic mean density, and is derived from summations over each grid point in the asymmetric unit of the cell.
The CATEGORY of data items used to describe atomic information used in crystallographic structure studies.
ATOM_ANALYTICAL_MASS_LOSS
The CATEGORY of data items used to describe information pertaining to mass loss during specimen preparation for the purposes of determining elemental composition information for use in crystallographic structure studies.
loop_ _atom_analytical_mass_loss.id _atom_analytical_mass_loss.meas_id _atom_analytical_mass_loss.percent _atom_analytical_mass_loss.temperature LOD1 a 2 328 LOI1 a 5 623 LOI2 a 10 1023 LOI3 a 15 1373 LOI4 b 5 673 LOI5 b 10 1123
Four mass-loss percentages are given for measurement 'a', and two for measurement 'b'. The mass losses were recorded after exposing the specimen to the listed temperatures. The mass lost at a lower temperature for the same measurement should be included in the higher temperatures; that is, for measurement 'a', the total mass loss after four measurements is 15 wt%, not (2+5+10+15) wt%.
AUDIT_AUTHOR
The CATEGORY of data items used for author(s) details.
CHEMICAL_CONN_ATOM
The CATEGORY of data items which describe the 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. In particular, 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 as to describe a complete chemical entity.
COMPUTING
The CATEGORY of data items used to record details of the computer programs used in the crystal structure analysis.
DIFFRN_MEASUREMENT
The CATEGORY of data items which specify the details of the diffraction measurement.
DIFFRN_REFLNS_CLASS
The CATEGORY of data items which specify different classes of reflections in the raw measured diffraction data.
DIFFRN_REFLNS
EXPTL_ABSORPT
The CATEGORY of data items used to specify the experimental details of the absorption measurements and corrections to the diffraction data.
EXPTL
FUNCTION
Functions
The crystallographic functions the invoked in the definition methods of CORE STRUCTURE data items defined and used within the Crystallographic Information Framework (CIF).
JOURNAL_COEDITOR
Category of items recording coeditor details.
JOURNAL_TECHEDITOR
Category of items recording details of the technical editor processing this publication.
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 textual content of other submissions. Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.
REFLNS_SCALE
The CATEGORY of data items which specify the scales needed to place measured structure factor coefficients on the same absolute scale.
REFLNS
SPACE_GROUP_SYMOP
The CATEGORY of data items used to describe symmetry equivalent sites in the crystal unit cell.
ATOM_ANALYTICAL
The CATEGORY of data items used to describe elemental composition information used in crystallographic structure studies.
loop_ _atom_analytical.id _atom_analytical.analyte _atom_analytical.meas_id _atom_analytical.chemical_species _atom_analytical.analyte_mass_percent _atom_analytical.chemical_species_mass_percent 1 Si a 'Si O2' ? 22.7 2 Al a 'Al2 O3' ? 27.4 3 Ti b 'Ti O2' ? 2.7 4 Si c . 10.5 . 5 Si d Si 11.7 11.7
There are three separate determinations of Si content, and one each of Al and Ti. The amount of Al is reported as the mass percent of Al2O3. The equivalent amount of Al is not given. There are four different measurements presented in this table.
CHEMICAL_FORMULA
The CATEGORY of data items which 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 parentheses. 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 or not carbon is present. 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. _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
DIFFRN_RADIATION_WAVELENGTH
The CATEGORY of data items which specify the wavelength of the radiation used in measuring diffraction intensities. Items may be looped to identify and assign weights to distinct wavelength components from a polychromatic beam.
DIFFRN_RADIATION
The CATEGORY of data items which specify information about the standard reflections used in the diffraction measurement process.
GEOM_CONTACT
['_geom_contact.atom_site_label_1', '_geom_contact.atom_site_label_2', '_geom_contact.site_symmetry_1', '_geom_contact.site_symmetry_2']
The CATEGORY of data items used to specify the interatomic contact distances in the structural model.
Loop m1 as model_site { rb = m1.radius_bond + _geom.bond_distance_incr rc = m1.radius_contact + _geom.contact_distance_incr Loop m2 as model_site { If (m2.symop != '1_555') Next radb = rb + m2.radius_bond radc = rc + m2.radius_contact label = m2.label Loop s as space_group_symop :ns { axyz = s.R * m2.fract_xyz + s.T Do i = -2,2 { Do j = -2,2 { Do k = -2,2 { # cell translations tran = List ([i,j,k]) bxyz = axyz + tran cxyz = _atom_sites_Cartn_transform.matrix * bxyz d = Norm (cxyz - m1.Cartn_xyz) If (d < radb or d > radc) Next geom_contact( .atom_site_label_1 = m1.label, .site_symmetry_1 = m1.symop, .atom_site_label_2 = label, .site_symmetry_2 = Symop(ns+1,tran), .distance = d ) } } } } } }
GEOM
PUBL_CONTACT_AUTHOR
Category of items describing contact author(s) details.
REFINE_LS_CLASS
REFINE_LS
PUBL_AUTHOR
Category of data items recording the author information.
VALENCE_PARAM
The CATEGORY of items for listing bond valences.
The CATEGORY of data items which specify the wavelength of the radiation used in measuring diffraction intensities. To identify and assign weights to distinct wavelength components from a polychromatic beam, see DIFFRN_RADIATION_WAVELENGTH.
DIFFRN_REFLNS_TRANSF_MATRIX
The CATEGORY of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. |11 12 13| (h k l) diffraction |21 22 23| = (h' k' l') |31 32 33|
The CATEGORY of data items used to specify the geometry of the structural model as derived from the atomic sites. The geometry is expressed in terms of the interatomic angles (GEOM_ANGLE data), covalent bond distances (GEOM_BOND data), contact distances (GEOM_CONTACT data), hydrogen bonds (GEOM_HBOND data) and torsion geometry (GEOM_TORSION 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.
JOURNAL_DATE
Category of items recording dates of publication processing.
The DICTIONARY group encompassing the CORE PUBLICATION data items defined and used within the Crystallographic Information Framework (CIF).
DATABASE_CODE
The CATEGORY of data items recording database deposition. These data items are assigned by database managers and should only appear in a CIF if they originate from that source.
DIFFRN_ORIENT_MATRIX
The CATEGORY of data items which specify the matrix specifying the orientation of the crystal axes to the diffractometer goniometer.
GEOM_BOND
['_geom_bond.atom_site_label_1', '_geom_bond.atom_site_label_2', '_geom_bond.site_symmetry_1', '_geom_bond.site_symmetry_2']
The CATEGORY of data items used to specify the geometry bonds in the structural model as derived from the atomic sites.
dmin = _geom.bond_distance_min Loop m1 as model_site :i { rad = m1.radius_bond + _geom.bond_distance_incr Loop m2 as model_site :j { If (i==j or m1.mole_index != m2.mole_index) Next d = Norm (m1.Cartn_xyz - m2.Cartn_xyz) If (d<dmin or d>(rad+m2.radius_bond)) Next geom_bond( .atom_site_label_1 = m1.label, .atom_site_label_2 = m2.label, .site_symmetry_1 = m1.symop, .site_symmetry_2 = m2.symop, .distance = d ) } }
REFLNS_CLASS
The CATEGORY of data items which specify the properties of reflections in specific classes of reflections.
The CATEGORY of data items used to record details about the creation and subsequent updating of the data block.
The CATEGORY of data items used to describe the measurement of the cell parameters.
CELL
DIFFRN_SOURCE
The CATEGORY of data items which specify information about the radiation source.
The CATEGORY of data items used to specify the experimental work prior to diffraction measurements. These include crystallization crystal measurements and absorption-correction techniques used.
GEOM_ANGLE
['_geom_angle.atom_site_label_1', '_geom_angle.atom_site_label_2', '_geom_angle.atom_site_label_3', '_geom_angle.site_symmetry_1', '_geom_angle.site_symmetry_2', '_geom_angle.site_symmetry_3']
The CATEGORY of data items used to specify the geometry angles in the structural model as derived from the atomic sites.
dmin = _geom.bond_distance_min Loop m1 as model_site :i { # loop vertex model site rad1 = m1.radius_bond + _geom.bond_distance_incr Loop m2 as model_site :j { # loop first target site If (i==j or m1.mole_index != m2.mole_index) Next v1 = m2.Cartn_xyz - m1.Cartn_xyz d1 = Norm (v1) If (d1<dmin or d1>(rad1+m2.radius_bond)) Next rad2 = m2.radius_bond + _geom.bond_distance_incr Loop m3 as model_site :k>j { # loop second target site If (i==k or m1.mole_index != m3.mole_index) Next v2 = m3.Cartn_xyz - m1.Cartn_xyz d2 = Norm (v2) If (d2<dmin or d2>(rad2+m3.radius_bond)) Next angle = Acosd ( v1*v2 / (d1*d2) ) geom_angle( .atom_site_label_1 = m2.label, .atom_site_label_2 = m1.label, .atom_site_label_3 = m3.label, .site_symmetry_1 = m2.symop, .site_symmetry_2 = m1.symop, .site_symmetry_3 = m3.symop, .distances = List ( d1, d2 ), .value = angle ) } } }
EXPTL_CRYSTAL_FACE
['_exptl_crystal_face.index_h', '_exptl_crystal_face.index_k', '_exptl_crystal_face.index_l']
The CATEGORY of data items which specify the dimensions of the crystal used in the diffraction measurements.
GEOM_TORSION
['_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.site_symmetry_1', '_geom_torsion.site_symmetry_2', '_geom_torsion.site_symmetry_3', '_geom_torsion.site_symmetry_4']
The CATEGORY of data items used to specify the torsion angles in the structural model as derived from the atomic sites.
dmin = _geom.bond_distance_min Loop m1 as model_site :i { rad1 = m1.radius_bond + _geom.bond_distance_incr Loop m2 as model_site :j { If (i==j or m2.mole_index!=m1.mole_index) Next v21 = m1.Cartn_xyz - m2.Cartn_xyz d21 = Norm (v21) If (d21 < dmin or d21 > (rad1+m2.radius_bond)) Next rad2 = m2.radius_bond + _geom.bond_distance_incr Loop m3 as model_site :k { If (k==i or k==j or m3.mole_index!=m2.mole_index) Next v23 = m3.Cartn_xyz - m2.Cartn_xyz d23 = Norm (v23) If (d23 < dmin or d23 > (rad2+m3.radius_bond)) Next rad3 = m3.radius_bond + _geom.bond_distance_incr Loop m4 as model_site :l { If (l==k or l==j or l==i or m4.mole_index!=m3.mole_index) Next v34 = m4.Cartn_xyz - m3.Cartn_xyz d34 = Norm (v34) If (d34 < dmin or d34 > (rad3+m4.radius_bond)) Next u1 = v21 ^ v23 u2 = v34 ^ v23 angle = Acosd ( u1 * u2 / ( Norm(u1) * Norm(u2) ) ) If ( (u1^u2)*v23 < 0 ) angle = -angle geom_torsion( .atom_site_label_1 = m1.label, .atom_site_label_2 = m2.label, .atom_site_label_3 = m3.label, .atom_site_label_4 = m4.label, .site_symmetry_1 = m1.symop, .site_symmetry_2 = m2.symop, .site_symmetry_3 = m3.symop, .site_symmetry_4 = m4.symop, .distances = List ( d21,d23,d34 ), .angle = angle ) } } } }
ATOM_TYPE
The CATEGORY of data items used to describe atomic type information used in crystallographic structure studies.
typelist = List() Loop a as atom_site { type = a.type_symbol If( type not in typelist ) typelist ++= type } For type in typelist { atom_type(.symbol = type, .number_in_cell = '?' ) }
DIFFRN_ORIENT_REFLN
['_diffrn_orient_refln.index_h', '_diffrn_orient_refln.index_k', '_diffrn_orient_refln.index_l']
The CATEGORY of data items which specify the reflections used to calculate the matrix which gives the orientation of the crystal axes to the diffractometer goniometer.
GEOM_HBOND
['_geom_hbond.atom_site_label_D', '_geom_hbond.atom_site_label_H', '_geom_hbond.atom_site_label_A', '_geom_hbond.site_symmetry_D', '_geom_hbond.site_symmetry_H', '_geom_hbond.site_symmetry_A']
The CATEGORY of data items used to specify the hydrogen bond distances in the structural model as derived from atomic sites.
REFLNS_SHELL
['_reflns_shell.d_res_low', '_reflns_shell.d_res_high']
The CATEGORY of data items which specify the information about reflections divided into shells bounded by d resolution limits.
PUBL_SECTION
Manuscript section data if submitted in parts. See also _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.
MODEL_SITE
['_model_site.label', '_model_site.symop']
The CATEGORY of data items used to describe atomic sites and connections in the proposed atomic model.
atomlist = List() Loop a as atom_site { axyz = a.fract_xyz cxyz = _atom_sites_Cartn_transform.matrix * axyz radb = _atom_type[a.type_symbol].radius_bond radc = _atom_type[a.type_symbol].radius_contact ls = List ( a.label, "1_555" ) atomlist ++= [ls, axyz, cxyz, radb, radc, 0] } molelist = List() dmin = _geom.bond_distance_min m = 0 n = 0 For [ls1,a1,c1,rb1,rc1,m1] in atomlist { If (m1 != 0) Next m += 1 n += 1 molelist ++= [ls1,a1,c1,rb1,rc1,n,m] atomlist --= [ls1,a1,c1,rb1,rc1,m] Repeat { connect = "no" For [ls2,a2,c2,rb2,rc2,n2,m2] in molelist { If (m2 != m) Next For [ls3,a3,c3,rb3,rc3,m3] in atomlist { dmax = rb2 + rb3 + _geom.bond_distance_incr Loop s as space_group_symop :ns { axyz = s.R * a3 + s.T tran = Closest (axyz, a2) bxyz = axyz + tran cxyz = _atom_sites_Cartn_transform.matrix *bxyz d = Norm (cxyz - c2) If (d > dmin and d < dmax) { ls = List ( ls3[0], Symop(ns+1, tran) ) If (ls not in Strip(molelist,0)) { n += 1 molelist ++= [ls,bxyz,cxyz,rb3,rc3,n,m] atomlist --= [ls3,a3,c3,rb3,rc3,m] connect = "yes" } } } } } If (connect == "no") Break } } For [ls,ax,cx,rb,rc,n,m] in molelist { model_site( .label = ls[0], .symop = ls[1], .fract_xyz = ax, .Cartn_xyz = cx, .radius_bond = rb, .radius_contact = rc, .index = n, .mole_index = m ) }
The CATEGORY of data items used to specify space group information about the crystal used in the diffraction measurements. Space-group types are identified by their number as listed in International Tables for Crystallography Volume A, or by their Schoenflies symbol. Specific settings of the space groups can be identified by their Hall symbol, by specifying their symmetry operations or generators, or by giving the transformation that relates the specific setting to the reference setting based on International Tables Volume A and stored in this dictionary. 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. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
The CATEGORY of data items used to specify parameters for the complete set of reflections used in the structure refinement process. Note that these parameters are often similar measures to those defined in the DIFFRN categories, but differ in that the parameters refer to the reduced/transformed reflections which have been used to refine the atom site data in the ATOM_SITE category. The DIFFRN definitions refer to the diffraction measurements and the raw reflection data.
Category of items recording 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 CATEGORY of data items which specify the overall reflection measurement information.
CITATION
Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.
ATOM_SITES_CARTN_TRANSFORM
The CATEGORY of data items used to describe the matrix elements used to transform fractional coordinates into Cartesian coordinates of all atom sites in a crystal structure.
ATOM_SITES_FRACT_TRANSFORM
The CATEGORY of data items used to describe the matrix elements used to transform Cartesian coordinates into fractional coordinates of all atom sites in a crystal structure.
The CATEGORY of data items used to describe the diffraction experiment.
The CATEGORY of data items used to specify information about crystals used in the diffraction measurements.
The CATEGORY of data items which describe the composition and chemical properties of the compound under study. The formula data items must be consistent with the density, unit-cell and Z values.
ATOM_TYPE_SCAT
The CATEGORY of data items used to describe atomic scattering information used in crystallographic structure studies.
DIFFRN_REFLN
The CATEGORY of data items which specify the reflection measurements, prior to data reduction and merging.
REFLN
['_refln.index_h', '_refln.index_k', '_refln.index_l']
The CATEGORY of data items used to describe the reflection data used in the refinement of a crystallographic structure model.
ATOM_SITE_ANISO
The CATEGORY of data items used to describe the anisotropic atomic displacement parameters of the atomic sites in a crystal structure.
ATOM_SITE
The CATEGORY of data items used to describe atom site information used in crystallographic structure studies.
['\n loop_\n _atom_site.label\n _atom_site.occupancy\n _atom_site.disorder_assembly\n _atom_site.disorder_group\n C1 1 . .\n H11A .5 M 1\n H12A .5 M 1\n H13A .5 M 1\n H11B .5 M 2\n H12B .5 M 2\n H13B .5 M 2', '\n loop_\n _atom_site.label\n _atom_site.type_symbol\n _atom_site.fract_x\n _atom_site.fract_y\n _atom_site.fract_z\n _atom_site.occupancy\n _atom_site.disorder_assembly\n _atom_site.disorder_group\n Cu1 Cu 0.78443(2) 0.88297(4) 0.37825(2) 1 . .\n Co1 Co 0.77504(2) 0.66957(4) 0.54249(2) 0.78(3) A 1\n Mn1 Mn 0.77504(2) 0.66957(4) 0.54249(2) 0.22(3) A 2\n O1 O 0.85532(9) 0.95747(19) 0.28965(9) 1 . .\n O2 O 0.84868(9) 0.94662(19) 0.14953(8) 1 . .\n # ...']
["\n A hypothetical example of a positional disorder description. Disorder\n assembly 'M' describes a methyl group with two alternative\n configurations '1' and '2':\n\n H11B H11A H13B\n . | .\n . | .\n . | .\n C1 --------C2---\n / . \\\n / . \\\n / . \\\n H12A H12B H13A", "\n An example of a compositional disorder description. Disorder assembly\n 'A' describes a site that is simultaneously occupied by Co and Mn\n atoms which are assigned to disorder group '1' and disorder group '2'\n respectively.\n\n The example was created based on data from:\n Li, Ang et al. (2021). Dalton Transactions, 50(2), 681-688.\n https://doi.org/10.1039/d0dt03269g"]
The CATEGORY of data items used to describe the parameters of the crystal unit cell.