############################################################################## # # # MAIN CIF DICTIONARY SHELL # # # ############################################################################## data_CIF_DIC _dictionary.title CIF_DIC _dictionary.class Instance _dictionary.version 1.2.06 _dictionary.date 2009-10-24 _dictionary.uri www.iucr.org/cif/dic/cif.dic _dictionary.ddl_conformance 3.7.13 _dictionary.namespace CifDic _description.text ; Dictionary shell for the complete set of COMCIFS-approved data-item definitions for use within the Crystallographic Information Framework. ; save_CIF_DIC _definition.id cif_dic _definition.scope Category _definition.class Head _definition.update 2006-06-30 _description.text ; The DICTIONARY group encompassing all data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id ddl_dic save_ #============================================================================= # Import definitions from all CIF dictionaries #============================================================================= save_CIF_CORE _definition.id cif_core _definition.scope Category _definition.class Head _definition.update 2006-06-30 _description.text ; The DICTIONARY group encompassing all CORE data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_dic save_ save_CORE_CRYSTAL _definition.id core_crystal _definition.scope Category _definition.class Head _definition.update 2006-06-20 _description.text ; The category encompassing the CORE CRYSTAL data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_core save_ save_CELL _definition.id cell _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the parameters of the crystal unit cell and their measurement. ; _category.parent_id exptl save_ save_cell.atomic_mass _definition.id '_cell.atomic_mass' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'Cell Atomic Mass' _name.category_id cell _name.object_id atomic_mass _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0.: _units.code daltons loop_ _method.purpose _method.expression Evaluation ; mass = 0. Loop t as atom_type { mass += t.number_in_cell * t.atomic_mass } _cell.atomic_mass = mass ; save_ save_cell.formula_units_Z _definition.id '_cell.formula_units_Z' _definition.update 2006-06-20 _description.text ; The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. ; _description.common 'CellFormulaZ' _name.category_id cell _name.object_id formula_units_Z _type.purpose Assigned _type.container Single _type.contents Integer _enumeration.range 1: save_ save_cell.metric_tensor _definition.id '_cell.metric_tensor' _definition.update 2008-06-24 _description.text ; The direct space (covariant) metric tensor used to transform vectors and coordinates from real (direct) to reciprocal space. ; _description.common 'CellMetricTensor' _name.category_id cell _name.object_id metric_tensor _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; with v as cell_vector _cell.metric_tensor = Array ([[ v.a*v.a, v.a*v.b, v.a*v.c ], [ v.b*v.a, v.b*v.b, v.b*v.c ], [ v.c*v.a, v.c*v.b, v.c*v.c ]]) ; save_ save_cell.orthogonal_matrix _definition.id '_cell.orthogonal_matrix' _definition.update 2008-06-24 _description.text ; 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. ; _description.common 'CellOthogMatrix' _name.category_id cell _name.object_id orthogonal_matrix _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With p as cell_length With q as cell_angle With r as cell_reciprocal_angle _cell.orthogonal_matrix = Array ([ [ p.a*Sind(q.beta)*Sind(r.gamma), 0, 0 ], [ -p.a*Sind(q.beta)*Cosd(r.gamma), p.b*Sind(q.alpha), 0 ], [ p.a*Cosd(q.beta), p.b*Cosd(q.alpha), p.c ]]) ; save_ save_cell.special_details _definition.id '_cell.special_details' _definition.update 2006-06-20 _description.text ; Description of special aspects of the cell choice, noting possible alternative settings. ; _description.common 'CellDetails' _name.category_id cell _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text save_ save_cell.volume _definition.id '_cell.volume' _definition.update 2006-06-20 _description.text ; Volume of the crystal unit cell. ; _description.common 'CellVolume' _name.category_id cell _name.object_id volume _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms_cubed loop_ _method.purpose _method.expression Evaluation ; With v as cell_vector _cell.volume = v.a * ( v.b ^ v.c ) ; save_ save_CELL_ANGLE _definition.id cell_angle _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the angles between the axes in the crystal unit cell. ; _category.parent_id cell save_ save_cell_angle.alpha _definition.id '_cell_angle.alpha' _definition.update 2006-06-20 _description.text ; The angle between the cell axes _cell_length.b and _cell_length.c. ; _description.common 'CellAngleAlpha' _name.category_id cell_angle _name.object_id alpha _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:180.0 _enumeration.default 90.0 _units.code degrees save_ save_cell_angle.beta _definition.id '_cell_angle.beta' _definition.update 2006-06-20 _description.text ; The angle between the cell axes _cell_length.a and _cell_length.c. ; _description.common 'CellAngleBeta' _name.category_id cell_angle _name.object_id beta _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:180.0 _enumeration.default 90.0 _units.code degrees save_ save_cell_angle.gamma _definition.id '_cell_angle.gamma' _definition.update 2006-06-20 _description.text ; The angle between the cell axes _cell_length.a and _cell_length.b. ; _description.common 'CellAngleGamma' _name.category_id cell_angle _name.object_id gamma _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:180.0 _enumeration.default 90.0 _units.code degrees save_ save_CELL_LENGTH _definition.id cell_length _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the lengths of the axes in the crystal unit cell. ; _category.parent_id cell save_ save_cell_length.a _definition.id '_cell_length.a' _definition.update 2008-06-24 _description.text ; The length of the crystal unit cell along the x-axis. ; _description.common 'CellLengthA' _name.category_id cell_length _name.object_id a _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms save_ save_cell_length.b _definition.id '_cell_length.b' _definition.update 2008-06-24 _description.text ; The length of the crystal unit cell along the y-axis. ; _description.common 'CellLengthB' _name.category_id cell_length _name.object_id b _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms save_ save_cell_length.c _definition.id '_cell_length.c' _definition.update 2008-06-24 _description.text ; The length of the crystal unit cell along the z-axis. ; _description.common 'CellLengthC' _name.category_id cell_length _name.object_id c _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms save_ save_CELL_VECTOR _definition.id cell_vector _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the axial vectors of the crystal unit cell. ; _category.parent_id cell save_ save_cell_vector.a _definition.id '_cell_vector.a' _definition.update 2008-06-24 _description.text ; The cell vector along the x axis. ; _description.common 'CellVectorA' _name.category_id cell_vector _name.object_id a _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _cell_vector.a = _cell.orthogonal_matrix * Array (1,0,0) ; save_ save_cell_vector.b _definition.id '_cell_vector.b' _definition.update 2008-06-24 _description.text ; The cell vector along the y axis. ; _description.common 'CellVectorB' _name.category_id cell_vector _name.object_id b _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _cell_vector.b = _cell.orthogonal_matrix * Array (0,1,0) ; save_ save_cell_vector.c _definition.id '_cell_vector.c' _definition.update 2008-06-24 _description.text ; The cell vector along the z axis. ; _description.common 'CellVectorC' _name.category_id cell_vector _name.object_id c _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _cell_vector.c = _cell.orthogonal_matrix * Array (0,0,1) ; save_ save_CELL_MEASUREMENT _definition.id cell_measurement _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the angles between the axes in the crystal unit cell. ; _category.parent_id cell save_ save_cell_measurement.pressure _definition.id '_cell_measurement.pressure' _definition.update 2006-06-20 _description.text ; The pressure at which the unit-cell parameters were measured (not the pressure used to synthesize the sample). ; _description.common 'CellMeasPressure' _name.category_id cell_measurement _name.object_id pressure _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kilopascals save_ save_cell_measurement.radiation _definition.id '_cell_measurement.radiation' _definition.update 2006-06-20 _description.text ; Description of the radiation used to measure the unit-cell data. ; _description.common 'CellMeasRadiation' _name.category_id cell_measurement _name.object_id radiation _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'neutron' 'X-ray tube' 'synchrotron' save_ save_cell_measurement.reflns_used _definition.id '_cell_measurement.reflns_used' _definition.update 2006-06-20 _description.text ; Number of reflections used to determine the unit cell. The reflections may be specified as cell_measurement_refln items. ; _description.common 'CellMeasReflnCount' _name.category_id cell_measurement _name.object_id reflns_used _type.purpose Assigned _type.container Single _type.contents Count save_ save_cell_measurement.temperature _definition.id '_cell_measurement.temperature' _definition.update 2006-06-20 _description.text ; The temperature at which the unit-cell parameters were measured (not the temperature of synthesis). ; _description.common 'CellMeasTemperature' _name.category_id cell_measurement _name.object_id temperature _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kelvins save_ save_cell_measurement.theta_max _definition.id '_cell_measurement.theta_max' _definition.update 2006-06-20 _description.text ; Maximum theta scattering angle of reflections used to measure the crystal unit cell. ; _description.common 'CellMeasThetaMax' _name.category_id cell_measurement _name.object_id theta_max _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_cell_measurement.theta_min _definition.id '_cell_measurement.theta_min' _definition.update 2006-06-20 _description.text ; Minimum theta scattering angle of reflections used to measure the crystal unit cell. ; _description.common 'CellMeasThetaMin' _name.category_id cell_measurement _name.object_id theta_min _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_cell_measurement.wavelength _definition.id '_cell_measurement.wavelength' _definition.update 2006-06-20 _description.text ; Wavelength of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be the same as that given in _diffrn_radiation_wavelength.value ; _description.common 'CellMeasWaveLength' _name.category_id cell_measurement _name.object_id wavelength _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_CELL_MEASUREMENT_REFLN _definition.id cell_measurement_refln _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe the reflection data used in the measurement of the crystal unit cell. ; _category.parent_id cell _category_key.generic '_cell_measurement_refln.key' save_ save_cell_measurement_refln.key _definition.id '_cell_measurement_refln.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of CELL_MEASUREMENT_REFLN items in a looped list. ; _description.common 'Key to cell measurement reflections' _name.category_id cell_measurement_refln _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _cell_measurement_refln.key = _cell_measurement_refln.hkl ; save_ save_cell_measurement_refln.hkl _definition.id '_cell_measurement_refln.hkl' _definition.update 2008-06-18 _description.text ; Miller indices of a reflection used to measure the unit cell. ; _description.common 'CellMeasReflnHkl' _name.category_id cell_measurement_refln _name.object_id hkl _type.purpose Identify _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With c as cell_measurement_refln _cell_measurement_refln.hkl = Array ([c.index_h, c.index_k, c.index_l]) ; save_ save_cell_measurement_refln.theta _definition.id '_cell_measurement_refln.theta' _definition.update 2006-06-20 _description.text ; Theta angle of reflection used to measure the crystal unit cell. ; _description.common 'CellMeasReflnTheta' _name.category_id cell_measurement_refln _name.object_id theta _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_cell_measurement_refln.index_h _definition.id '_cell_measurement_refln.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id cell_measurement_refln _name.object_id index_h save_ save_cell_measurement_refln.index_k _definition.id '_cell_measurement_refln.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id cell_measurement_refln _name.object_id index_k save_ save_cell_measurement_refln.index_l _definition.id '_cell_measurement_refln.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id cell_measurement_refln _name.object_id index_l save_ save_CELL_RECIPROCAL _definition.id cell_reciprocal _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the unit cell data in reciprocal space. ; _category.parent_id cell save_ save_cell_reciprocal.convert_U_to_beta _definition.id '_cell_reciprocal.convert_U_to_beta' _definition.update 2008-08-24 _description.text ; 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 -2pi**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 - ( beta11 h h + ............ 2 beta23 k l ) The conversion of the U or B matrices to the beta matrix beta = C U C = C B C /8pi**2 where C is conversion matrix defined here. ; _description.common 'CellRecipConvertUtoBeta' _name.category_id cell_reciprocal _name.object_id convert_U_to_beta _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With r as cell_reciprocal_length _cell_reciprocal.convert_U_to_beta = 1.4142 * Pi * Array ([[ r.a, 0, 0 ], [ 0, r.b, 0 ], [ 0, 0, r.c ]]) ; save_ save_cell_reciprocal.metric_tensor _definition.id '_cell_reciprocal.metric_tensor' _definition.update 2008-08-24 _description.text ; The reciprocal (contravariant) metric tensor used to transform vectors and coordinates from reciprocal space to real (direct) space. ; _description.common 'CellRecipMetricTensor' _name.category_id cell_reciprocal _name.object_id metric_tensor _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; with r as cell_reciprocal_vector _cell_reciprocal.metric_tensor = Array ([[ r.a*r.a, r.a*r.b, r.a*r.c ], [ r.b*r.a, r.b*r.b, r.b*r.c ], [ r.c*r.a, r.c*r.b, r.c*r.c ]]) ; save_ save_cell_reciprocal.orthogonal_matrix _definition.id '_cell_reciprocal.orthogonal_matrix' _definition.update 2008-06-24 _description.text ; 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 ; _description.common 'HklOthogMatrix' _name.category_id cell_reciprocal _name.object_id orthogonal_matrix _type.purpose Assigned _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal.orthogonal_matrix = Inverse( Transpose( _cell.orthogonal_matrix )) ; save_ save_CELL_RECIPROCAL_ANGLE _definition.id cell_reciprocal_angle _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the unit cell angles in reciprocal space. ; _category.parent_id cell save_ save_cell_reciprocal_angle.alpha _definition.id '_cell_reciprocal_angle.alpha' _definition.update 2006-06-24 _description.text ; Reciprocal of the angle between _cell_length.b and _cell_length.c. ; _description.common 'CellRecipAngleAlpha' _name.category_id cell_reciprocal_angle _name.object_id alpha _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_angle.alpha = 180. - _cell_angle.alpha ; save_ save_cell_reciprocal_angle.beta _definition.id '_cell_reciprocal_angle.beta' _definition.update 2006-06-24 _description.text ; Reciprocal of the angle between _cell_length.a and _cell_length.c. ; _description.common 'CellRecipAngleBeta' _name.category_id cell_reciprocal_angle _name.object_id beta _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_angle.beta = 180. - _cell_angle.beta ; save_ save_cell_reciprocal_angle.gamma _definition.id '_cell_reciprocal_angle.gamma' _definition.update 2006-06-24 _description.text ; Reciprocal of the angle between _cell_length.a and _cell_length.b. ; _description.common 'CellRecipAngleGamma' _name.category_id cell_reciprocal_angle _name.object_id gamma _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_angle.gamma = 180. - _cell_angle.gamma ; save_ save_CELL_RECIPROCAL_LENGTH _definition.id cell_reciprocal_length _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the unit cell lengths in reciprocal space. ; _category.parent_id cell save_ save_cell_reciprocal_length.a _definition.id '_cell_reciprocal_length.a' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_length.a. ; _description.common 'CellRecipLengthA' _name.category_id cell_reciprocal_length _name.object_id a _type.purpose Measured _type.container Single _type.contents Real _units.code reciprocal_angstroms loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_length.a = Norm ( _cell_reciprocal_vector.a ) ; save_ save_cell_reciprocal_length.b _definition.id '_cell_reciprocal_length.b' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_length.b. ; _description.common 'CellRecipLengthB' _name.category_id cell_reciprocal_length _name.object_id b _type.purpose Measured _type.container Single _type.contents Real _units.code reciprocal_angstroms loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_length.b = Norm ( _cell_reciprocal_vector.b ) ; save_ save_cell_reciprocal_length.c _definition.id '_cell_reciprocal_length.c' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_length.c. ; _description.common 'CellRecipLengthC' _name.category_id cell_reciprocal_length _name.object_id c _type.purpose Measured _type.container Single _type.contents Real _units.code reciprocal_angstroms loop_ _method.purpose _method.expression Evaluation ; _cell_reciprocal_length.c = Norm ( _cell_reciprocal_vector.c ) ; save_ save_CELL_RECIPROCAL_VECTOR _definition.id cell_reciprocal_vector _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe the unit cell vectors in reciprocal space. ; _category.parent_id cell save_ save_cell_reciprocal_vector.a _definition.id '_cell_reciprocal_vector.a' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_vector.a. ; _description.common 'CellRecipVectorA' _name.category_id cell_reciprocal_vector _name.object_id a _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With c as cell_vector _cell_reciprocal_vector.a = c.b ^ c.c / _cell.volume ; save_ save_cell_reciprocal_vector.b _definition.id '_cell_reciprocal_vector.b' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_vector.b. ; _description.common 'CellRecipVectorB' _name.category_id cell_reciprocal_vector _name.object_id b _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With c as cell_vector _cell_reciprocal_vector.b = c.c ^ c.a / _cell.volume ; save_ save_cell_reciprocal_vector.c _definition.id '_cell_reciprocal_vector.c' _definition.update 2006-06-24 _description.text ; Reciprocal of the _cell_vector.c. ; _description.common 'CellRecipVectorC' _name.category_id cell_reciprocal_vector _name.object_id c _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With c as cell_vector _cell_reciprocal_vector.c = c.a ^ c.b / _cell.volume ; save_ save_CHEMICAL _definition.id chemical _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; 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. ; _category.parent_id exptl save_ save_chemical.absolute_configuration _definition.id '_chemical.absolute_configuration' _definition.update 2006-06-20 _description.text ; Codes identifying the assignment of absolute structure. In the enumerated codes Set_E is defined to be the set of non-centrosymmetric crystal classes {1, 2, 3, 4, 6, 222, 32, 422, 622, 23, 432}, x(su) is the value of the Flack (1983) parameter as given by data item _refine_ls.abs_structure_Flack. Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. ; _description.common 'ChemAbsConfigCode' _name.category_id chemical _name.object_id absolute_configuration _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail rm ; 'reference molecule' To be valid the crystal class must be in Set_E and the source of the chiral reference substance of known absolute configuration must be reported. The optical activity in solution or liquid state must be non-zero. ; ad ; 'anomalous dispersion' The absolute configuration established by anomalous dispersion effects in diffraction measurements on the crystal. To be valid the crystal class must be in Set_E and |x/su| < 1.6 and |(1-x)/su| > 5.0. The optical activity in solution or liquid state must be non-zero. ; rmad ; 'rm + ad' Established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous dispersion effects in diffraction measurements on the crystal. To be valid the conditions of both 'rm' and 'ad' must be fulfilled. The optical activity in solution or liquid state must be non-zero. ; syn ; 'synthetic' The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure. To be valid the crystal class must be in Set_E and the chiral centre used to assign the enantiomer must be reported. The optical activity in solution or liquid state must be non-zero. ; unk ; 'unknown' An arbitrary choice of enantiomer has been made. To be valid the crystal class must be in Set_E. The optical activity in solution or liquid state must be non-zero. ; save_ save_chemical.compound_source _definition.id '_chemical.compound_source' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemCompoundSource' _name.category_id chemical _name.object_id compound_source _type.purpose Describe _type.container Single _type.contents Text save_ save_chemical.melting_point _definition.id '_chemical.melting_point' _definition.update 2006-06-20 _description.text ; The temperature at which a crystalline solid changes to a liquid. ; _description.common 'ChemMeltingPoint' _name.category_id chemical _name.object_id melting_point _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kelvins save_ save_chemical.name_common _definition.id '_chemical.name_common' _definition.update 2006-06-20 _description.text ; Trivial name by which the compound is commonly known. ; _description.common 'ChemCommonName' _name.category_id chemical _name.object_id name_common _type.purpose Assigned _type.container Single _type.contents Text save_ save_chemical.name_mineral _definition.id '_chemical.name_mineral' _definition.update 2006-06-20 _description.text ; Mineral name accepted by the International Mineralogical Association. ; _description.common 'ChemMineralName' _name.category_id chemical _name.object_id name_mineral _type.purpose Assigned _type.container Single _type.contents Text save_ save_chemical.name_structure_type _definition.id '_chemical.name_structure_type' _definition.update 2006-06-20 _description.text ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; _description.common 'ChemStructuralName' _name.category_id chemical _name.object_id name_structure_type _type.purpose Assigned _type.container Single _type.contents Text save_ save_chemical.name_systematic _definition.id '_chemical.name_systematic' _definition.update 2006-06-20 _description.text ; IUPAC or Chemical Abstracts full name of compound. ; _description.common 'ChemSystemName' _name.category_id chemical _name.object_id name_systematic _type.purpose Assigned _type.container Single _type.contents Text save_ save_chemical.optical_rotation _definition.id '_chemical.optical_rotation' _definition.update 2006-06-20 _description.text ; The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC in g, and SOLV is the chemical formula of the solvent. ; _description.common 'ChemOpticalRotDetails' _name.category_id chemical _name.object_id optical_rotation _type.purpose Assigned _type.container Single _type.contents Text loop_ _description_example.case '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)' save_ save_CHEMICAL_CONN_ATOM _definition.id chemical_conn_atom _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; 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. ; _description.common 'Chemical Connectivity List' _category.parent_id chemical _category_key.generic '_chemical_conn_atom.key' save_ save_chemical_conn_atom.key _definition.id '_chemical_conn_atom.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of CHEMICAL_CONN_ATOM items in a looped list. ; _description.common 'Chemical Connectivity List' _name.category_id chemical_conn_atom _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; chemical_conn_atom.key = chemical_conn_atom.number ; save_ save_chemical_conn_atom.charge _definition.id '_chemical_conn_atom.charge' _definition.update 2006-06-20 _description.text ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _description.common 'ChemConnAtomCharge' _name.category_id chemical_conn_atom _name.object_id charge _type.purpose Assigned _type.container Single _type.contents Integer _enumeration.range -6:6 _enumeration.default 0 save_ save_chemical_conn_atom.display_x _definition.id '_chemical_conn_atom.display_x' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemConnDisplayX' _name.category_id chemical_conn_atom _name.object_id display_x _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_chemical_conn_atom.display_y _definition.id '_chemical_conn_atom.display_y' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemConnDisplayY' _name.category_id chemical_conn_atom _name.object_id display_y _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_chemical_conn_atom.NCA _definition.id '_chemical_conn_atom.NCA' _definition.update 2006-06-20 _description.text ; The number of connected atoms excluding terminal hydrogen atoms. ; _description.common 'ChemConnAtomNCA' _name.category_id chemical_conn_atom _name.object_id NCA _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: save_ save_chemical_conn_atom.NH _definition.id '_chemical_conn_atom.NH' _definition.update 2006-06-20 _description.text ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the atom_site list. This number will be the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the atom_site list. ; _description.common 'ChemConnAtomNH' _name.category_id chemical_conn_atom _name.object_id NH _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: save_ save_chemical_conn_atom.number _definition.id '_chemical_conn_atom.number' _definition.update 2007-02-09 _description.text ; The chemical sequence number to be associated with this atom. ; _description.common 'ChemConnAtomNumber' _name.category_id chemical_conn_atom _name.object_id number _type.purpose Assigned _type.container Single _type.contents Index _enumeration.range 1: save_ save_chemical_conn_atom.type_symbol _definition.id '_chemical_conn_atom.type_symbol' _definition.update 2006-06-20 _description.text ; A code identifying the atom type. ; _description.common 'ChemConnAtomType' _name.category_id chemical_conn_atom _name.object_id type_symbol _name.linked_item_id '_atom_type.symbol' _type.purpose Link _type.container Single _type.contents Code save_ save_CHEMICAL_CONN_BOND _definition.id chemical_conn_bond _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; 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. ; _description.common 'ChemConnBondList' _category.parent_id chemical _category_key.generic '_chemical_conn_bond.key' save_ save_chemical_conn_bond.key _definition.id '_chemical_conn_bond.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of CHEMICAL_CONN_BOND items in a looped list. ; _description.common 'Chemical Connectivity Bond List' _name.category_id chemical_conn_bond _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _chemical_conn_bond.key = _chemical_conn_bond.id ; save_ save_chemical_conn_bond.atom_1 _definition.id '_chemical_conn_bond.atom_1' _definition.update 2006-06-20 _description.text ; Sequence numbers that form the bond connecting two atom sites. ; _name.category_id chemical_conn_bond _name.object_id atom_1 _name.linked_item_id '_chemical_conn_atom.number' _type.purpose Link _type.container Single _type.contents Integer save_ save_chemical_conn_bond.atom_2 _definition.id '_chemical_conn_bond.atom_2' _definition.update 2006-06-20 _description.text ; Sequence numbers that form the bond connecting two atom sites. ; _name.category_id chemical_conn_bond _name.linked_item_id '_chemical_conn_atom.number' _name.object_id atom_2 _type.purpose Link _type.container Single _type.contents Integer save_ save_chemical_conn_bond.id _definition.id '_chemical_conn_bond.id' _definition.update 2008-06-18 _description.text ; Bond identifier composed of a tuple of two sequence numbers specified as _chemical_conn_atom.number values. ; _description.common 'ChemConnBondId' _name.category_id chemical_conn_bond _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With c as chemical_conn_bond _chemical_conn_bond.id = Tuple ( c.atom_1, c.atom_2 ) ; save_ save_chemical_conn_bond.type _definition.id '_chemical_conn_bond.type' _definition.update 2006-06-20 _description.text ; Code for the chemical bond type. ; _description.common 'ChemConnBondType' _name.category_id chemical_conn_bond _name.object_id type _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' _enumeration.default sing save_ save_CHEMICAL_FORMULA _definition.id chemical_formula _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; 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 alphabetic 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 ; _category.parent_id chemical save_ save_chemical_formula.analytical _definition.id '_chemical_formula.analytical' _definition.update 2006-06-20 _description.text ; Formula determined by standard chemical analysis including trace elements. Parentheses are used only for standard uncertainties (su's). ; _description.common 'ChemFormulaAnalytical' _name.category_id chemical_formula _name.object_id analytical _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case 'Fe2.45(2) Ni1.60(3) S4' save_ save_chemical_formula.iupac _definition.id '_chemical_formula.iupac' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemFormulaIupac' _name.category_id chemical_formula _name.object_id iupac _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' save_ save_chemical_formula.moiety _definition.id '_chemical_formula.moiety' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemFormulaMoiety' _name.category_id chemical_formula _name.object_id moiety _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case '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)" save_ save_chemical_formula.structural _definition.id '_chemical_formula.structural' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemFormulaStructural' _name.category_id chemical_formula _name.object_id structural _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' save_ save_chemical_formula.sum _definition.id '_chemical_formula.sum' _definition.update 2006-06-20 _description.text ; 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. ; _description.common 'ChemFormulaSum' _name.category_id chemical_formula _name.object_id sum _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case 'C18 H19 N7 O8 S' save_ save_chemical_formula.weight _definition.id '_chemical_formula.weight' _definition.update 2006-06-20 _description.text ; Mass of the formula specified in one or more of the chemical_formula data items which leads to the density in _exptl_crystal.density_diffrn. ; _description.common 'ChemFormulaWeight' _name.category_id chemical_formula _name.object_id weight _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 1.0: _units.code daltons save_ save_chemical_formula.weight_meas _definition.id '_chemical_formula.weight_meas' _definition.update 2006-06-20 _description.text ; Formula mass measured by a non-diffraction experiment. ; _description.common 'ChemFormulaWeightMeas' _name.category_id chemical_formula _name.object_id weight_meas _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 1.0: _units.code daltons save_ save_EXPTL _definition.id exptl _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the experimental work prior to diffraction measurements. These include crystallization and crystal measurements. ; _category.parent_id core_crystal _category_key.generic '_exptl.key' save_ save_exptl.key _definition.id '_exptl.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of exptl items in a looped list. ; _description.common 'Experimental List' _name.category_id exptl _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited save_ save_exptl.crystals_number _definition.id '_exptl.crystals_number' _definition.update 2006-06-20 _description.text ; Number of crystals used in the measurement of intensities. ; _description.common 'CrystalsCount' _name.category_id exptl _name.object_id crystals_number _type.purpose Assigned _type.container Single _type.contents Index _enumeration.range 1: save_ save_exptl.special_details _definition.id '_exptl.special_details' _definition.update 2006-06-20 _description.text ; Details of the experiment prior to intensity measurement. See also _exptl_crystal.preparation ; _description.common 'SpecialExptlDetails' _name.category_id exptl _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text save_ save_EXPTL_ABSORPT _definition.id exptl_absorpt _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to specify the experimental details of the absorption measurements and corrections to the diffraction data. ; _category.parent_id exptl save_ save_exptl_absorpt.coefficient_mu _definition.id '_exptl_absorpt.coefficient_mu' _definition.update 2006-06-20 _description.text ; Absorption coefficient mu calculated from the atomic content of the cell, the density and the radiation wavelength. ; _description.common 'AbsorbCoeffMu' _name.category_id exptl_absorpt _name.object_id coefficient_mu _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code reciprocal_millimetres save_ save_exptl_absorpt.correction_T_max _definition.id '_exptl_absorpt.correction_T_max' _definition.update 2008-03-28 _description.text ; Maximum transmission factor for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. ; _description.common 'AbsorbTmax' _name.category_id exptl_absorpt _name.object_id correction_T_max _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_exptl_absorpt.correction_T_min _definition.id '_exptl_absorpt.correction_T_min' _definition.update 2008-03-28 _description.text ; Minimum transmission factor for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. ; _description.common 'AbsorbTmin' _name.category_id exptl_absorpt _name.object_id correction_T_min _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_exptl_absorpt.correction_type _definition.id '_exptl_absorpt.correction_type' _definition.update 2006-06-20 _description.text ; Code identifying the absorption correction type and method. ; _description.common 'AbsorbCorrectType' _name.category_id exptl_absorpt _name.object_id correction_type _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail analytical 'analytical from crystal shape' cylinder 'cylindrical' empirical 'empirical from intensities' gaussian 'Gaussian from crystal shape' integration 'integration from crystal shape' multi-scan 'symmetry-related measurements' none 'no absorption correction applied' numerical 'numerical from crystal shape' psi-scan 'psi-scan corrections' refdelf 'refined from delta-F' sphere 'spherical' _enumeration.default none save_ save_exptl_absorpt.process_details _definition.id '_exptl_absorpt.process_details' _definition.update 2006-06-20 _description.text ; Description of the absorption correction process applied to the measured intensities. A literature reference should be supplied for psi-scan or multi-scan techniques. ; _description.common 'AbsorbCorrectDetails' _name.category_id exptl_absorpt _name.object_id process_details _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'Tompa analytical' 'MolEN (Fair, 1990)' '(North, Phillips & Mathews, 1968)' save_ save_EXPTL_CRYSTAL _definition.id exptl_crystal _definition.scope Category _definition.class List _definition.update 2008-06-19 _description.text ; The CATEGORY of data items used to specify information about the crystals used in the diffraction measurements. ; _category.parent_id exptl _category_key.generic '_exptl_crystal.key' save_ save_exptl_crystal.key _definition.id '_exptl_crystal.key' _definition.update 2008-06-19 _description.text ; Value is a unique key to a set of EXPTL_CRYSTAL items in a looped list. ; _description.common 'Key to exptl_crystal values' _name.category_id exptl_crystal _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _exptl_crystal.key = _exptl_crystal.id ; save_ save_exptl_crystal.colour _definition.id '_exptl_crystal.colour' _definition.update 2006-06-20 _description.text ; Colour and appearance of the crystal. ; _description.common 'CrystalColour' _name.category_id exptl_crystal _name.object_id colour _type.purpose Assigned _type.container Tuple _type.contents Code loop_ _description_example.case "(transluscent, pale, green)" loop_ _method.purpose _method.expression Evaluation ; With c as exptl_crystal_appearance _exptl_crystal.colour = Tuple ( c.general, c.intensity, c.hue ) ; save_ save_exptl_crystal.density_diffrn _definition.id '_exptl_crystal.density_diffrn' _definition.update 2006-06-20 _description.text ; Crystal density calculated from crystal unit cell and atomic content. ; _description.common 'CrystalDensityDiffrn' _name.category_id exptl_crystal _name.object_id density_diffrn _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code megagrams_per_metres_cubed loop_ _method.purpose _method.expression Evaluation ; _exptl_crystal.density_diffrn = 1.6605 * _cell.atomic_mass / _cell.volume ; save_ save_exptl_crystal.density_meas _definition.id '_exptl_crystal.density_meas' _definition.update 2006-06-20 _description.text ; Crystal density measured using standard chemical and physical methods. ; _description.common 'CrystalDensityMeas' _name.category_id exptl_crystal _name.object_id density_meas _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code megagrams_per_metres_cubed save_ save_exptl_crystal.density_meas_temp _definition.id '_exptl_crystal.density_meas_temp' _definition.update 2006-06-20 _description.text ; Temperature at which _exptl_crystal.density_meas was determined. ; _description.common 'CrystalDensityTemperature' _name.category_id exptl_crystal _name.object_id density_meas_temp _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kelvins save_ save_exptl_crystal.density_method _definition.id '_exptl_crystal.density_method' _definition.update 2006-06-20 _description.text ; Description of method used to measure _exptl_crystal.density_meas. ; _description.common 'CrystalDensityMethod' _name.category_id exptl_crystal _name.object_id density_method _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'flotation in aqueous KI' save_ save_exptl_crystal.description _definition.id '_exptl_crystal.description' _definition.update 2006-06-20 _description.text ; Description of the quality and habit of the crystal. The crystal dimensions should appear in the exptl_crystal_size category. ; _description.common 'CrystalDescription' _name.category_id exptl_crystal _name.object_id description _type.purpose Describe _type.container Single _type.contents Text save_ save_exptl_crystal.F_000 _definition.id '_exptl_crystal.F_000' _definition.update 2006-06-20 _description.text ; 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 theta = 0 f~i~ = imaginary part of the scattering factors at theta = 0 the sum is taken over each atom in the unit cell ; _description.common 'F(000)expected' _name.category_id exptl_crystal _name.object_id F_000 _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_exptl_crystal.id _definition.id '_exptl_crystal.id' _definition.update 2006-06-20 _description.text ; Name identifying a crystal if multiple crystals are used. ; _description.common 'CrystalId' _name.category_id exptl_crystal _name.object_id id _type.purpose Identify _type.container Single _type.contents Text save_ save_exptl_crystal.preparation _definition.id '_exptl_crystal.preparation' _definition.update 2006-06-20 _description.text ; Details of crystal growth and preparation of the crystals. ; _description.common 'CrystalPreparation' _name.category_id exptl_crystal _name.object_id preparation _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'mounted in an argon-filled quartz capillary' save_ save_exptl_crystal.pressure_history _definition.id '_exptl_crystal.pressure_history' _definition.update 2006-06-20 _description.text ; Details concerning the pressure history of the crystals. ; _description.common 'CrystalOriginPressure' _name.category_id exptl_crystal _name.object_id pressure_history _type.purpose Describe _type.container Single _type.contents Text save_ save_exptl_crystal.size_length _definition.id '_exptl_crystal.size_length' _definition.update 2006-06-20 _description.text ; The length of needle crystals. ; _name.category_id exptl_crystal _name.object_id size_length _description.common 'CrystalNeedleLength' _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.: _units.code millimetres save_ save_exptl_crystal.size_max _definition.id '_exptl_crystal.size_max' _definition.update 2006-06-20 _description.text ; The maximum dimension of a crystal. ; _name.category_id exptl_crystal _name.object_id size_max _description.common 'CrystalSizeMax' _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.: _units.code millimetres save_ save_exptl_crystal.size_mid _definition.id '_exptl_crystal.size_mid' _definition.update 2006-06-20 _description.text ; The medium dimension of a crystal. ; _name.category_id exptl_crystal _name.object_id size_mid _description.common 'CrystalSizeMedial' _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.: _units.code millimetres save_ save_exptl_crystal.size_min _definition.id '_exptl_crystal.size_min' _definition.update 2006-06-20 _description.text ; The minimum dimension of a crystal. ; _name.category_id exptl_crystal _name.object_id size_min _description.common 'CrystalSizeMin' _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.: _units.code millimetres save_ save_exptl_crystal.size_rad _definition.id '_exptl_crystal.size_rad' _definition.update 2006-06-20 _description.text ; The radius of a spherical crystal. ; _name.category_id exptl_crystal _name.object_id size_rad _description.common 'CrystalRadius' _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.: _units.code millimetres save_ save_exptl_crystal.thermal_history _definition.id '_exptl_crystal.thermal_history' _definition.update 2006-06-20 _description.text ; Details concerning the thermal history of the crystals. ; _description.common 'CrystalOriginThermal' _name.category_id exptl_crystal _name.object_id thermal_history _type.purpose Describe _type.container Single _type.contents Text save_ save_EXPTL_CRYSTAL_FACE _definition.id exptl_crystal_face _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the dimensions of the crystals used in the diffraction measurements. ; _category.parent_id exptl_crystal _category_key.generic '_exptl_crystal_face.key' save_ save_exptl_crystal_face.key _definition.id '_exptl_crystal_face.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of EXPTL_CRYSTAL items in a looped list. ; _description.common 'Crystal Faces List' _name.category_id exptl_crystal_face _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _exptl_crystal_face.key = _exptl_crystal_face.id ; save_ save_exptl_crystal_face.crystal_id _definition.id '_exptl_crystal_face.crystal_id' _definition.update 2008-06-19 _description.text ; Name identifying a crystal if multiple crystals are used. ; _description.common 'CrystalFaceCrystalId' _name.category_id exptl_crystal_face _name.object_id crystal_id _name.linked_item_id '_exptl_crystal.id' _type.purpose Link _type.container Single _type.contents Text save_ save_exptl_crystal_face.diffr_chi _definition.id '_exptl_crystal_face.diffr_chi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id exptl_crystal_face _name.object_id diffr_chi save_ save_exptl_crystal_face.diffr_kappa _definition.id '_exptl_crystal_face.diffr_kappa' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id exptl_crystal_face _name.object_id diffr_kappa save_ save_exptl_crystal_face.diffr_phi _definition.id '_exptl_crystal_face.diffr_phi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id exptl_crystal_face _name.object_id diffr_phi save_ save_exptl_crystal_face.diffr_psi _definition.id '_exptl_crystal_face.diffr_psi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id exptl_crystal_face _name.object_id diffr_psi save_ save_exptl_crystal_face.hkl _definition.id '_exptl_crystal_face.hkl' _definition.update 2007-02-07 _description.text ; Miller indices of the crystal face. ; _description.common 'Crystal face hkl' _name.category_id exptl_crystal_face _name.object_id hkl _type.purpose Identify _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With f as exptl_crystal_face _exptl_crystal_face.hkl = Array ([f.index_h, f.index_h, f.index_l]) ; save_ save_exptl_crystal_face.index_h _definition.id '_exptl_crystal_face.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id exptl_crystal_face _name.object_id index_h save_ save_exptl_crystal_face.index_k _definition.id '_exptl_crystal_face.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id exptl_crystal_face _name.object_id index_k save_ save_exptl_crystal_face.index_l _definition.id '_exptl_crystal_face.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id exptl_crystal_face _name.object_id index_l save_ save_exptl_crystal_face.id _definition.id '_exptl_crystal_face.id' _definition.update 2008-06-18 _description.text ; Identifier which combines the crystal id and the face indices as a tuple. This is the key item of the category. ; _description.common 'Crystal face id code' _name.category_id exptl_crystal_face _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Text,Array(Index,Index,Index) loop_ _method.purpose _method.expression Evaluation ; With f as exptl_crystal_face _exptl_crystal_face.id = Tuple ( f.crystal_id, f.hkl ) ; save_ save_exptl_crystal_face.perp_dist _definition.id '_exptl_crystal_face.perp_dist' _definition.update 2006-06-20 _description.text ; Perpendicular distance of face to the centre of rotation of the crystal. ; _description.common 'Crystal face perp distance' _name.category_id exptl_crystal_face _name.object_id perp_dist _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code millimetres save_ save_EXPTL_CRYSTAL_APPEARANCE _definition.id exptl_crystal_appearance _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of ENUMERATION items used to specify information about the crystal colour and appearance. ; _category.parent_id exptl_crystal save_ save_exptl_crystal_appearance.general _definition.id '_exptl_crystal_appearance.general' _definition.update 2006-06-20 _description.text ; Appearance of the crystal. ; _description.common 'CrystalColourAppearance' _name.category_id exptl_crystal_appearance _name.object_id general _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state 'metallic' 'lustrous' 'transparent' 'transluscent' 'opaque' ' ' _enumeration.default ' ' save_ save_exptl_crystal_appearance.intensity _definition.id '_exptl_crystal_appearance.intensity' _definition.update 2006-06-20 _description.text ; Colour intensity of the crystal. ; _description.common 'CrystalColourIntensity' _name.category_id exptl_crystal_appearance _name.object_id intensity _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state 'dark' 'light' 'intense' 'pale' ' ' _enumeration.default ' ' save_ save_exptl_crystal_appearance.hue _definition.id '_exptl_crystal_appearance.hue' _definition.update 2008-02-07 _description.text ; Colour hue of the crystal as an enumerated set of codes. ; _description.common 'CrystalHue' _name.category_id exptl_crystal_appearance _name.object_id hue _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail black [ 000, 000, 000 ] white [ 255, 255, 255 ] grey [ 192, 192, 192 ] grey_light [ 211, 211, 211 ] grey_slate [ 112, 128, 144 ] blue [ 000, 000, 255 ] blue_light [ 176, 224, 230 ] blue_medium [ 000, 000, 205 ] blue_dark [ 025, 025, 112 ] blue_navy [ 000, 000, 128 ] blue_royal [ 065, 105, 225 ] blue_sky [ 135, 206, 235 ] blue_steel [ 070, 130, 180 ] turquoise [ 064, 224, 208 ] cyan [ 000, 255, 255 ] cyan_light [ 224, 255, 255 ] green [ 000, 255, 000 ] green_light [ 152, 251, 152 ] green_dark [ 000, 100, 000 ] green_sea [ 046, 139, 087 ] green_lime [ 050, 205, 050 ] green_olive [ 107, 142, 035 ] green_khaki [ 240, 230, 140 ] yellow [ 255, 255, 000 ] yellow_light [ 255, 255, 224 ] yellow_gold [ 255, 215, 000 ] brown [ 165, 042, 042 ] brown_sienna [ 160, 082, 045 ] brown_beige [ 245, 245, 220 ] brown_tan [ 210, 180, 140 ] salmon [ 250, 128, 114 ] salmon_light [ 255, 160, 122 ] salmon_dark [ 233, 150, 122 ] orange [ 255, 165, 000 ] orange_dark [ 255, 140, 000 ] red [ 255, 000, 000 ] red_coral [ 255, 127, 080 ] red_tomato [ 255, 099, 071 ] red_orange [ 255, 069, 000 ] red_violet [ 219, 112, 147 ] red_maroon [ 176, 048, 096 ] pink [ 255, 192, 203 ] pink_light [ 255, 182, 193 ] pink_deep [ 255, 020, 147 ] pink_hot [ 255, 105, 180 ] violet [ 238, 130, 238 ] violet_red [ 208, 032, 144 ] violet_magenta [ 255, 000, 255 ] violet_dark [ 148, 000, 211 ] violet_blue [ 138, 043, 226 ] _enumeration.default 'white' save_ save_SYMMETRY _definition.id symmetry _definition.scope Category _definition.class Set _definition.update 2006-06-20 _description.text ; The CATEGORY of data items used to describe symmetry information used in crystallographic structure studies. ; _category.parent_id exptl save_ save_symmetry.cell_setting _definition.id '_symmetry.cell_setting' _definition.update 2006-06-20 _description.text ; Code for cell settings for this space-group symmetry. ; _description.common 'SymmetryCellSetting' _name.category_id symmetry _name.object_id cell_setting _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic _enumeration.default triclinic save_ save_symmetry.Int_Tables_number _definition.id '_symmetry.Int_Tables_number' _definition.update 2006-06-20 _description.text ; Space-group number from International Tables for Crystallography, Vol. A. ; _description.common 'SymmetryIntTabNumber' _name.category_id symmetry _name.object_id Int_Tables_number _type.purpose Assigned _type.container Single _type.contents Index _enumeration.range 1:230 save_ save_symmetry.multiplicity _definition.id '_symmetry.multiplicity' _definition.update 2006-06-20 _description.text ; Number of unique symmetry elements in the space group. ; _description.common 'SymmetryMultiplicity' _name.category_id symmetry _name.object_id multiplicity _type.purpose Observed _type.container Single _type.contents Index _enumeration.range 1:192 loop_ _method.purpose _method.expression Evaluation ; n = 0 Loop s as symmetry_equiv n += 1 _symmetry.multiplicity = n ; save_ save_symmetry.space_group_name_Hall _definition.id '_symmetry.space_group_name_Hall' _definition.update 2008-06-19 _description.text ; Space-group symbol as described by Hall. This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525. ; _description.common 'SpaceGroupSymbolHall' _name.category_id symmetry _name.object_id space_group_name_Hall _type.purpose Assigned _type.container Single _type.contents Text loop_ _description_example.case 'P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' save_ save_symmetry.space_group_name_H_M _definition.id '_symmetry.space_group_name_H_M' _definition.update 2006-06-20 loop_ _alias.definition_id '_symmetry.space_group_name_H-M' _description.text ; Hermann-Mauguin space-group symbol. Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1987) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol specify the _symmetry_equiv.pos_as_xyz or *_Hall data items as well. Leave spaces between symbols referring to different axes. ; _description.common 'SpaceGroupSymbolH-M' _name.category_id symmetry _name.object_id space_group_name_H_M _type.purpose Assigned _type.container Single _type.contents Text loop_ _description_example.case 'P 1 21/m 1' 'P 2/n 2/n 2/n (origin at -1)' 'R -3 2/m' save_ save_SYMMETRY_EQUIV _definition.id symmetry_equiv _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe symmetry equivalent sites in the crystal unit cell. ; _category.parent_id symmetry _category_key.generic '_symmetry_equiv.key' save_ save_symmetry_equiv.key _definition.id '_symmetry_equiv.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of SYMMETRY_EQUIV items in a looped list. ; _description.common 'Symmetry Equivalent Position List' _name.category_id symmetry_equiv _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _symmetry_equiv.key = _symmetry_equiv.pos_site_id ; save_ save_symmetry_equiv.pos_as_xyz _definition.id '_symmetry_equiv.pos_as_xyz' _definition.update 2006-06-20 _description.text ; Symmetry equivalent position in the 'xyz' representation. Except for the space group P1, this data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography, Vol. A. (1987). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. ; _description.common 'SymmetryEquivPosXyz' _name.category_id symmetry_equiv _name.object_id pos_as_xyz _type.purpose Assigned _type.container Single _type.contents Formula loop_ _description_example.case -y+x,-y,1/3+z save_ save_symmetry_equiv.pos_site_id _definition.id '_symmetry_equiv.pos_site_id' _definition.update 2008-06-18 _description.text ; A code identifying each entry in the _symmetry_equiv.pos_as_xyz list. It is normally the sequence number of the entry in that list, and should be identified with the code 'n' in the geometry symmetry codes of the form 'n_klm'. ; _description.common 'SymmetryEquivPosNumber' _name.category_id symmetry_equiv _name.object_id pos_site_id _type.purpose Identify _type.container Single _type.contents Index save_ save_symmetry_equiv.R _definition.id '_symmetry_equiv.R' _definition.update 2008-06-24 _description.text ; A matrix containing the symmetry rotation operations of a space group | r11 r12 r13 | R = | r21 r22 r23 | | r31 r32 r33 | ; _description.common 'SymmetryRotMatrix' _name.category_id symmetry_equiv _name.object_id R _type.purpose Assigned _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; sm = _symmetry_equiv.Seitz_matrix _symmetry_equiv.R = Array ([[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]]]) ; save_ save_symmetry_equiv.RT _definition.id '_symmetry_equiv.RT' _definition.update 2008-06-24 _description.text ; The TRANSFORM of the symmetry rotation matrix representing the point group opertions of the space group | r11 r21 r31 | RT = | r12 r22 r32 | | r13 r23 r33 | ; _description.common 'SymmetryRotMatrix' _name.category_id symmetry_equiv _name.object_id RT _type.purpose Assigned _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _symmetry_equiv.RT = Transpose (_symmetry_equiv.R) ; save_ save_symmetry_equiv.Seitz_matrix _definition.id '_symmetry_equiv.Seitz_matrix' _definition.update 2008-06-24 _description.text ; 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 | ; _description.common 'SymmetrySeitzMatrix' _name.category_id symmetry_equiv _name.object_id Seitz_matrix _type.purpose Assigned _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _symmetry_equiv.Seitz_matrix = SeitzFromJones (_symmetry_equiv.pos_as_xyz) ; save_ save_symmetry_equiv.T _definition.id '_symmetry_equiv.T' _definition.update 2006-06-20 _description.text ; A vector containing the symmetry translation operations of a space group. ; _description.common 'SymmetryTranslVector' _name.category_id symmetry_equiv _name.object_id T _type.purpose Assigned _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; sm = _symmetry_equiv.Seitz_matrix _symmetry_equiv.T = Array ( [sm[0,3],sm[1,3],sm[2,3]] ) ; save_ save_CORE_DIFFRACTION _definition.id core_diffraction _definition.scope Category _definition.class Head _definition.update 2006-12-14 _description.text ; The DICTIONARY group encompassing the CORE DIFFRACTION data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_core save_ save_DIFFRN _definition.id diffrn _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to describe the diffraction experiment. ; _category.parent_id core_diffraction save_ save_diffrn.ambient_pressure _definition.id '_diffrn.ambient_pressure' _definition.update 2006-12-14 _description.text ; The mean pressure at which the diffraction intensities were measured. ; _description.common 'AmbientPressure' _name.category_id diffrn _name.object_id ambient_pressure _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kilopascals save_ save_diffrn.ambient_temperature _definition.id '_diffrn.ambient_temperature' _definition.update 2006-12-14 _description.text ; The mean temperature at which the diffraction intensities were measured. ; _description.common 'AmbientTemperature' _name.category_id diffrn _name.object_id ambient_temperature _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kelvins save_ save_diffrn.crystal_treatment _definition.id '_diffrn.crystal_treatment' _definition.update 2006-12-14 _description.text ; Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. ; _description.common 'CrystalTreatment' _name.category_id diffrn _name.object_id crystal_treatment _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream' save_ save_diffrn.special_details _definition.id '_diffrn.special_details' _definition.update 2006-12-14 _description.text ; Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation, etc. ; _description.common 'DiffrnMeasDetails' _name.category_id diffrn _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case ; The results may not be entirely reliable as the measurement was made during a heat wave when the air-conditioning had failed. ; save_ save_diffrn.symmetry_description _definition.id '_diffrn.symmetry_description' _definition.update 2006-12-14 _description.text ; Observed diffraction point symmetry, systematic absences and possible space group(s) or superspace group(s) compatible with these. ; _description.common 'DiffrnSymmetryDetails' _name.category_id diffrn _name.object_id symmetry_description _type.purpose Describe _type.container Single _type.contents Text save_ save_DIFFRN_ATTENUATOR _definition.id diffrn_attenuator _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the attenuators used in the diffraction source. ; _category.parent_id diffrn _category_key.generic '_diffrn_attenuator.key' save_ save_diffrn_attenuator.key _definition.id '_diffrn_attenuator.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_ATTENUATOR items in a looped list. ; _description.common 'Key to beam attenuator values' _name.category_id diffrn_attenuator _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_attenuator.key = _diffrn_attenuator.code ; save_ save_diffrn_attenuator.code _definition.id '_diffrn_attenuator.code' _definition.update 2008-06-19 _description.text ; Name identifying a particular attenuator setting; referenced by the _diffrn_refln.attenuator_code which is stored with the intensities. ; _description.common 'DiffrnAttenuatorCode' _name.category_id diffrn_attenuator _name.object_id code _type.purpose Identify _type.container Single _type.contents Text save_ save_diffrn_attenuator.material _definition.id '_diffrn_attenuator.material' _definition.update 2006-12-14 _description.text ; Description of the material from which the attenuator is made. ; _description.common 'DiffrnAttenuator' _name.category_id diffrn_attenuator _name.object_id material _type.purpose Describe _type.container Single _type.contents Text save_ save_diffrn_attenuator.scale _definition.id '_diffrn_attenuator.scale' _definition.update 2006-12-14 _description.text ; The scale factor applied to a measured intensity if it is reduced by an attenuator identified by _diffrn_attenuator.code. ; _description.common 'DiffrnAttenuatorScale' _name.category_id diffrn_attenuator _name.object_id scale _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 1.0: save_ save_DIFFRN_DETECTOR _definition.id diffrn_detector _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the detectors used in the in the measurement of diffraction intensities. ; _category.parent_id diffrn save_ save_diffrn_detector.description _definition.id '_diffrn_detector.description' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_radiation.detector' _description.text ; Description of the type of diffraction radiation detector. ; _description.common 'DetectorClass' _name.category_id diffrn_detector _name.object_id description _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' save_ save_diffrn_detector.area_resol_mean _definition.id '_diffrn_detector.area_resol_mean' _definition.update 2006-12-14 _description.text ; The resolution limit of an area diffraction radiation detector. ; _description.common 'DetectorResolLimit' _name.category_id diffrn_detector _name.object_id area_resol_mean _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code pixels_per_millimetre save_ save_diffrn_detector.details _definition.id '_diffrn_detector.details' _definition.update 2006-12-14 _description.text ; Description of special aspects of the radiation detector. ; _description.common 'DetectorDetails' _name.category_id diffrn_detector _name.object_id details _type.purpose Describe _type.container Single _type.contents Text save_ save_diffrn_detector.dtime _definition.id '_diffrn_detector.dtime' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_radiation.detector_dtime' _description.text ; The maximum time between two detector signals that cannot be resolved. ; _description.common 'DetectorDeadTime' _name.category_id diffrn_detector _name.object_id dtime _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code microseconds save_ save_diffrn_detector.make _definition.id '_diffrn_detector.make' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_detector.type' _description.text ; The make, model or name of the diffraction radiation detector. ; _description.common 'DetectorMake' _name.category_id diffrn_detector _name.object_id make _type.purpose Describe _type.container Single _type.contents Text save_ save_DIFFRN_MEASUREMENT _definition.id diffrn_measurement _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the details of the diffraction measurement. ; _category.parent_id diffrn save_ save_diffrn.measurement_details _definition.id '_diffrn.measurement_details' _definition.update 2006-12-14 _description.text ; Description of special aspects of the diffraction measurement. ; _description.common 'DiffrnMeasDetails' _name.category_id diffrn _name.object_id measurement_details _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case '440 frames of 0.25\%' save_ save_diffrn.measurement_device_class _definition.id '_diffrn.measurement_device_class' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn.measurement_device' _description.text ; Type of goniometer device used to mount and orient the specimen. ; _description.common 'DiffrnMeasDeviceClass' _name.category_id diffrn _name.object_id measurement_device_class _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'three-circle diffractometer' 'four-circle diffractometer' '\k-geometry diffractometer' 'oscillation camera' 'precession camera' save_ save_diffrn.measurement_device_details _definition.id '_diffrn.measurement_device_details' _definition.update 2006-12-14 _description.text ; Details of the goniometer device used in the diffraction experiment. ; _description.common 'DiffrnMeasDeviceDetails' _name.category_id diffrn _name.object_id measurement_device_details _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case ; commercial goniometer modified locally to allow for 90\% \t arc ; save_ save_diffrn.measurement_device_make _definition.id '_diffrn.measurement_device_make' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn.measurement_device_type' _description.text ; The make, model or name of the goniometer device used. ; _description.common 'DiffrnMeasDeviceMake' _name.category_id diffrn _name.object_id measurement_device_make _type.purpose Describe _type.container Single _type.contents Text save_ save_diffrn.measurement_method _definition.id '_diffrn.measurement_method' _definition.update 2006-12-14 _description.text ; Description of scan method used to measure diffraction intensities. ; _description.common 'DiffrnMeasMethod' _name.category_id diffrn _name.object_id measurement_method _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'profile data from \q/2\q scans' save_ save_diffrn.measurement_specimen_support _definition.id '_diffrn.measurement_specimen_support' _definition.update 2006-12-14 _description.text ; Mounting method for the crystal specimum during data collection. ; _description.common 'DiffrnSpecimumMount' _name.category_id diffrn _name.object_id measurement_specimen_support _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ save_DIFFRN_ORIENT _definition.id diffrn_orient _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the orientation of the crystal axes to the diffractometer goniometer. ; _category.parent_id diffrn save_ save_DIFFRN_ORIENT_MATRIX _definition.id diffrn_orient_matrix _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the matrix specifying the orientation of the crystal axes to the diffractometer goniometer. ; _category.parent_id diffrn_orient save_ save_diffrn_orient_matrix.type _definition.id '_diffrn_orient_matrix.type' _definition.update 2006-12-14 _description.text ; Description of orientation matrix and how it should be applied to define the orientation of the crystal with respect to the diffractometer axes. ; _description.common 'DiffrnOrientMatrixType' _name.category_id diffrn_orient_matrix _name.object_id type _type.purpose Describe _type.container Single _type.contents Text save_ save_diffrn_orient_matrix.UBIJ _definition.id '_diffrn_orient_matrix.UBIJ' _definition.update 2008-06-24 _description.text ; The 3x3 matrix specifying the orientation of the crystal with respect to the diffractometer axes. ; _description.common 'DiffrnOrientMatrix' _name.category_id diffrn_orient_matrix _name.object_id UBIJ _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With o as diffrn_orient_matrix _diffrn_orient_matrix.UBIJ = Array ([[ 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 ]]) ; save_ save_diffrn_orient_matrix.UB_11 _definition.id '_diffrn_orient_matrix.UB_11' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_11 save_ save_diffrn_orient_matrix.UB_12 _definition.id '_diffrn_orient_matrix.UB_12' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_12 save_ save_diffrn_orient_matrix.UB_13 _definition.id '_diffrn_orient_matrix.UB_13' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_13 save_ save_diffrn_orient_matrix.UB_21 _definition.id '_diffrn_orient_matrix.UB_21' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_21 save_ save_diffrn_orient_matrix.UB_22 _definition.id '_diffrn_orient_matrix.UB_22' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_22 save_ save_diffrn_orient_matrix.UB_23 _definition.id '_diffrn_orient_matrix.UB_23' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_23 save_ save_diffrn_orient_matrix.UB_31 _definition.id '_diffrn_orient_matrix.UB_31' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_31 save_ save_diffrn_orient_matrix.UB_32 _definition.id '_diffrn_orient_matrix.UB_32' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_32 save_ save_diffrn_orient_matrix.UB_33 _definition.id '_diffrn_orient_matrix.UB_33' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix of the orientation of the crystal axes to the diffractometer goniometer. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_orient_matrix _name.object_id UB_33 save_ save_DIFFRN_ORIENT_REFLN _definition.id diffrn_orient_refln _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; 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. ; _category.parent_id diffrn_orient _category_key.generic '_diffrn_orient_refln.key' save_ save_diffrn_orient_refln.key _definition.id '_diffrn_orient_refln.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_ORIENT_REFLN items in a looped list. ; _description.common 'Key to orientation reflections' _name.category_id diffrn_orient_refln _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_orient_refln.key = _diffrn_orient_refln.hkl ; save_ save_diffrn_orient_refln.angle_chi _definition.id '_diffrn_orient_refln.angle_chi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_chi save_ save_diffrn_orient_refln.angle_kappa _definition.id '_diffrn_orient_refln.angle_kappa' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_kappa save_ save_diffrn_orient_refln.angle_omega _definition.id '_diffrn_orient_refln.angle_omega' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_omega save_ save_diffrn_orient_refln.angle_phi _definition.id '_diffrn_orient_refln.angle_phi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_phi save_ save_diffrn_orient_refln.angle_psi _definition.id '_diffrn_orient_refln.angle_psi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_psi save_ save_diffrn_orient_refln.angle_theta _definition.id '_diffrn_orient_refln.angle_theta' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_orient_refln _name.object_id angle_theta save_ save_diffrn_orient_refln.hkl _definition.id '_diffrn_orient_refln.hkl' _definition.update 2006-12-14 _description.text ; Miller indices of a reflection used to define the orientation matrix. ; _description.common 'DiffrnOrientReflnHkl' _name.category_id diffrn_orient_refln _name.object_id hkl _type.purpose Identify _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With a as diffrn_orient_refln _diffrn_orient_refln.hkl = Array ([a.index_h, a.index_k, a.index_l]) ; save_ save_diffrn_orient_refln.index_h _definition.id '_diffrn_orient_refln.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_orient_refln _name.object_id index_h save_ save_diffrn_orient_refln.index_k _definition.id '_diffrn_orient_refln.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_orient_refln _name.object_id index_k save_ save_diffrn_orient_refln.index_l _definition.id '_diffrn_orient_refln.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_orient_refln _name.object_id index_l save_ save_DIFFRN_RADIATION _definition.id diffrn_radiation _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; 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. ; _category.parent_id diffrn save_ save_diffrn_radiation.collimation _definition.id '_diffrn_radiation.collimation' _definition.update 2006-12-14 _description.text ; Description of the collimation or focusing applied to the radiation. ; _description.common 'RadCollimator' _name.category_id diffrn_radiation _name.object_id collimation _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' save_ save_diffrn_radiation.filter_edge _definition.id '_diffrn_radiation.filter_edge' _definition.update 2006-12-14 _description.text ; Absorption edge of the radiation filter used. ; _description.common 'RadFilter' _name.category_id diffrn_radiation _name.object_id filter_edge _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_diffrn_radiation.inhomogeneity _definition.id '_diffrn_radiation.inhomogeneity' _definition.update 2006-12-14 _description.text ; Half-width of the incident beam perpendicular to the diffraction plane. ; _description.common 'RadHalfWidth' _name.category_id diffrn_radiation _name.object_id inhomogeneity _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code millimetres save_ save_diffrn_radiation.monochromator _definition.id '_diffrn_radiation.monochromator' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'RadMonochromator' _name.category_id diffrn_radiation _name.object_id monochromator _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' save_ save_diffrn_radiation.polarisn_norm _definition.id '_diffrn_radiation.polarisn_norm' _definition.update 2006-12-14 _description.text ; The angle, as viewed from the specimen, between the perpendicular component of the polarisation and the diffraction plane. ; _description.common 'RadPolarizNorm' _name.category_id diffrn_radiation _name.object_id polarisn_norm _type.purpose Measured _type.container Single _type.contents Real _enumeration.range -180.0:180.0 _units.code degrees save_ save_diffrn_radiation.polarisn_ratio _definition.id '_diffrn_radiation.polarisn_ratio' _definition.update 2006-12-14 _description.text ; 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). ; _description.common 'RadPolarizRatio' _name.category_id diffrn_radiation _name.object_id polarisn_ratio _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_diffrn_radiation.probe _definition.id '_diffrn_radiation.probe' _definition.update 2006-12-14 _description.text ; General description of the radiation used (i.e. name of subatomic particle or region of the electromagnetic spectrum). ; _description.common 'RadDescription' _name.category_id diffrn_radiation _name.object_id probe _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state x-ray neutron electron gamma _enumeration.default x-ray save_ save_diffrn_radiation.type _definition.id '_diffrn_radiation.type' _definition.update 2006-12-14 _description.text ; Description of the radiation type. Detailed information on the description in _diffrn_radiation.probe. ; _description.common 'RadType' _name.category_id diffrn_radiation _name.object_id type _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail Cu 'Copper tube' Mo 'Molybdinum tube' Ag 'Silver tube' white 'unfiltered radiation' synch 'synchrotron radiation' save_ save_diffrn_radiation.xray_symbol _definition.id '_diffrn_radiation.xray_symbol' _definition.update 2006-12-14 _description.text ; IUPAC symbol for the X-ray wavelength for probe radiation. ; _description.common 'RadXraySymbol' _name.category_id diffrn_radiation _name.object_id xray_symbol _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail K-L~3~ 'K\a~1~ in older Siegbahn notation' K-L~2~ 'K\a~2~ in older Siegbahn notation' K-M~3~ 'K\b~1~ in older Siegbahn notation' K-L~2,3~ 'use where K-L~3~ and K-L~2~ are not resolved' _enumeration.default K-L~3~ save_ save_DIFFRN_RADIATION_WAVELENGTH _definition.id diffrn_radiation_wavelength _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; 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. ; _category.parent_id diffrn_radiation _category_key.generic '_diffrn_radiation_wavelength.key' save_ save_diffrn_radiation_wavelength.key _definition.id '_diffrn_radiation_wavelength.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_RADIATION_WAVELENGTH items in a looped list. ; _description.common 'Key to radiation wavelengths' _name.category_id diffrn_radiation_wavelength _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_radiation_wavelength.key = _diffrn_radiation_wavelength.id ; save_ save_diffrn_radiation_wavelength.value _definition.id '_diffrn_radiation_wavelength.value' _definition.update 2006-12-14 # _alias.definition_id '_diffrn_radiation_wavelength' #Now a category!! _description.text ; Wavelength of radiation used in diffraction measurements. ; _description.common 'RadWaveLength' _name.category_id diffrn_radiation_wavelength _name.object_id value _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_diffrn_radiation_wavelength.id _definition.id '_diffrn_radiation_wavelength.id' _definition.update 2008-06-19 _description.text ; Name identifying a radiation used in the diffraction measurements. This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id ; _description.common 'RadWaveLengthId' _name.category_id diffrn_radiation_wavelength _name.object_id id _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case "x2" save_ save_diffrn_radiation_wavelength.wt _definition.id '_diffrn_radiation_wavelength.wt' _definition.update 2006-12-14 _description.text ; Relative intensity of a radiation used in the diffraction measurements. ; _description.common 'RadWaveLengthWeight' _name.category_id diffrn_radiation_wavelength _name.object_id wt _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0.0:1.0 _enumeration.default 1.0 save_ save_DIFFRN_REFLN _definition.id diffrn_refln _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the reflection measurements, prior to data reduction and merging. ; _description.common 'Measured reflection data' _category.parent_id diffrn _category_key.generic '_diffrn_refln.key' save_ save_diffrn_refln.key _definition.id '_diffrn_refln.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_REFLN items in a looped list. ; _description.common 'Key to measured reflection data' _name.category_id diffrn_refln _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_refln.key = _diffrn_refln.hkl ; save_ save_diffrn_refln.angle_chi _definition.id '_diffrn_refln.angle_chi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_chi save_ save_diffrn_refln.angle_kappa _definition.id '_diffrn_refln.angle_kappa' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_kappa save_ save_diffrn_refln.angle_omega _definition.id '_diffrn_refln.angle_omega' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_omega save_ save_diffrn_refln.angle_phi _definition.id '_diffrn_refln.angle_phi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_phi save_ save_diffrn_refln.angle_psi _definition.id '_diffrn_refln.angle_psi' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_psi save_ save_diffrn_refln.angle_theta _definition.id '_diffrn_refln.angle_theta' _definition.update 2006-06-29 _description.text ; A diffractometer angle value. ; _type.purpose Observed _type.container Single _type.contents Real _units.code degrees _enumeration.range -180.:180. _name.category_id diffrn_refln _name.object_id angle_theta save_ save_diffrn_refln.attenuator_code _definition.id '_diffrn_refln.attenuator_code' _definition.update 2008-06-19 _description.text ; Name identifying any attenuator setting for this reflection. ; _description.common 'DiffrnReflnAttenCode' _name.category_id diffrn_refln _name.object_id attenuator_code _name.linked_item_id '_diffrn_attenuator.code' _type.purpose Link _type.container Single _type.contents Text save_ save_diffrn_refln.class_code _definition.id '_diffrn_refln.class_code' _definition.update 2008-06-19 _description.text ; Name identifying a relection class, if assigned. e.g. modulated structures ; _description.common 'DiffrnReflnClass' _name.category_id diffrn_refln _name.object_id class_code _name.linked_item_id '_diffrn_reflns_class.code' _type.purpose Link _type.container Single _type.contents Text save_ save_diffrn_refln.counts_bg_1 _definition.id '_diffrn_refln.counts_bg_1' _definition.update 2006-06-29 _description.text ; The set of data items which specify the diffractometer counts. Background counts before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; _type.purpose Observed _type.container Single _type.contents Integer _enumeration.range 0: _name.category_id diffrn_refln _name.object_id counts_bg_1 _description.common 'DiffrnReflnCountsBg1' save_ save_diffrn_refln.counts_bg_2 _definition.id '_diffrn_refln.counts_bg_2' _definition.update 2006-06-29 _description.text ; The set of data items which specify the diffractometer counts. Background counts before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; _type.purpose Observed _type.container Single _type.contents Integer _enumeration.range 0: _name.category_id diffrn_refln _name.object_id counts_bg_2 _description.common 'DiffrnReflnCountsBg2' save_ save_diffrn_refln.counts_net _definition.id '_diffrn_refln.counts_net' _definition.update 2006-06-29 _description.text ; The set of data items which specify the diffractometer counts. Background counts before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; _type.purpose Observed _type.container Single _type.contents Integer _enumeration.range 0: _name.category_id diffrn_refln _name.object_id counts_net _description.common 'DiffrnReflnCountsNet' save_ save_diffrn_refln.counts_peak _definition.id '_diffrn_refln.counts_peak' _definition.update 2006-06-29 _description.text ; The set of data items which specify the diffractometer counts. Background counts before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; _type.purpose Observed _type.container Single _type.contents Integer _enumeration.range 0: _name.category_id diffrn_refln _name.object_id counts_peak _description.common 'DiffrnReflnCountsPeak' save_ save_diffrn_refln.counts_total _definition.id '_diffrn_refln.counts_total' _definition.update 2006-06-29 _description.text ; The set of data items which specify the diffractometer counts. Background counts before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; _type.purpose Observed _type.container Single _type.contents Integer _enumeration.range 0: _name.category_id diffrn_refln _name.object_id counts_total _description.common 'DiffrnReflnCountsTotal' save_ save_diffrn_refln.crystal_id _definition.id '_diffrn_refln.crystal_id' _definition.update 2008-06-19 _description.text ; Name identifying each crystal if multiple crystals are used. ; _description.common 'DiffrnReflnCrystalId' _name.category_id diffrn_refln _name.object_id crystal_id _name.linked_item_id '_exptl_crystal.id' _type.purpose Link _type.container Single _type.contents Text save_ save_diffrn_refln.detect_slit_horiz _definition.id '_diffrn_refln.detect_slit_horiz' _definition.update 2006-12-14 _description.text ; Total slit aperture angle in the diffraction plane. ; _description.common 'DiffrnReflnDetectSlitHoriz' _name.category_id diffrn_refln _name.object_id detect_slit_horiz _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_diffrn_refln.detect_slit_vert _definition.id '_diffrn_refln.detect_slit_vert' _definition.update 2006-12-14 _description.text ; Total slit aperture angle perpendicular to the diffraction plane. ; _description.common 'DiffrnReflnDetectSlitVert' _name.category_id diffrn_refln _name.object_id detect_slit_vert _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_diffrn_refln.elapsed_time _definition.id '_diffrn_refln.elapsed_time' _definition.update 2006-12-14 _description.text ; Elapsed time from the start to the end of the intensity measurement. ; _description.common 'DiffrnReflnElapseTime' _name.category_id diffrn_refln _name.object_id elapsed_time _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code minutes save_ save_diffrn_refln.hkl _definition.id '_diffrn_refln.hkl' _definition.update 2008-06-18 _description.text ; 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. ; _description.common 'DiffrnReflnHkl' _name.category_id diffrn_refln _name.object_id hkl _type.purpose Identify _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With a as diffrn_refln _diffrn_refln.hkl = Array ( [a.index_h, a.index_h, a.index_l] ) ; save_ save_diffrn_refln.index_h _definition.id '_diffrn_refln.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_refln _name.object_id index_h save_ save_diffrn_refln.index_k _definition.id '_diffrn_refln.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_refln _name.object_id index_k save_ save_diffrn_refln.index_l _definition.id '_diffrn_refln.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_refln _name.object_id index_l save_ save_diffrn_refln.intensity_net _definition.id '_diffrn_refln.intensity_net' _definition.update 2006-12-14 _description.text ; Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _description.common 'DiffrnReflnInet' _name.category_id diffrn_refln _name.object_id intensity_net _type.purpose Measured _type.container Single _type.contents Real save_ save_diffrn_refln.scale_group_code _definition.id '_diffrn_refln.scale_group_code' _definition.update 2008-06-19 _description.text ; Name identifying the scale applying to this reflection. ; _description.common 'DiffrnReflnScaleGroup' _name.category_id diffrn_refln _name.object_id scale_group_code _name.linked_item_id '_diffrn_scale_group.code' _type.purpose Link _type.container Single _type.contents Text save_ save_diffrn_refln.scan_mode _definition.id '_diffrn_refln.scan_mode' _definition.update 2006-12-14 _description.text ; Code identifying the mode of scanning with a diffractometer. See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. ; _description.common 'DiffrnReflnScanMode' _name.category_id diffrn_refln _name.object_id scan_mode _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail om 'omega scan' ot 'omega/2theta scan' q 'Q-scans (arbitrary reciprocal directions)' _enumeration.default ot save_ save_diffrn_refln.scan_mode_backgd _definition.id '_diffrn_refln.scan_mode_backgd' _definition.update 2006-12-14 _description.text ; Code identifying mode of scanning to measure the background intensity. ; _description.common 'DiffrnReflnScanModeBgd' _name.category_id diffrn_refln _name.object_id scan_mode_backgd _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail st 'stationary counter background' mo 'moving counter background' _enumeration.default st save_ save_diffrn_refln.scan_rate _definition.id '_diffrn_refln.scan_rate' _definition.update 2006-12-14 _description.text ; Angular rate of scanning a reflection to measure the intensity. ; _description.common 'DiffrnReflnScanRate' _name.category_id diffrn_refln _name.object_id scan_rate _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code degrees_per_minute save_ save_diffrn_refln.scan_time_backgd _definition.id '_diffrn_refln.scan_time_backgd' _definition.update 2006-12-14 _description.text ; Time spent measuring background counts. ; _description.common 'DiffrnReflnScanTimeBgd' _name.category_id diffrn_refln _name.object_id scan_time_backgd _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code seconds save_ save_diffrn_refln.scan_width _definition.id '_diffrn_refln.scan_width' _definition.update 2006-12-14 _description.text ; Angular scan width when measuring the peak intensity. ; _description.common 'DiffrnReflnScanWidth' _name.category_id diffrn_refln _name.object_id scan_width _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_diffrn_refln.sin_theta_over_lambda _definition.id '_diffrn_refln.sin_theta_over_lambda' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_refln.sint/lambda' _description.text ; (sin theta)/lambda value for this reflection. ; _description.common 'DiffrnReflnSinTheta/Lambda' _name.category_id diffrn_refln _name.object_id sin_theta_over_lambda _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code reciprocal_angstroms save_ save_diffrn_refln.standard_code _definition.id '_diffrn_refln.standard_code' _definition.update 2008-06-19 _description.text ; Name identifying if reflection was measured as a standard intensity. Must be '.' or match one of the _diffrn_standard_refln.code values. ; _description.common 'DiffrnReflnStandCode' _name.category_id diffrn_refln _name.object_id standard_code _name.linked_item_id '_diffrn_standard_refln.code' _type.purpose Link _type.container Single _type.contents Text save_ save_diffrn_refln.wavelength _definition.id '_diffrn_refln.wavelength' _definition.update 2006-12-14 _description.text ; Mean wavelength of radiation used to measure this intensity. ; _description.common 'DiffrnReflnWaveLength' _name.category_id diffrn_refln _name.object_id wavelength _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_diffrn_refln.wavelength_id _definition.id '_diffrn_refln.wavelength_id' _definition.update 2008-06-19 _description.text ; Name identifying the wavelength in the diffrn_radiation_wavelength list. ; _description.common 'DiffrnReflnRadId' _name.category_id diffrn_refln _name.object_id wavelength_id _name.linked_item_id '_diffrn_radiation_wavelength.id' _type.purpose Link _type.container Single _type.contents Text save_ save_DIFFRN_REFLNS _definition.id diffrn_reflns _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the overall reflection measurement information. ; _category.parent_id diffrn save_ save_diffrn_reflns.av_R_equivalents _definition.id '_diffrn_reflns.av_R_equivalents' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'DiffrnResid(EquivI)' _name.category_id diffrn_reflns _name.object_id av_R_equivalents _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_diffrn_reflns.av_sigmaI_over_netI _definition.id '_diffrn_reflns.av_sigmaI_over_netI' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_reflns.av_sigmaI/netI' _description.text ; Measured [sum su(net I)|/sum|net I|] for all measured reflections. ; _description.common 'DiffrnRatio(sigI/netI)' _name.category_id diffrn_reflns _name.object_id av_sigmaI_over_netI _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_diffrn_reflns.fraction_theta_full _definition.id '_diffrn_reflns.fraction_theta_full' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn.measured_fraction_theta_full' _description.text ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns.theta_full. ; _description.common 'DiffrnCompletionThetaFull' _name.category_id diffrn_reflns _name.object_id fraction_theta_full _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0:1.0 save_ save_diffrn_reflns.fraction_theta_max _definition.id '_diffrn_reflns.fraction_theta_max' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn.measured_fraction_theta_max' _description.text ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns.theta_max. ; _description.common 'DiffrnCompletionThetaMax' _name.category_id diffrn_reflns _name.object_id fraction_theta_max _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0:1.0 save_ save_diffrn_reflns.limit_h_max _definition.id '_diffrn_reflns.limit_h_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_h_max save_ save_diffrn_reflns.limit_h_min _definition.id '_diffrn_reflns.limit_h_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_h_min save_ save_diffrn_reflns.limit_k_max _definition.id '_diffrn_reflns.limit_k_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_k_max save_ save_diffrn_reflns.limit_k_min _definition.id '_diffrn_reflns.limit_k_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_k_min save_ save_diffrn_reflns.limit_l_max _definition.id '_diffrn_reflns.limit_l_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_l_max save_ save_diffrn_reflns.limit_l_min _definition.id '_diffrn_reflns.limit_l_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_reflns _name.object_id limit_l_min save_ save_diffrn_reflns.number _definition.id '_diffrn_reflns.number' _definition.update 2006-12-14 _description.text ; Total number of measured intensities, excluding reflections that are classed as systematically absent arising from translational symmetry in the crystal unit cell. ; _description.common 'DiffrnReflnsCount' _name.category_id diffrn_reflns _name.object_id number _type.purpose Measured _type.container Single _type.contents Count _enumeration.range 0: save_ save_diffrn_reflns.reduction_process _definition.id '_diffrn_reflns.reduction_process' _definition.update 2006-12-14 _description.text ; Description of how intensities were reduced to structure-factor magnitudes. ; _description.common 'DiffrnReflnsReductionDetails' _name.category_id diffrn_reflns _name.object_id reduction_process _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'data averaged using Fisher test' save_ save_diffrn_reflns.theta_full _definition.id '_diffrn_reflns.theta_full' _definition.update 2006-12-14 _description.text ; 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_reflns.fraction_theta_full. ; _description.common 'DiffrnThetaFull' _name.category_id diffrn_reflns _name.object_id theta_full _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_diffrn_reflns.theta_max _definition.id '_diffrn_reflns.theta_max' _definition.update 2006-12-14 _description.text ; Maximum theta angle of the measured reflections. ; _description.common 'DiffrnThetaMax' _name.category_id diffrn_reflns _name.object_id theta_max _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_diffrn_reflns.theta_min _definition.id '_diffrn_reflns.theta_min' _definition.update 2006-12-14 _description.text ; Minimum theta angle of the measured reflections. ; _description.common 'DiffrnThetaMin' _name.category_id diffrn_reflns _name.object_id theta_min _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:90.0 _units.code degrees save_ save_DIFFRN_REFLNS_TRANSF_MATRIX _definition.id diffrn_reflns_transf_matrix _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; 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| ; _category.parent_id diffrn_reflns save_ save_diffrn_reflns_transf_matrix.TIJ _definition.id '_diffrn_reflns_transf_matrix.TIJ' _definition.update 2008-06-24 _description.text ; 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| ; _description.common 'DiffrnReflnsTransformMatrix' _name.category_id diffrn_reflns_transf_matrix _name.object_id TIJ _type.purpose Observed _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With t as diffrn_reflns_transf_matrix _diffrn_reflns_transf_matrix.TIJ = Array ([[t.11, t.12, t.13], [t.21, t.22, t.23], [t.31, t.32, t.33]]) ; save_ save_diffrn_reflns_transf_matrix.11 _definition.id '_diffrn_reflns_transf_matrix.11' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 11 save_ save_diffrn_reflns_transf_matrix.12 _definition.id '_diffrn_reflns_transf_matrix.12' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 12 save_ save_diffrn_reflns_transf_matrix.13 _definition.id '_diffrn_reflns_transf_matrix.13' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 13 save_ save_diffrn_reflns_transf_matrix.21 _definition.id '_diffrn_reflns_transf_matrix.21' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 21 save_ save_diffrn_reflns_transf_matrix.22 _definition.id '_diffrn_reflns_transf_matrix.22' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 22 save_ save_diffrn_reflns_transf_matrix.23 _definition.id '_diffrn_reflns_transf_matrix.23' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 23 save_ save_diffrn_reflns_transf_matrix.31 _definition.id '_diffrn_reflns_transf_matrix.31' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 31 save_ save_diffrn_reflns_transf_matrix.32 _definition.id '_diffrn_reflns_transf_matrix.32' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 32 save_ save_diffrn_reflns_transf_matrix.33 _definition.id '_diffrn_reflns_transf_matrix.33' _definition.update 2006-06-29 _description.text ; The set of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. ; _type.purpose Observed _type.container Single _type.contents Real _name.category_id diffrn_reflns_transf_matrix _name.object_id 33 save_ save_DIFFRN_REFLNS_CLASS _definition.id diffrn_reflns_class _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify different classes of reflections in the raw measured diffraction data. ; _category.parent_id diffrn_reflns _category_key.generic '_diffrn_reflns_class.key' save_ save_diffrn_reflns_class.key _definition.id '_diffrn_reflns_class.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_REFLNS_CLASS items in a looped list. ; _description.common 'Key to class of measured refns' _name.category_id diffrn_reflns_class _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_reflns_class.key = _diffrn_reflns_class.code ; save_ save_diffrn_reflns_class.av_R_eq _definition.id '_diffrn_reflns_class.av_R_eq' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'DiffrnShellResid(I)' _name.category_id diffrn_reflns_class _name.object_id av_R_eq _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_diffrn_reflns_class.av_uI_over_I _definition.id '_diffrn_reflns_class.av_uI_over_I' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_reflns_class.av_sgI/I' _description.text ; Measured [sum|su(net I)|/sum|net I|] for intensities in a reflection class. ; _description.common 'DiffrnShellRatio(suI/netI)' _name.category_id diffrn_reflns_class _name.object_id av_uI_over_I _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_diffrn_reflns_class.code _definition.id '_diffrn_reflns_class.code' _definition.update 2008-06-19 _description.text ; Name identifying a reflection class. ; _description.common 'DiffrnShellCode' _name.category_id diffrn_reflns_class _name.object_id code _type.purpose Assigned _type.container Single _type.contents Text loop_ _description_example.case "m2" save_ save_diffrn_reflns_class.description _definition.id '_diffrn_reflns_class.description' _definition.update 2006-12-14 _description.text ; Description of a reflection class. ; _description.common 'DiffrnShellDetails' _name.category_id diffrn_reflns_class _name.object_id description _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'm=1 first order satellites' save_ save_diffrn_reflns_class.d_res_high _definition.id '_diffrn_reflns_class.d_res_high' _definition.update 2006-12-14 _description.text ; Highest resolution in reflection class i.e. smallest d value in class. ; _description.common 'DiffrnShellResolHi' _name.category_id diffrn_reflns_class _name.object_id d_res_high _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_diffrn_reflns_class.d_res_low _definition.id '_diffrn_reflns_class.d_res_low' _definition.update 2006-12-14 _description.text ; Lowest resolution in reflection class i.e. largest d value in class. ; _description.common 'DiffrnShellResolLo' _name.category_id diffrn_reflns_class _name.object_id d_res_low _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_diffrn_reflns_class.number _definition.id '_diffrn_reflns_class.number' _definition.update 2006-12-14 _description.text ; Number of measured intensities for a reflection class, excluding the systematic absences arising from centring translations. ; _description.common 'DiffrnShellNumber' _name.category_id diffrn_reflns_class _name.object_id number _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_DIFFRN_SCALE_GROUP _definition.id diffrn_scale_group _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the groups of reflections in the raw measured diffraction data with different relative scales. ; _description.common 'ScaleGroupList' _category.parent_id diffrn_reflns _category_key.generic '_diffrn_scale_group.key' save_ save_diffrn_scale_group.key _definition.id '_diffrn_scale_group.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_SCALE_GROUP items in a looped list. ; _description.common 'Key to intensity scaling groups' _name.category_id diffrn_scale_group _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_scale_group.key = _diffrn_scale_group.code ; save_ save_diffrn_scale_group.code _definition.id '_diffrn_scale_group.code' _definition.update 2008-06-19 _description.text ; Name identifying a specific scale group of reflections. ; _description.common 'ScaleGroupCode' _name.category_id diffrn_scale_group _name.object_id code _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case "A" save_ save_diffrn_scale_group.I_net _definition.id '_diffrn_scale_group.I_net' _definition.update 2006-12-14 _description.text ; Scale for a specific measurement group of eflections. Is multiplied with the net intensity to place all intensities on a common scale. ; _description.common 'ScaleGroupInet' _name.category_id diffrn_scale_group _name.object_id I_net _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_DIFFRN_SOURCE _definition.id diffrn_source _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify information about the radiation source. ; _category.parent_id diffrn save_ save_diffrn_source.device _definition.id '_diffrn_source.device' _definition.update 2006-12-14 _description.text ; Identification of the device providing the source of radiation. ; _description.common 'RadSourceDevice' _name.category_id diffrn_source _name.object_id device _type.purpose State _type.container Single _type.contents Code loop_ _description_example.case 'sealed X-ray tube' 'nuclear reactor' 'spallation source' 'electron microscope' 'rotating-anode X-ray tube' 'synchrotron' save_ save_diffrn_source.current _definition.id '_diffrn_source.current' _definition.update 2006-12-14 _description.text ; Generator current at which the radiation source device was operated. ; _description.common 'RadSourceCurrent' _name.category_id diffrn_source _name.object_id current _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code milliamperes save_ save_diffrn_source.details _definition.id '_diffrn_source.details' _definition.update 2006-12-14 _description.text ; General description of the radiation source device. ; _description.common 'RadSourceDetails' _name.category_id diffrn_source _name.object_id details _type.purpose Describe _type.container Single _type.contents Text save_ save_diffrn_source.power _definition.id '_diffrn_source.power' _definition.update 2006-12-14 _description.text ; Generator power at which the radiation source device was operated. ; _description.common 'RadSourcePower' _name.category_id diffrn_source _name.object_id power _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kilowatts save_ save_diffrn_source.size _definition.id '_diffrn_source.size' _definition.update 2006-12-14 _description.text ; Description of the collimated source beam as viewed from the sample. ; _description.common 'RadSourceSize' _name.category_id diffrn_source _name.object_id size _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case '8mm x 0.4 mm fine-focus' 'broad focus' save_ save_diffrn_source.target _definition.id '_diffrn_source.target' _definition.update 2006-12-14 _description.text ; Chemical element symbol for the radiation source target (usually the anode). This can be used also for spallation sources. ; _description.common 'RadTargetElement' _name.category_id diffrn_source _name.object_id target _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail Ac Actinium Ag Silver Al Aluminum Am Americium Ar Argon As Arsenic At Astatine Au Gold B Boron Ba Barium Be Beryllium Bh Bohrium Bi Bismuth Bk Berkelium Br Bromine C Carbon Ca Calcium Cd Cadmium Ce Cerium Cf Californium Cl Chlorine Cm Curium Co Cobalt Cr Chromium Cs Cesium Cu Copper Db Dubnium Ds Darmstadtium Dy Dysprosium Er Erbium Es Einsteinium Eu Europium F Fluorine Fe Iron Fm Fermium Fr Francium Ga Gallium Gd Gadolinium Ge Germanium H Hydrogen He Helium Hf Hafnium Hg Mercury Ho Holmium Hs Hassium I Iodine In Indium Ir Iridium K Potassium Kr Krypton La Lanthanum Li Lithium Lr Lawrencium Lu Lutetium Md Mendelevium Mg Magnesium Mn Manganese Mo Molybdenum Mt Meitnerium N Nitrogen Na Sodium Ne Neon Nb Niobium Nd Neodymium Ni Nickel No Nobelium Np Neptunium O Oxygen Os Osmium P Phosphorus Pd Palladium Po Polonium Pb Lead Pt Platinum Pr Praseodymium Pm Promethium Pu Plutonium Pa Protactinium Ra Radium Rb Rubidium Re Rhenium Rf Rutherfordium Rh Rhodium Rn Radon Ru Ruthenium S Sulfur Sb Antimony Sc Scandium Se Selenium Sg Seaborgium Si Silicon Sm Samarium Sn Tin Sr Strontium Ta Tantalum Tb Terbium Tc Technetium Te Tellurium Th Thorium Ti Titanium Tl Thallium Tm Thulium U Uranium Uub Ununbium Uun Ununnilium Uuu Ununumium V Vanadium W Tungsten Xe Xenon Y Yttrium Yb Ytterbium Zn Zinc Zr Zirconium _enumeration.default C save_ save_diffrn_source.make _definition.id '_diffrn_source.make' _definition.update 2006-12-14 _description.text ; Description of the make, model or name of the source device. ; _description.common 'RadDeviceMake' _name.category_id diffrn_source _name.object_id make _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'NSLS beamline X8C' 'Rigaku RU200' save_ save_diffrn_source.voltage _definition.id '_diffrn_source.voltage' _definition.update 2006-12-14 _description.text ; Generator voltage at which the radiation source device was operated. ; _description.common 'RadSourceVoltage' _name.category_id diffrn_source _name.object_id voltage _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code kilovolts save_ save_DIFFRN_STANDARDS _definition.id diffrn_standards _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify information about the standard reflections used in the diffraction measurement process. ; _category.parent_id diffrn save_ save_diffrn_standards.decay_percent _definition.id '_diffrn_standards.decay_percent' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_standards.decay_%' _description.text ; 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. ; _description.common 'DiffrnStandDecay%' _name.category_id diffrn_standards _name.object_id decay_percent _type.purpose Measured _type.container Single _type.contents Real _enumeration.range :100 save_ save_diffrn_standards.interval_count _definition.id '_diffrn_standards.interval_count' _definition.update 2007-02-09 _description.text ; Reflection count between the standard reflection measurements. ; _description.common 'DiffrnStandIntCount' _name.category_id diffrn_standards _name.object_id interval_count _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: save_ save_diffrn_standards.interval_time _definition.id '_diffrn_standards.interval_time' _definition.update 2006-12-14 _description.text ; Time between the standard reflection measurements. ; _description.common 'DiffrnStandIntTime' _name.category_id diffrn_standards _name.object_id interval_time _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0.: _units.code seconds save_ save_diffrn_standards.number _definition.id '_diffrn_standards.number' _definition.update 2007-02-09 _description.text ; Count of unique standard reflections used in the diffraction measurements. ; _description.common 'DiffrnStandCount' _name.category_id diffrn_standards _name.object_id number _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: save_ save_diffrn_standards.scale_su _definition.id '_diffrn_standards.scale_su' _definition.update 2006-12-14 loop_ _alias.definition_id '_diffrn_standards.scale_sigma' _description.text ; Standard uncertainty (e.s.d.) of the individual mean standard scales applied to the intensity data. ; _description.common 'DiffrnStandScaleSu' _name.category_id diffrn_standards _name.object_id scale_su _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_DIFFRN_STANDARD_REFLN _definition.id diffrn_standard_refln _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; 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. ; _description.common 'StandReflnList' _category.parent_id diffrn_standards _category_key.generic '_diffrn_standard_refln.key' save_ save_diffrn_standard_refln.key _definition.id '_diffrn_standard_refln.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of DIFFRN_STANDARD_REFLN items in a looped list. ; _description.common 'Key to standard reflections list' _name.category_id diffrn_standard_refln _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _diffrn_standard_refln.key = _diffrn_standard_refln.code ; save_ save_diffrn_standard_refln.code _definition.id '_diffrn_standard_refln.code' _definition.update 2008-06-19 _description.text ; Name identifying a standard reflection indices. ; _description.common 'StandReflnCode' _name.category_id diffrn_standard_refln _name.object_id code _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case "s1" save_ save_diffrn_standard_refln.hkl _definition.id '_diffrn_standard_refln.hkl' _definition.update 2006-12-14 _description.text ; Miller indices of a standard reflection. ; _description.common 'StandReflnHkl' _name.category_id diffrn_standard_refln _name.object_id hkl _type.purpose Observed _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With d as diffrn_standard_refln _diffrn_standard_refln.hkl = Array ([d.index_h, d.index_h, d.index_l]) ; save_ save_diffrn_standard_refln.index_h _definition.id '_diffrn_standard_refln.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_standard_refln _name.object_id index_h save_ save_diffrn_standard_refln.index_k _definition.id '_diffrn_standard_refln.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_standard_refln _name.object_id index_k save_ save_diffrn_standard_refln.index_l _definition.id '_diffrn_standard_refln.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id diffrn_standard_refln _name.object_id index_l save_ save_REFLN _definition.id refln _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe the reflection data used in the refinement of a crystallographic structure model. ; _description.common 'ReflnList' _category.parent_id core_diffraction _category_key.generic '_refln.key' save_ save_refln.key _definition.id '_refln.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of REFLN items in a looped list. ; _description.common 'Key to refinement reflection list' _name.category_id refln _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _refln.key = _refln.hkl ; save_ save_refln.A_calc _definition.id '_refln.A_calc' _definition.update 2006-12-14 _description.text ; The calculated real structure-factor component A =|Fcalc|cos(phase) ; _description.common 'ReflnCalcA' _name.category_id refln _name.object_id A_calc _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _refln.A_calc = Real ( _refln.F_complex ) ; save_ save_refln.A_meas _definition.id '_refln.A_meas' _definition.update 2006-12-14 _description.text ; The measured real structure-factor component A =|Fmeas|cos(phase) ; _description.common 'ReflnMeasA' _name.category_id refln _name.object_id A_meas _type.purpose Measured _type.container Single _type.contents Real save_ save_refln.B_calc _definition.id '_refln.B_calc' _definition.update 2006-12-14 _description.text ; The calculated imaginary structure-factor component B =|Fcalc|sin(phase) ; _description.common 'ReflnCalcB' _name.category_id refln _name.object_id B_calc _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _refln.B_calc = Imag ( _refln.F_complex ) ; save_ save_refln.B_meas _definition.id '_refln.B_meas' _definition.update 2006-12-14 _description.text ; The measured imaginary structure-factor component B =|Fmeas|sin(phase) ; _description.common 'ReflnMeasB' _name.category_id refln _name.object_id B_meas _type.purpose Measured _type.container Single _type.contents Real save_ save_refln.class_code _definition.id '_refln.class_code' _definition.update 2008-06-19 _description.text ; Name 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. ; _description.common 'ReflnClassCode' _name.category_id refln _name.object_id class_code _name.linked_item_id '_reflns_class.code' _type.purpose Link _type.container Single _type.contents Text save_ save_refln.crystal_id _definition.id '_refln.crystal_id' _definition.update 2008-06-19 _description.text ; Code identifying each crystal if multiple crystals are used. Is used to link with crystals identified by _exptl_crystal.id. ; _description.common 'ReflnCrystalId' _name.category_id refln _name.object_id crystal_id _name.linked_item_id '_exptl_crystal.id' _type.purpose Link _type.container Single _type.contents Text save_ save_refln.d_spacing _definition.id '_refln.d_spacing' _definition.update 2006-12-14 _description.text ; The distance in angstroms between lattice planes in the crystal with the indices _refln.hkl for this reflection. ; _description.common 'ReflnDspacing' _name.category_id refln _name.object_id d_spacing _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; _refln.d_spacing = 2. / _refln.sin_theta_over_lambda ; save_ save_refln.F_calc _definition.id '_refln.F_calc' _definition.update 2006-12-14 _description.text ; The structure factor amplitude for the reflection calculated from the atom site data. ; _description.common 'ReflnCalcF' _name.category_id refln _name.object_id F_calc _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") {_units.code = "femtometres" } Else If (_diffrn_radiation.probe == "electron"){_units.code = "volts" } Else {_units.code = "electrons" } ; Evaluation ; _refln.F_calc = Magn ( _refln.F_complex ) ; save_ save_refln.F_complex _definition.id '_refln.F_complex' _definition.update 2006-12-14 _description.text ; The structure factor vector for the reflection calculated from the atom site data. ; _description.common 'ReflnComplexF' _name.category_id refln _name.object_id F_complex _type.purpose Measured _type.container Single _type.contents Complex loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") {_units.code = "femtometres" } Else If (_diffrn_radiation.probe == "electron"){_units.code = "volts" } Else {_units.code = "electrons" } ; Evaluation ; With r as refln fc = Complex (0., 0.) h = r.hkl bb = r.sin_theta_over_lambda **2 uu = 8*Pi**2 * bb Loop a as atom_site { x = a.fract_xyz f = ( r.form_factor_table [a.type_symbol] * a.symmetry_multiplicity * a.occupancy ) If (a.adp_type == 'uiso') t = Exp(-a.U_iso_or_equiv * uu) Else If (a.adp_type == 'biso') t = Exp(-a.B_iso_or_equiv * bb) Else u = a.matrix_beta Loop s as symmetry_equiv { If (a.adp_type == 'uani') t = Exp(-h * s.R * u * s.RT * h) fc += f * t * ExpImag( TwoPi * ( h * ( s.R * x + s.T))) } } _refln.F_complex = fc / _symmetry.multiplicity ; save_ save_refln.F_meas _definition.id '_refln.F_meas' _definition.update 2006-12-14 _description.text ; The structure factor amplitude for the reflection derived from the measured intensities. ; _description.common 'ReflnMeasF' _name.category_id refln _name.object_id F_meas _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") {_units.code = "femtometres" } Else If (_diffrn_radiation.probe == "electron"){_units.code = "volts" } Else {_units.code = "electrons" } ; Evaluation ; _refln.F_meas = Sqrt ( _refln.F_squared_meas ) ; save_ save_refln.F_sigma ## <<<<<<< to be discussed as a Measure issue _definition.id '_refln.F_sigma' _definition.update 2006-12-14 _description.text ; The standard uncertainty of the measured structure factor amplitude. This item has been replaced by the implicit su of _refln.F_meas. ; _description.common 'ReflnSigmaF' _name.category_id refln _name.object_id F_sigma _type.purpose Observed _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") {_units.code = "femtometres" } Else If (_diffrn_radiation.probe == "electron"){_units.code = "volts" } Else {_units.code = "electrons" } ; Evaluation ; _refln.F_sigma = _refln.F_squared_sigma / 2 ; save_ save_refln.F_squared_calc _definition.id '_refln.F_squared_calc' _definition.update 2006-12-14 _description.text ; The structure factor amplitude squared for the reflection calculated from the atom site data. ; _description.common 'ReflnCalcFsqd' _name.category_id refln _name.object_id F_squared_calc _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") { _units.code = "femtometres_squared" } Else If (_diffrn_radiation.probe == "electron") { _units.code = "volts_squared" } Else {_units.code = "electrons_squared" } ; Evaluation ; _refln.F_squared_calc = _refln.F_calc **2 ; save_ save_refln.F_squared_meas _definition.id '_refln.F_squared_meas' _definition.update 2006-12-14 _description.text ; The structure factor amplitude for the reflection derived from the measured intensities. ; _description.common 'ReflnMeasFsqd' _name.category_id refln _name.object_id F_squared_meas _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") { _units.code = "femtometres_squared" } Else If (_diffrn_radiation.probe == "electron") { _units.code = "volts_squared" } Else {_units.code = "electrons_squared" } ; Evaluation ; _refln.F_squared_meas = _refln.F_meas **2 ; save_ save_refln.F_squared_sigma ## <<<<<<<<< discuss as a Measure issue _definition.id '_refln.F_squared_sigma' _definition.update 2006-12-14 _description.text ; The standard uncertainty of the measured structure factor squared. This item has been replaced by the implicit su of _refln.F_squared_meas. ; _name.category_id refln _name.object_id F_squared_sigma _type.purpose Observed _type.container Single _type.contents Real loop_ _method.purpose _method.expression Definition ; If (_diffrn_radiation.probe == "neutron") { _units.code = "femtometres_squared" } Else If (_diffrn_radiation.probe == "electron") { _units.code = "volts_squared" } Else {_units.code = "electrons_squared" } ; Evaluation ; _refln.F_squared_sigma = 2. * _refln.F_sigma ; save_ save_refln.form_factor_table _definition.id '_refln.form_factor_table' _definition.update 2006-12-14 _description.text ; Atomic scattering factor table for the scattering angle of this diffraction vector and atom types in structure. ; _description.common 'ReflnFormFactorTable' _name.category_id refln _name.object_id form_factor_table _type.purpose Assigned _type.container Table _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With r as refln table = Table () s = r.sin_theta_over_lambda Loop t as atom_type { If (_diffrn_radiation.probe == 'neutron') { f = t.length_neutron } Else If (s < 2.0 ) { c = t.Cromer_Mann_coeffs f = (c[0] + c[1] * Exp (-c[2] * s*s) + c[3] * Exp (-c[4] * s*s) + c[5] * Exp (-c[6] * s*s) + c[7] * Exp (-c[8] * s*s)) } Else { c = t.hi_ang_Fox_coeffs f = Exp ( c[0] + c[1]*s + c[2]*s*s + c[3]*s*s*s ) } table [ t.symbol ] = f } _refln.form_factor_table = table ; save_ save_refln.include_status _definition.id '_refln.include_status' _definition.update 2006-12-14 loop_ _alias.definition_id '_refln.observed_status' _description.text ; Code indicating how the reflection was included in the refinement and R-factor calculations. ; _description.common 'ReflnRefineInclusion' _name.category_id refln _name.object_id include_status _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail o 'included in all; > _reflns.threshold_expression; within d-res limits' < 'included partly; < _reflns.threshold_expression; within d-res limits' - 'systematically absent reflection' x 'unreliable measurement -- not used' h '> _refine_ls.d_res_high' l '< _refine_ls.d_res_low' _enumeration.default o save_ save_refln.hkl _definition.id '_refln.hkl' _definition.update 2008-06-18 _description.text ; The Miller indices as a reciprocal space vector. ; _description.common 'ReflnHkl' _name.category_id refln _name.object_id hkl _type.purpose Identify _type.container Array _type.contents Integer loop_ _method.purpose _method.expression Evaluation ; With r as refln _refln.hkl = Array ( [r.index_h, r.index_k, r.index_l] ) ; save_ save_refln.index_h _definition.id '_refln.index_h' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id refln _name.object_id index_h save_ save_refln.index_k _definition.id '_refln.index_k' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id refln _name.object_id index_k save_ save_refln.index_l _definition.id '_refln.index_l' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id refln _name.object_id index_l save_ save_refln.intensity_calc _definition.id '_refln.intensity_calc' _definition.update 2006-12-14 _description.text ; The intensity of the reflection calculated from the atom site data. ; _description.common 'ReflnCalcI' _name.category_id refln _name.object_id intensity_calc _type.purpose Measured _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; _refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor ; save_ save_refln.intensity_meas _definition.id '_refln.intensity_meas' _definition.update 2006-12-14 _description.text ; The intensity of the reflection derived from the diffraction measurements. ; _description.common 'ReflnMeasI' _name.category_id refln _name.object_id intensity_meas _type.purpose Measured _type.container Single _type.contents Real save_ save_refln.Lp_factor _definition.id '_refln.Lp_factor' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnLpFactor' _name.category_id refln _name.object_id Lp_factor _type.purpose Measured _type.container Single _type.contents Real save_ save_refln.mean_path_length_tbar _definition.id '_refln.mean_path_length_tbar' _definition.update 2006-12-14 _description.text ; Mean path length through the crystal for this diffraction vector. ; _description.common 'ReflnMeanPathLength' _name.category_id refln _name.object_id mean_path_length_tbar _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code millimetres save_ save_refln.phase_calc _definition.id '_refln.phase_calc' _definition.update 2006-12-14 _description.text ; The phase of the calculated structure-factor. ; _description.common 'ReflnCalcPhase' _name.category_id refln _name.object_id phase_calc _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; _refln.phase_calc = Atan2d ( _refln.B_calc, _refln.A_calc ) ; save_ save_refln.phase_meas _definition.id '_refln.phase_meas' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnMeasPhase' _name.category_id refln _name.object_id phase_meas _type.purpose Measured _type.container Single _type.contents Real _units.code degrees save_ save_refln.refinement_status _definition.id '_refln.refinement_status' _definition.update 2006-12-14 _description.text ; Status code of reflection in the structure refinement process. ; _description.common 'ReflnRefineStatus' _name.category_id refln _name.object_id refinement_status _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction' _enumeration.default incl save_ save_refln.scale_group_code _definition.id '_refln.scale_group_code' _definition.update 2008-06-19 _description.text ; Name identifying the scale (if there is more than one scale) used convert the measured structure factor to a common absolute value. ; _description.common 'ReflnScaleCode' _name.category_id refln _name.object_id scale_group_code _name.linked_item_id '_reflns_scale.group_code' _type.purpose Link _type.container Single _type.contents Text save_ save_refln.sin_theta_over_lambda _definition.id '_refln.sin_theta_over_lambda' _definition.update 2006-12-14 loop_ _alias.definition_id '_refln.sint/lambda' _description.text ; The (sin theta)/lambda value for this reflection. ; _description.common 'ReflnSinTheta/Lambda' _name.category_id refln _name.object_id sin_theta_over_lambda _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code reciprocal_angstroms loop_ _method.purpose _method.expression Evaluation ; With r as refln h = r.hkl G = _cell_reciprocal.metric_tensor r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2. ; save_ save_refln.symmetry_epsilon _definition.id '_refln.symmetry_epsilon' _definition.update 2006-12-14 _description.text ; The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. ; _description.common 'ReflnSymmetryEpsilon' _name.category_id refln _name.object_id symmetry_epsilon _type.purpose Observed _type.container Single _type.contents Index _enumeration.range 1:48 save_ save_refln.symmetry_multiplicity _definition.id '_refln.symmetry_multiplicity' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnSymmetryMultiplicity' _name.category_id refln _name.object_id symmetry_multiplicity _type.purpose Observed _type.container Single _type.contents Index _enumeration.range 1:48 save_ save_refln.wavelength _definition.id '_refln.wavelength' _definition.update 2006-12-14 _description.text ; The mean wavelength in angstroms of radiation used to measure this reflection. This is an template_idarameter for data collected using energy-dispersive detectors or the Laue method. ; _description.common 'ReflnWavelength' _name.category_id refln _name.object_id wavelength _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_refln.wavelength_id _definition.id '_refln.wavelength_id' _definition.update 2008-06-19 _description.text ; Name identifying the wavelength in the DIFFRN_RADIATION_WAVELENGTH list. ; _description.common 'ReflnWavelengthId' _name.category_id refln _name.object_id wavelength_id _name.linked_item_id '_diffrn_radiation_wavelength.id' _type.purpose Link _type.container Single _type.contents Text save_ save_REFLNS _definition.id reflns _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; 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 simmilar 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.parent_id core_diffraction save_ save_reflns.d_resolution_high _definition.id '_reflns.d_resolution_high' _definition.update 2006-12-14 _description.text ; Highest resolution for the final REFLN data set. This corresponds to the smallest interpanar d value. ; _description.common 'ReflnsResolHigh' _name.category_id reflns _name.object_id d_resolution_high _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns.d_resolution_low _definition.id '_reflns.d_resolution_low' _definition.update 2006-12-14 _description.text ; Lowest resolution for the final REFLN data set. This corresponds to the largest interpanar d value. ; _description.common 'ReflnsResolLow' _name.category_id reflns _name.object_id d_resolution_low _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns.Friedel_coverage _definition.id '_reflns.Friedel_coverage' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnsFriedelCoverage' _name.category_id reflns _name.object_id Friedel_coverage _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_reflns.limit_h_max _definition.id '_reflns.limit_h_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_h_max save_ save_reflns.limit_h_min _definition.id '_reflns.limit_h_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_h_min save_ save_reflns.limit_k_max _definition.id '_reflns.limit_k_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_k_max save_ save_reflns.limit_k_min _definition.id '_reflns.limit_k_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_k_min save_ save_reflns.limit_l_max _definition.id '_reflns.limit_l_max' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_l_max save_ save_reflns.limit_l_min _definition.id '_reflns.limit_l_min' _definition.update 2008-06-18 _description.text ; The index of a reciprocal space vector. ; _type.purpose Identify _type.container Single _type.contents Integer _name.category_id reflns _name.object_id limit_l_min save_ save_reflns.number_gt _definition.id '_reflns.number_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns.number_observed' _description.text ; 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 to the nature of the structure and the procedures used. ; _description.common 'ReflnsGtCount' _name.category_id reflns _name.object_id number_gt _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns.number_total _definition.id '_reflns.number_total' _definition.update 2006-12-14 _description.text ; 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 to the nature of the structure and the procedures used. ; _description.common 'ReflnsTotalCount' _name.category_id reflns _name.object_id number_total _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns.special_details _definition.id '_reflns.special_details' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnsSpecialDetails' _name.category_id reflns _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text save_ save_reflns.threshold_expression _definition.id '_reflns.threshold_expression' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns.observed_criterion' _description.text ; 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. ; _description.common 'ReflnsThesholdExpression' _name.category_id reflns _name.object_id threshold_expression _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'I>2u(I)' save_ save_REFLNS_CLASS _definition.id reflns_class _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the properties of reflections in specific classes of reflections. ; _category.parent_id reflns _category_key.generic '_reflns_class.key' save_ save_reflns_class.key _definition.id '_reflns_class.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of REFLNS_CLASS items in a looped list. ; _description.common 'Key to reflection classes' _name.category_id reflns_class _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _reflns_class.key = _reflns_class.code ; save_ save_reflns_class.code _definition.id '_reflns_class.code' _definition.update 2008-06-19 _description.text ; Name identifying a reflection class. ; _description.common 'ReflnsClassCode' _name.category_id reflns_class _name.object_id code _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case 'c1' save_ save_reflns_class.description _definition.id '_reflns_class.description' _definition.update 2006-12-14 _description.text ; Description of a reflection class. ; _description.common 'ReflnsClassDetails' _name.category_id reflns_class _name.object_id description _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'H0L0 common projection reflections' save_ save_reflns_class.d_res_high _definition.id '_reflns_class.d_res_high' _definition.update 2006-12-14 _description.text ; Highest resolution for the reflections in this class. This corresponds to the smallest interpanar d value. ; _description.common 'ReflnsClassResolHigh' _name.category_id reflns_class _name.object_id d_res_high _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns_class.d_res_low _definition.id '_reflns_class.d_res_low' _definition.update 2006-12-14 _description.text ; Lowest resolution for the reflections in this class. This corresponds to the largest interpanar d value. ; _description.common 'ReflnsClassResolLow' _name.category_id reflns_class _name.object_id d_res_low _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns_class.number_gt _definition.id '_reflns_class.number_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_class.number_observed' _description.text ; 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 to the nature of the structure and the procedures used. ; _description.common 'ReflnsClassGtCount' _name.category_id reflns_class _name.object_id number_gt _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_class.number_total _definition.id '_reflns_class.number_total' _definition.update 2006-12-14 _description.text ; 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 to the nature of the structure and the procedures used. ; _description.common 'ReflnsClassTotalCount' _name.category_id reflns_class _name.object_id number_total _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_class.R_factor_all _definition.id '_reflns_class.R_factor_all' _definition.update 2006-12-14 _description.text ; Residual factor for reflections in this class included in the refinement. See _refine_ls.R_factor_all definition for details. ; _description.common 'ReflnsClassR(F)All' _name.category_id reflns_class _name.object_id R_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_class.R_factor_gt _definition.id '_reflns_class.R_factor_gt' _definition.update 2006-12-14 _description.text ; Residual factor for the reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_factor_all definition for details. ; _description.common 'ReflnsClassR(F)Gt' _name.category_id reflns_class _name.object_id R_factor_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_class.R_Fsqd_factor _definition.id '_reflns_class.R_Fsqd_factor' _definition.update 2006-12-14 _description.text ; Residual factor R(F^2^) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_Fsqd_factor definition for details. ; _description.common 'ReflnsClassR(Fsqd)Gt' _name.category_id reflns_class _name.object_id R_Fsqd_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_class.R_I_factor _definition.id '_reflns_class.R_I_factor' _definition.update 2006-12-14 _description.text ; Residual factor R(I) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_I_factor definition for details. ; _description.common 'ReflnsClassR(I)Gt' _name.category_id reflns_class _name.object_id R_I_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_class.wR_factor_all _definition.id '_reflns_class.wR_factor_all' _definition.update 2006-12-14 _description.text ; Weight residual for all reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.wR_factor_all definition for details. ; _description.common 'ReflnsClassWR(F)All' _name.category_id reflns_class _name.object_id wR_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_REFLNS_SCALE _definition.id reflns_scale _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the scales needed to place measured structure factor coefficients on the same absolute scale. ; _category.parent_id reflns _category_key.generic '_reflns_scale.key' save_ save_reflns_scale.key _definition.id '_reflns_scale.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of REFLNS_SCALE items in a looped list. ; _description.common 'Key to reflection scale groups' _name.category_id reflns_scale _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _reflns_scale.key = _reflns_scale.group_code ; save_ save_reflns_scale.group_code _definition.id '_reflns_scale.group_code' _definition.update 2008-06-19 _description.text ; Name identifying a reflection scale group. These names need not correspond to _diffrn_scale_group.code names. ; _description.common 'ReflnsScaleCode' _name.category_id reflns_scale _name.object_id group_code _type.purpose Identify _type.container Single _type.contents Text save_ save_reflns_scale.meas_F _definition.id '_reflns_scale.meas_F' _definition.update 2006-12-14 _description.text ; Structure factor scale for this scale group. ; _description.common 'ReflnsScaleMeasF' _name.category_id reflns_scale _name.object_id meas_F _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_scale.meas_F_squared _definition.id '_reflns_scale.meas_F_squared' _definition.update 2006-12-14 _description.text ; Structure factor squared scale for this scale group. ; _description.common 'ReflnsScaleMeasFsqd' _name.category_id reflns_scale _name.object_id meas_F_squared _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_reflns_scale.meas_intensity _definition.id '_reflns_scale.meas_intensity' _definition.update 2006-12-14 _description.text ; Net intensity scale for this scale group. ; _description.common 'ReflnsScaleMeasI' _name.category_id reflns_scale _name.object_id meas_intensity _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_REFLNS_SHELL _definition.id reflns_shell _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items which specify the information about reflections divided into shells bounded by d resolution limits. ; _category.parent_id reflns _category_key.generic '_reflns_shell.key' save_ save_reflns_shell.key _definition.id '_reflns_shell.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of REFLNS_SHELL items in a looped list. ; _description.common 'Key to reflection shells' _name.category_id reflns_shell _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _reflns_shell.key = _reflns_shell.d_res_limits ; save_ save_reflns_shell.d_res_high _definition.id '_reflns_shell.d_res_high' _definition.update 2006-12-14 _description.text ; Highest resolution for the reflections in this shell. This corresponds to the smallest interpanar d value. ; _description.common 'ReflnsShellResolHigh' _name.category_id reflns_shell _name.object_id d_res_high _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns_shell.d_res_limits _definition.id '_reflns_shell.d_res_limits' _definition.update 2006-12-14 _description.text ; Resolution for the reflections in this shell stored as the tuple of lowest and highest values. This is the category key. ; _description.common 'ReflnsShellResolLimits' _name.category_id reflns_shell _name.object_id d_res_limits _type.purpose Observed _type.container Tuple _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With s as reflns_shell _reflns_shell.d_res_limits = Tuple ( s.d_res_low, s.d_res_high ) ; save_ save_reflns_shell.d_res_low _definition.id '_reflns_shell.d_res_low' _definition.update 2006-12-14 _description.text ; Lowest resolution for the reflections in this shell. This corresponds to the largest interpanar d value. ; _description.common 'ReflnsShellResolLow' _name.category_id reflns_shell _name.object_id d_res_low _type.purpose Observed _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_reflns_shell.meanI_over_uI_all _definition.id '_reflns_shell.meanI_over_uI_all' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.meanI_over_sigI_all' _description.text ; Ratio of the mean intensity in a shell to the mean standard uncertainty of the intensities in the shell. ; _description.common 'ReflnsShellMean(I/suI)All' _name.category_id reflns_shell _name.object_id meanI_over_uI_all _type.purpose Measured _type.container Single _type.contents Real save_ save_reflns_shell.meanI_over_uI_gt _definition.id '_reflns_shell.meanI_over_uI_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.meanI_over_sigI_obs' '_reflns_shell.meanI_over_sigI_gt' _description.text ; 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. ; _description.common 'ReflnsShellMean(I/suI)Gt' _name.category_id reflns_shell _name.object_id meanI_over_uI_gt _type.purpose Measured _type.container Single _type.contents Real save_ save_reflns_shell.number_measured_all _definition.id '_reflns_shell.number_measured_all' _definition.update 2006-12-14 _description.text ; Total count of reflections measured for this resolution shell. ; _description.common 'ReflnsShellCountAll' _name.category_id reflns_shell _name.object_id number_measured_all _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_shell.number_measured_gt _definition.id '_reflns_shell.number_measured_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.number_measured_obs' _description.text ; Number of reflections measured for this resolution shell which are significantly intense (see _reflns.threshold_expression). ; _description.common 'ReflnsShellCountGt' _name.category_id reflns_shell _name.object_id number_measured_gt _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_shell.number_possible _definition.id '_reflns_shell.number_possible' _definition.update 2006-12-14 _description.text ; Count of symmetry-unique reflections possible in this reflection shell. ; _description.common 'ReflnsShellUniqueCountEst' _name.category_id reflns_shell _name.object_id number_possible _type.purpose Observed _type.container Single _type.contents Count save_ save_reflns_shell.number_unique_all _definition.id '_reflns_shell.number_unique_all' _definition.update 2006-12-14 _description.text ; Count of symmetry-unique reflections present in this reflection shell. ; _description.common 'ReflnsShellUniqueCountAll' _name.category_id reflns_shell _name.object_id number_unique_all _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_shell.number_unique_gt _definition.id '_reflns_shell.number_unique_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.number_unique_obs' _description.text ; Number of symmetry-unique reflections present in this reflection shell which are significantly intense (see _reflns.threshold_expression). ; _description.common 'ReflnsShellUniqueCountGt' _name.category_id reflns_shell _name.object_id number_unique_gt _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_reflns_shell.percent_possible_all _definition.id '_reflns_shell.percent_possible_all' _definition.update 2006-12-14 _description.text ; Percentage of reflections present in this shell over that possible. ; _description.common 'ReflnsShellCoverageAll' _name.category_id reflns_shell _name.object_id percent_possible_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:100.0 save_ save_reflns_shell.percent_possible_gt _definition.id '_reflns_shell.percent_possible_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.percent_possible_obs' _description.text ; Percentage of reflections present in this shell which are significantly intense (see _reflns.threshold_expression), over that possible. ; _description.common 'ReflnsShellCoverageGt' _name.category_id reflns_shell _name.object_id percent_possible_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:100.0 save_ save_reflns_shell.Rmerge_F_all _definition.id '_reflns_shell.Rmerge_F_all' _definition.update 2006-12-14 _description.text ; Rmerge(F) for all reflections in a given shell. sum~i~ ( sum~j~ | F~j~ - | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ ) F~j~ = the amplitude of the jth observation of reflection i = 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. ; _description.common 'ReflnsShellMergeR(F)All' _name.category_id reflns_shell _name.object_id Rmerge_F_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0 save_ save_reflns_shell.Rmerge_F_gt _definition.id '_reflns_shell.Rmerge_F_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.Rmerge_F_obs' _description.text ; 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. ; _description.common 'ReflnsShellMergeR(F)Gt' _name.category_id reflns_shell _name.object_id Rmerge_F_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0 save_ save_reflns_shell.Rmerge_I_all _definition.id '_reflns_shell.Rmerge_I_all' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'ReflnsShellMergeR(I)All' _name.category_id reflns_shell _name.object_id Rmerge_I_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0 save_ save_reflns_shell.Rmerge_I_gt _definition.id '_reflns_shell.Rmerge_I_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_reflns_shell.Rmerge_I_obs' _description.text ; 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. ; _description.common 'ReflnsShellMergeR(I)Gt' _name.category_id reflns_shell _name.object_id Rmerge_I_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0 save_ save_CORE_STRUCTURE _definition.id core_structure _definition.scope Category _definition.class Head _definition.update 2006-12-14 _description.text ; The DICTIONARY group encompassing the CORE STRUCTURE data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_core save_ save_ATOM_SITE _definition.id atom_site _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe atomic site information used in crystallographic structure studies. ; _description.common 'AtomSiteList' _category.parent_id core_structure _category_key.generic '_atom_site.key' save_ save_atom_site.key _definition.id '_atom_site.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of ATOM_SITE items in a looped list. ; _description.common 'Key to list of atomic sites' _name.category_id atom_site _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _atom_site.key = _atom_site.label ; save_ save_atom_site.adp_type _definition.id '_atom_site.adp_type' _definition.update 2006-12-14 loop_ _alias.definition_id '_atom_site.thermal_displace_type' _description.text ; Code for type of atomic displacement parameters used for the site. ; _description.common 'AtomSiteAdpType' _name.category_id atom_site _name.object_id adp_type _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' _enumeration.default Uiso save_ save_atom_site.attached_hydrogens _definition.id '_atom_site.attached_hydrogens' _definition.update 2006-12-14 _description.text ; The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given. ; _description.common 'AtomSiteAttachedH' _name.category_id atom_site _name.object_id attached_hydrogens _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0:8 _enumeration.default 0 loop_ _description_example.case _description_example.detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen' save_ save_atom_site.B_equiv_geom_mean _definition.id '_atom_site.B_equiv_geom_mean' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'AtomSiteBisoMean' _name.category_id atom_site _name.object_id B_equiv_geom_mean _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms_squared save_ save_atom_site.B_iso_or_equiv _definition.id '_atom_site.B_iso_or_equiv' _definition.update 2006-12-14 _description.text ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated from anisotropic temperature factor parameters. B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)] a = the real-space cell lengths a* = the reciprocal-space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _description.common 'AtomSiteBisoEquiv' _name.category_id atom_site _name.object_id B_iso_or_equiv _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms_squared save_ save_atom_site.calc_attached_atom _definition.id '_atom_site.calc_attached_atom' _definition.update 2006-12-14 _description.text ; The _atom_site.label of the atom site to which the 'geometry- calculated' atom site is attached. ; _description.common 'AtomSiteParentAtom' _name.category_id atom_site _name.object_id calc_attached_atom _name.linked_item_id '_atom_site.label' _type.purpose Link _type.container Single _type.contents Label save_ save_atom_site.calc_flag _definition.id '_atom_site.calc_flag' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'AtomSiteCalcStatus' _name.category_id atom_site _name.object_id calc_flag _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail d 'determined from diffraction measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates' _enumeration.default d save_ save_atom_site.Cartn_xyz _definition.id '_atom_site.Cartn_xyz' _definition.update 2006-12-14 _description.text ; Vector of Cartesian (orthogonal angstrom) atom site coordinates. ; _description.common 'AtomSiteCartnXyz' _name.category_id atom_site _name.object_id Cartn_xyz _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With a as atom_site _atom_site.Cartn_xyz = Array ( [a.Cartn_x, a.Cartn_y, a.Cartn_z] ) ; save_ save_atom_site.Cartn_x _definition.id '_atom_site.Cartn_x' _definition.update 2006-06-29 _description.text ; The atom site coordinates in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the _atom_sites_Cartn_transform.axes description. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms _name.category_id atom_site _name.object_id Cartn_x save_ save_atom_site.Cartn_y _definition.id '_atom_site.Cartn_y' _definition.update 2006-06-29 _description.text ; The atom site coordinates in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the _atom_sites_Cartn_transform.axes description. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms _name.category_id atom_site _name.object_id Cartn_y save_ save_atom_site.Cartn_z _definition.id '_atom_site.Cartn_z' _definition.update 2006-06-29 _description.text ; The atom site coordinates in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the _atom_sites_Cartn_transform.axes description. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms _name.category_id atom_site _name.object_id Cartn_z save_ save_atom_site.chemical_conn_number _definition.id '_atom_site.chemical_conn_number' _definition.update 2006-12-14 _description.text ; This number links an atom site to the chemical connectivity list. It must match a number specified by _chemical_conn_atom.number. ; _description.common 'AtomSiteChemConnLink' _name.category_id atom_site _name.object_id chemical_conn_number _name.linked_item_id '_chemical_conn_atom.number' _type.purpose Link _type.container Single _type.contents Index _enumeration.range 1: save_ save_atom_site.constraints _definition.id '_atom_site.constraints' _definition.update 2006-12-14 _description.text ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine_ls.number_constraints. ; _description.common 'AtomSiteConstraints' _name.category_id atom_site _name.object_id constraints _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'pop=1.0-pop(Zn3)' save_ save_atom_site.description _definition.id '_atom_site.description' _definition.update 2006-12-14 _description.text ; A description of special aspects of this site. See also _atom_site.refinement_flags. ; _description.common 'AtomSiteDetails' _name.category_id atom_site _name.object_id description _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'Ag/Si disordered' save_ save_atom_site.disorder_assembly _definition.id '_atom_site.disorder_assembly' _definition.update 2008-06-19 _description.text ; A code which identifies a cluster of atoms that show long range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. ; _description.common 'AtomSiteDisorderCode' _name.category_id atom_site _name.object_id disorder_assembly _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case _description_example.detail A 'disordered methyl assembly with groups 1 and 2' B 'disordered sites related by a mirror' S 'disordered sites independent of symmetry' save_ save_atom_site.disorder_group _definition.id '_atom_site.disorder_group' _definition.update 2008-06-19 _description.text ; A code that identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the H atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. "-1") is used to indicate sites disordered about a special position. ; _description.common 'AtomSiteDisorderGroup' _name.category_id atom_site _name.object_id disorder_group _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case _description_example.detail 2 'unique disordered site in group 2' -1 'symmetry-independent disordered site' save_ save_atom_site.fract_xyz _definition.id '_atom_site.fract_xyz' _definition.update 2006-12-14 _description.text ; Vector of atom site coordinates projected onto the crystal unit cell as fractions of the cell lengths. ; _description.common 'AtomSiteFractXyz' _name.category_id atom_site _name.object_id fract_xyz _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With a as atom_site atom_site.fract_xyz = Array ( [a.fract_x, a.fract_y, a.fract_z] ) ; save_ save_atom_site.fract_x _definition.id '_atom_site.fract_x' _definition.update 2006-06-29 _description.text ; Atom site coordinates as fractions of the cell length values. ; _type.purpose Measured _type.container Single _type.contents Real _name.category_id atom_site _name.object_id fract_x save_ save_atom_site.fract_y _definition.id '_atom_site.fract_y' _definition.update 2006-06-29 _description.text ; Atom site coordinates as fractions of the cell length values. ; _type.purpose Measured _type.container Single _type.contents Real _name.category_id atom_site _name.object_id fract_y save_ save_atom_site.fract_z _definition.id '_atom_site.fract_z' _definition.update 2006-06-29 _description.text ; Atom site coordinates as fractions of the cell length values. ; _type.purpose Measured _type.container Single _type.contents Real _name.category_id atom_site _name.object_id fract_z save_ save_atom_site.label _definition.id '_atom_site.label' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _description.common 'AtomSiteLabel' _name.category_id atom_site _name.object_id label save_ save_atom_site.label_component_0 _definition.id '_atom_site.label_component_0' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_0 save_ save_atom_site.label_component_1 _definition.id '_atom_site.label_component_1' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_1 save_ save_atom_site.label_component_2 _definition.id '_atom_site.label_component_2' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_2 save_ save_atom_site.label_component_3 _definition.id '_atom_site.label_component_3' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_3 save_ save_atom_site.label_component_4 _definition.id '_atom_site.label_component_4' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_4 save_ save_atom_site.label_component_5 _definition.id '_atom_site.label_component_5' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_5 save_ save_atom_site.label_component_6 _definition.id '_atom_site.label_component_6' _definition.update 2006-06-29 _description.text ; Component_0 is normally a code which matches identically with one of the _atom_type.symbol codes. If this is the case then the rules governing the _atom_type.symbol code apply. If, however, the data item _atom_site.type_symbol is also specified in the atom site list, component 0 need not match this symbol or adhere to any of the _atom_type.symbol rules. Component_1 is referred to as the "atom number". When component 0 is the atom type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components_2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underline. ; _type.purpose Assigned _type.container Single _type.contents Label _name.category_id atom_site _name.object_id label_component_6 save_ save_atom_site.occupancy _definition.id '_atom_site.occupancy' _definition.update 2006-12-14 _description.text ; 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). ; _description.common 'AtomSiteOccupancy' _name.category_id atom_site _name.object_id occupancy _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 _enumeration.default 1.0 save_ save_atom_site.refinement_flags _definition.id '_atom_site.refinement_flags' _definition.update 2006-12-14 _description.text ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. ; _description.common 'AtomSiteRefineFlags' _name.category_id atom_site _name.object_id refinement_flags _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail S 'special position constraint on site' G 'rigid group refinement of site' R 'riding-atom site attached to non-riding atom' D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint' save_ save_atom_site.restraints _definition.id '_atom_site.restraints' _definition.update 2006-12-14 _description.text ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine_ls.number_restraints. ; _description.common 'AtomSiteRestraints' _name.category_id atom_site _name.object_id restraints _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'restrained to planar ring' save_ save_atom_site.symmetry_multiplicity _definition.id '_atom_site.symmetry_multiplicity' _definition.update 2006-12-14 _description.text ; The site multiplicity is the number of times that a site is repeated in a cell due to the space-group symmetry. For sites related by the general symmetry equivalent this number will be the total number of unique symmetry positions in the space group. For special sites this will be a lesser number. The permitted numbers for each space group are given in given in International Tables for Crystallography, Vol. A (1987). ; _description.common 'AtomSiteMultiplicity' _name.category_id atom_site _name.object_id symmetry_multiplicity _type.purpose Observed _type.container Single _type.contents Index _enumeration.range 1:192 loop_ _method.purpose _method.expression Evaluation ; With a as atom_site mul = 1 xyz = a.fract_xyz Loop s as symmetry_equiv { 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.symmetry_multiplicity = mul ; save_ save_atom_site.type_symbol _definition.id '_atom_site.type_symbol' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'AtomSiteTypeSymbol' _name.category_id atom_site _name.object_id type_symbol _name.linked_item_id '_atom_type.symbol' _type.purpose Link _type.container Single _type.contents Code loop_ _description_example.case Cu Cu2+ dummy S- H* H(SDS) loop_ _method.purpose _method.expression Evaluation ; _atom_site.type_symbol = AtomType ( _atom_site.label ) ; save_ save_atom_site.U_equiv_geom_mean _definition.id '_atom_site.U_equiv_geom_mean' _definition.update 2006-12-14 _description.text ; 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^ ; _description.common 'AtomSiteUisoMean' _name.category_id atom_site _name.object_id U_equiv_geom_mean _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms_squared save_ save_atom_site.U_iso_or_equiv _definition.id '_atom_site.U_iso_or_equiv' _definition.update 2006-12-14 _description.text ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U(equiv), in angstroms squared, calculated from anisotropic atomic displacement parameters. U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)] a = the real-space cell lengths a* = the reciprocal-space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. ; _description.common 'AtomSiteUisoEquiv' _name.category_id atom_site _name.object_id U_iso_or_equiv _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms_squared save_ save_atom_site.Wyckoff_symbol _definition.id '_atom_site.Wyckoff_symbol' _definition.update 2008-06-19 _description.text ; The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). ; _description.common 'AtomSiteWyckoff' _name.category_id atom_site _name.object_id Wyckoff_symbol _type.purpose Assigned _type.container Single _type.contents Text save_ save_ATOM_SITE_ANISO _definition.id atom_site_aniso _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe the anisotropic thermal parameters of the atomic sites in a crystal structure. ; _description.common 'Anisotropic thermal parameters' _category.parent_id atom_site _category.parent_join Yes _category_key.generic '_atom_site_aniso.key' save_ save_atom_site_aniso.key _definition.id '_atom_site_aniso.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of ATOM_SITE_ANISO items in a looped list. ; _description.common 'Key to list of atomic sites' _name.category_id atom_site_aniso _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _atom_site_aniso.key = _atom_site_aniso.label ; save_ save_atom_site_aniso.label _definition.id '_atom_site_aniso.label' _definition.update 2008-06-18 _description.text ; The atom site label used if the anisotropic atomic displacement parameters are stored as a separate list. ; _description.common 'AtomSiteAnisoLabel' _name.category_id atom_site_aniso _name.object_id label _type.purpose Identify _type.container Single _type.contents Label save_ save_atom_site_aniso.ratio _definition.id '_atom_site_aniso.ratio' _definition.update 2006-12-14 _description.text ; Ratio of the maximum to minimum eigenvalues of the atomic displacement (thermal) ellipsoids. ; _description.common 'AtomSiteAnisoRatio' _name.category_id atom_site_aniso _name.object_id ratio _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 1.0: save_ save_atom_site_aniso.type_symbol _definition.id '_atom_site_aniso.type_symbol' _definition.update 2006-12-14 _description.text ; This _atom_type.symbol code links the anisotropic atom parameters to the atom type data associated with this site and must match one of the _atom_type.symbol codes in this list. ; _description.common 'AtomSiteAnisoTypeSymbol' _name.category_id atom_site_aniso _name.object_id type_symbol _name.linked_item_id '_atom_type.symbol' _type.purpose Link _type.container Single _type.contents Code loop_ _method.purpose _method.expression Evaluation ; _atom_site_aniso.type_symbol = AtomType ( _atom_site_aniso.label ) ; save_ save_atom_site_aniso.matrix_beta _definition.id '_atom_site_aniso.matrix_beta' _definition.update 2008-06-24 _description.text ; The symmetric anisotropic atomic displacement matrix beta(IJ) appears in a structure factor expression as: t = exp - ( beta11 h h + ............ 2 beta23 k l ) It is related to the adp matrices U(IJ) and B(IJ) as follows: t = exp -2pi**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* ) ; _description.common 'AtomSiteAnisoBetaIJ' _name.category_id atom_site_aniso _name.object_id matrix_beta _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With a as atom_site_aniso If (a.adp_type == 'uani') { C = _cell_reciprocal.convert_U_to_beta B = C * _atom_site_aniso.matrix_U * C } Else If (a.adp_type == 'bani') { C = _cell_reciprocal.convert_U_to_beta / (2.828427 * Pi) B = C * _atom_site_aniso.matrix_B * C } Else { If (a.adp_type == 'uiso') b = a.U_iso_or_equiv Else b = a.B_iso_or_equiv / (8 * Pi**2) C = _cell_reciprocal.convert_U_to_beta B = C * Array ([[b,0,0],[0,b,0],[0,0,b]]) * C } _atom_site_aniso.matrix_beta = B ; save_ save_atom_site_aniso.matrix_B _definition.id '_atom_site_aniso.matrix_B' _definition.update 2008-06-24 _description.text ; The symmetric anisotropic atomic displacement matrix B. ; _description.common 'AtomSiteAnisoBIJ' _name.category_id atom_site_aniso _name.object_id matrix_B _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With a as atom_site_aniso a.matrix_B = Array ([[ 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 ]]) ; save_ save_atom_site_aniso.B_11 _definition.id '_atom_site_aniso.B_11' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_11 save_ save_atom_site_aniso.B_12 _definition.id '_atom_site_aniso.B_12' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_12 save_ save_atom_site_aniso.B_13 _definition.id '_atom_site_aniso.B_13' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_13 save_ save_atom_site_aniso.B_22 _definition.id '_atom_site_aniso.B_22' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_22 save_ save_atom_site_aniso.B_23 _definition.id '_atom_site_aniso.B_23' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_23 save_ save_atom_site_aniso.B_33 _definition.id '_atom_site_aniso.B_33' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id B_33 save_ save_atom_site_aniso.matrix_U _definition.id '_atom_site_aniso.matrix_U' _definition.update 2008-06-24 _description.text ; The symmetric anisotropic atomic displacement matrix U. ; _description.common 'AtomSiteAnisoUIJ' _name.category_id atom_site_aniso _name.object_id matrix_U _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With a as atom_site_aniso a.matrix_U = Array ([[ 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 ]]) ; save_ save_atom_site_aniso.U_11 _definition.id '_atom_site_aniso.U_11' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_11 save_ save_atom_site_aniso.U_12 _definition.id '_atom_site_aniso.U_12' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_12 save_ save_atom_site_aniso.U_13 _definition.id '_atom_site_aniso.U_13' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_13 save_ save_atom_site_aniso.U_22 _definition.id '_atom_site_aniso.U_22' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_22 save_ save_atom_site_aniso.U_23 _definition.id '_atom_site_aniso.U_23' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_23 save_ save_atom_site_aniso.U_33 _definition.id '_atom_site_aniso.U_33' _definition.update 2006-06-29 _description.text ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure factor term: T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms_squared _name.category_id atom_site_aniso _name.object_id U_33 save_ save_ATOM_SITES _definition.id atom_sites _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to describe information which applies to all atom sites in a crystal structure. ; _category.parent_id core_structure save_ save_atom_sites.solution_primary _definition.id '_atom_sites.solution_primary' _definition.update 2006-12-14 _description.text ; Codes which identify the methods used to locate the first atomic sites determined. ; _description.common 'MethodologySolnPrimary' _name.category_id atom_sites _name.object_id solution_primary _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' _enumeration.default direct save_ save_atom_sites.solution_secondary _definition.id '_atom_sites.solution_secondary' _definition.update 2006-12-14 _description.text ; Code which identifies the methods used to locate the remaining non-hydrogen sites determined. ; _description.common 'MethodologySolnSecondary' _name.category_id atom_sites _name.object_id solution_secondary _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail difmap 'difference Fourier map' geom 'inferred from neighbouring sites' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' _enumeration.default difmap save_ save_atom_sites.solution_hydrogens _definition.id '_atom_sites.solution_hydrogens' _definition.update 2006-12-14 _description.text ; Code which identifies the methods used to locate the hydrogen atomic sites determined. ; _description.common 'methodologySolnHatoms' _name.category_id atom_sites _name.object_id solution_hydrogens _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail difmap 'difference Fourier map' geom 'inferred from neighbouring sites' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' _enumeration.default difmap save_ save_ATOM_SITES_CARTN_TRANSFORM _definition.id atom_sites_Cartn_transform _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to describe the matrix elements used to transform Cartesion coordinates into fractional coordinates of all atom sites in a crystal structure. ; _category.parent_id atom_sites save_ save_atom_sites_Cartn_transform.axes _definition.id '_atom_sites_Cartn_transform.axes' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'AtomSitesCartnTransfAxes' _name.category_id atom_sites_Cartn_transform _name.object_id axes _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'a parallel to x; b in the plane of y & z' save_ save_atom_sites_Cartn_transform.matrix _definition.id '_atom_sites_Cartn_transform.matrix' _definition.update 2008-06-24 _description.text ; Matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform.axes. The 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 + | 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. ; _description.common 'AtomSitesCartnTransfMatrix' _name.category_id atom_sites_Cartn_transform _name.object_id matrix _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With l as cell_length With a as cell_angle With r as cell_reciprocal_angle _atom_sites_Cartn_transform.matrix = Array ([ [ l.a*Sind(a.beta)*Sind(r.gamma), 0, 0 ], [ -l.a*Sind(a.beta)*Cosd(r.gamma), l.b*Sind(a.alpha), 0 ], [ l.a*Cosd(a.beta), l.b*Cosd(a.alpha), l.c ]]) ; save_ save_atom_sites_Cartn_transform.vector _definition.id '_atom_sites_Cartn_transform.vector' _definition.update 2006-12-14 _description.text ; Matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform.axes. The 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 + | 2 | z' |31 32 33| z | 3 | ; _description.common 'AtomSitesCartnTransfVector' _name.category_id atom_sites_Cartn_transform _name.object_id vector _type.purpose Measured _type.container Array _type.contents Real save_ save_ATOM_TYPE _definition.id atom_type _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe atomic type information used in crystallographic structure studies. ; _description.common 'AtomTypeList' _category.parent_id core_structure _category_key.generic '_atom_type.key' save_ save_atom_type.key _definition.id '_atom_type.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of ATOM_TYPE items in a looped list. ; _description.common 'Key to list of atomic types' _name.category_id atom_type _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _atom_type.key = _atom_type.symbol ; save_ save_atom_type.analytical_mass_percent _definition.id '_atom_type.analytical_mass_percent' _definition.update 2006-12-14 loop_ _alias.definition_id '_atom_type.analytical_mass_%' _description.text ; Mass percentage of this atom type derived from chemical analysis. ; _description.common 'AtomTypeComposition%' _name.category_id atom_type _name.object_id analytical_mass_percent _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:100. save_ save_atom_type.atomic_mass _definition.id '_atom_type.atomic_mass' _definition.update 2006-12-14 _description.text ; Mass of this atom type. ; _description.common 'AtomTypeMass' _name.category_id atom_type _name.object_id atomic_mass _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 1.008 D 2.008 H1- 1.008 He 4.003 Li 6.941 Li1+ 6.941 Be 9.012 Be2+ 9.012 B 10.811 C 12.011 N 14.007 O 15.999 O1- 15.999 F 18.998 F1- 18.998 Ne 20.179 Na 22.990 Na1+ 22.990 Mg 24.305 Mg2+ 24.305 Al 26.982 Al3+ 26.982 Si 28.086 Si4+ 28.086 P 30.974 S 32.066 Cl 35.453 Cl1- 35.453 Ar 39.948 K 39.098 K1+ 39.098 Ca 40.078 Ca2+ 40.078 Sc 44.956 Sc3+ 44.956 Ti 47.88 Ti2+ 47.88 Ti3+ 47.88 Ti4+ 47.88 V 50.942 V2+ 50.942 V3+ 50.942 V5+ 50.942 Cr 51.996 Cr2+ 51.996 Cr3+ 51.996 Mn 54.938 Mn2+ 54.938 Mn3+ 54.938 Mn4+ 54.938 Fe 55.847 Fe2+ 55.847 Fe3+ 55.847 Co 58.933 Co2+ 58.933 Co3+ 58.933 Ni 58.69 Ni2+ 58.69 Ni3+ 58.69 Cu 63.546 Cu1+ 63.546 Cu2+ 63.546 Zn 65.39 Zn2+ 65.39 Ga 69.723 Ga3+ 69.723 Ge 72.59 Ge4+ 72.59 As 74.922 Se 78.96 Br 79.904 Br1- 79.904 Kr 83.80 Rb 85.468 Rb1+ 85.468 Sr 87.62 Sr2+ 87.62 Y 88.906 Y3+ 88.906 Zr 91.224 Zr4+ 91.224 Nb 92.906 Nb3+ 92.906 Nb5+ 92.906 Mo 95.94 Mo3+ 95.94 Mo5+ 95.94 Mo6+ 95.94 Tc 98.906 Ru 101.07 Ru3+ 101.07 Ru4+ 101.07 Rh 102.906 Rh3+ 102.906 Rh4+ 102.906 Pd 106.42 Pd2+ 106.42 Pd4+ 106.42 Ag 107.868 Ag1+ 107.868 Ag2+ 107.868 Cd 112.41 Cd2+ 112.41 In 114.82 In3+ 114.82 Sn 118.71 Sn2+ 118.71 Sn4+ 118.71 Sb 121.75 Sb3+ 121.75 Sb5+ 121.75 Te 127.60 I 126.905 I1- 126.905 Xe 131.29 Cs 132.905 Cs1+ 132.905 Ba 137.33 Ba2+ 137.33 La 138.906 La3+ 138.906 Ce 140.12 Ce3+ 140.12 Ce4+ 140.12 Pr 140.908 Pr3+ 140.908 Pr4+ 140.908 Nd 144.24 Nd3+ 144.24 Pm 147. Sm 150.36 Sm3+ 150.36 Eu 151.96 Eu2+ 151.96 Eu3+ 151.96 Gd 157.25 Gd3+ 157.25 Tb 158.926 Tb3+ 158.926 Dy 162.5 Dy3+ 162.5 Ho 164.93 Ho3+ 164.93 Er 167.26 Er3+ 167.26 Tm 168.934 Tm3+ 168.934 Yb 173.04 Yb2+ 173.04 Yb3+ 173.04 Lu 174.967 Lu3+ 174.967 Hf 178.49 Hf4+ 178.49 Ta 180.948 Ta5+ 180.948 W 183.85 W6+ 183.85 Re 186.207 Os 190.2 Os4+ 190.2 Ir 192.22 Ir3+ 192.22 Ir4+ 192.22 Pt 195.08 Pt2+ 195.08 Pt4+ 195.08 Au 196.966 Au1+ 196.966 Au3+ 196.966 Hg 200.59 Hg1+ 200.59 Hg2+ 200.59 Tl 204.383 TL1+ 204.383 Tl3+ 204.383 Pb 207.2 Pb2+ 207.2 Pb4+ 207.2 Bi 208.980 Bi3+ 208.980 Bi5+ 208.980 Po 209. At 210. Rn 222. Fr 223. Ra 226.025 Ra2+ 226.025 Ac 227. Ac3+ 227. Th 232.038 Th4+ 232.038 Pa 231.036 U 238.029 U3+ 238.029 U4+ 238.029 U6+ 238.029 Np 237.048 Np3+ 237.048 Np4+ 237.048 Np6+ 237.048 Pu 242. Pu3+ 242. Pu4+ 242. Pu6+ 242. Am 243. Cm 247. Bk 247. Cf 249. _enumeration.def_index_id '_atom_type.element_symbol' _units.code daltons save_ save_atom_type.atomic_number _definition.id '_atom_type.atomic_number' _definition.update 2006-12-14 _description.text ; Atomic number of this atom type. ; _description.common 'AtomTypeNumber' _name.category_id atom_type _name.object_id atomic_number _type.purpose Assigned _type.container Single _type.contents Index loop_ _enumeration_default.index _enumeration_default.value H 01 D 01 H1- 01 He 02 Li 03 Li1+ 03 Be 04 Be2+ 04 B 05 C 06 N 07 O 08 O1- 08 F 09 F1- 09 Ne 10 Na 11 Na1+ 11 Mg 12 Mg2+ 12 Al 13 Al3+ 13 Si 14 Si4+ 14 P 15 S 16 Cl 17 Cl1- 17 Ar 18 K 19 K1+ 19 Ca 20 Ca2+ 20 Sc 21 Sc3+ 21 Ti 22 Ti2+ 22 Ti3+ 22 Ti4+ 22 V 23 V2+ 23 V3+ 23 V5+ 23 Cr 24 Cr2+ 24 Cr3+ 24 Mn 25 Mn2+ 25 Mn3+ 25 Mn4+ 25 Fe 26 Fe2+ 26 Fe3+ 26 Co 27 Co2+ 27 Co3+ 27 Ni 28 Ni2+ 28 Ni3+ 28 Cu 29 Cu1+ 29 Cu2+ 29 Zn 30 Zn2+ 30 Ga 31 Ga3+ 31 Ge 32 Ge4+ 32 As 33 Se 34 Br 35 Br1- 35 Kr 36 Rb 37 Rb1+ 37 Sr 38 Sr2+ 38 Y 39 Y3+ 39 Zr 40 Zr4+ 40 Nb 41 Nb3+ 41 Nb5+ 41 Mo 42 Mo3+ 42 Mo5+ 42 Mo6+ 42 Tc 43 Ru 44 Ru3+ 44 Ru4+ 44 Rh 45 Rh3+ 45 Rh4+ 45 Pd 46 Pd2+ 46 Pd4+ 46 Ag 47 Ag1+ 47 Ag2+ 47 Cd 48 Cd2+ 48 In 49 In3+ 49 Sn 50 Sn2+ 50 Sn4+ 50 Sb 51 Sb3+ 51 Sb5+ 51 Te 52 I 53 I1- 53 Xe 54 Cs 55 Cs1+ 55 Ba 56 Ba2+ 56 La 57 La3+ 57 Ce 58 Ce3+ 58 Ce4+ 58 Pr 59 Pr3+ 59 Pr4+ 59 Nd 60 Nd3+ 60 Pm 61 Sm 62 Sm3+ 62 Eu 63 Eu2+ 63 Eu3+ 63 Gd 64 Gd3+ 64 Tb 65 Tb3+ 65 Dy 66 Dy3+ 66 Ho 67 Ho3+ 67 Er 68 Er3+ 68 Tm 69 Tm3+ 69 Yb 70 Yb2+ 70 Yb3+ 70 Lu 71 Lu3+ 71 Hf 72 Hf4+ 72 Ta 73 Ta5+ 73 W 74 W6+ 74 Re 75 Os 76 Os4+ 76 Ir 77 Ir3+ 77 Ir4+ 77 Pt 78 Pt2+ 78 Pt4+ 78 Au 79 Au1+ 79 Au3+ 79 Hg 80 Hg1+ 80 Hg2+ 80 Tl 81 TL1+ 81 Tl3+ 81 Pb 82 Pb2+ 82 Pb4+ 82 Bi 83 Bi3+ 83 Bi5+ 83 Po 84 At 85 Rn 86 Fr 87 Ra 88 Ra2+ 88 Ac 89 Ac3+ 89 Th 90 Th4+ 90 Pa 91 U 92 U3+ 92 U4+ 92 U6+ 92 Np 93 Np3+ 93 Np4+ 93 Np6+ 93 Pu 94 Pu3+ 94 Pu4+ 94 Pu6+ 94 Am 95 Cm 96 Bk 97 Cf 98 _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type.description _definition.id '_atom_type.description' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'AtomTypeDetails' _name.category_id atom_type _name.object_id description _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case deuterium save_ save_atom_type.display_colour _definition.id '_atom_type.display_colour' _definition.update 2006-12-14 _description.text ; The display colour assigned to this atom type. Note that the possible colours are enumerated in the display_colour list category of items. ; _description.common 'AtomTypeColour' _name.category_id atom_type _name.object_id display_colour _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail black [ 000, 000, 000 ] white [ 255, 255, 255 ] grey [ 192, 192, 192 ] grey_light [ 211, 211, 211 ] grey_slate [ 112, 128, 144 ] blue [ 000, 000, 255 ] blue_light [ 176, 224, 230 ] blue_medium [ 000, 000, 205 ] blue_dark [ 025, 025, 112 ] blue_navy [ 000, 000, 128 ] blue_royal [ 065, 105, 225 ] blue_sky [ 135, 206, 235 ] blue_steel [ 070, 130, 180 ] turquoise [ 064, 224, 208 ] cyan [ 000, 255, 255 ] cyan_light [ 224, 255, 255 ] green [ 000, 255, 000 ] green_light [ 152, 251, 152 ] green_dark [ 000, 100, 000 ] green_sea [ 046, 139, 087 ] green_lime [ 050, 205, 050 ] green_olive [ 107, 142, 035 ] green_khaki [ 240, 230, 140 ] yellow [ 255, 255, 000 ] yellow_light [ 255, 255, 224 ] yellow_gold [ 255, 215, 000 ] brown [ 165, 042, 042 ] brown_sienna [ 160, 082, 045 ] brown_beige [ 245, 245, 220 ] brown_tan [ 210, 180, 140 ] salmon [ 250, 128, 114 ] salmon_light [ 255, 160, 122 ] salmon_dark [ 233, 150, 122 ] orange [ 255, 165, 000 ] orange_dark [ 255, 140, 000 ] red [ 255, 000, 000 ] red_coral [ 255, 127, 080 ] red_tomato [ 255, 099, 071 ] red_orange [ 255, 069, 000 ] red_violet [ 219, 112, 147 ] red_maroon [ 176, 048, 096 ] pink [ 255, 192, 203 ] pink_light [ 255, 182, 193 ] pink_deep [ 255, 020, 147 ] pink_hot [ 255, 105, 180 ] violet [ 238, 130, 238 ] violet_red [ 208, 032, 144 ] violet_magenta [ 255, 000, 255 ] violet_dark [ 148, 000, 211 ] violet_blue [ 138, 043, 226 ] loop_ _enumeration_default.index _enumeration_default.value H white D blue_light H1- white He unknown Li unknown Li1+ unknown Be unknown Be2+ unknown B unknown C steel_grey N blue O red O1- red F green F1- green Ne unknown Na magenta Na1+ magenta Mg magenta Mg2+ magenta Al magenta Al3+ magenta Si unknown Si4+ unknown P magenta S yellow Cl green Cl1- green Ar unknown K magenta K1+ magenta Ca magenta Ca2+ magenta Sc unknown Sc3+ unknown Ti magenta Ti2+ magenta Ti3+ magenta Ti4+ magenta V magenta V2+ magenta V3+ magenta V5+ magenta Cr magenta Cr2+ magenta Cr3+ magenta Mn magenta Mn2+ magenta Mn3+ magenta Mn4+ magenta Fe magenta Fe2+ magenta Fe3+ magenta Co magenta Co2+ magenta Co3+ magenta Ni magenta Ni2+ magenta Ni3+ magenta Cu magenta Cu1+ magenta Cu2+ magenta Zn magenta Zn2+ magenta Ga magenta Ga3+ magenta Ge magenta Ge4+ magenta As magenta Se yellow Br green Br1- green Kr unknown Rb unknown Rb1+ unknown Sr unknown Sr2+ unknown Y unknown Y3+ unknown Zr unknown Zr4+ unknown Nb unknown Nb3+ unknown Nb5+ unknown Mo unknown Mo3+ magenta Mo5+ magenta Mo6+ magenta Tc unknown Ru unknown Ru3+ unknown Ru4+ unknown Rh unknown Rh3+ unknown Rh4+ unknown Pd unknown Pd2+ unknown Pd4+ unknown Ag magenta Ag1+ magenta Ag2+ magenta Cd magenta Cd2+ magenta In unknown In3+ unknown Sn magenta Sn2+ magenta Sn4+ magenta Sb magenta Sb3+ magenta Sb5+ magenta Te unknown I green I1- green Xe unknown Cs unknown Cs1+ unknown Ba unknown Ba2+ unknown La unknown La3+ unknown Ce unknown Ce3+ unknown Ce4+ unknown Pr unknown Pr3+ unknown Pr4+ unknown Nd unknown Nd3+ unknown Pm unknown Sm unknown Sm3+ unknown Eu unknown Eu2+ unknown Eu3+ unknown Gd unknown Gd3+ unknown Tb unknown Tb3+ unknown Dy unknown Dy3+ unknown Ho unknown Ho3+ unknown Er unknown Er3+ unknown Tm unknown Tm3+ unknown Yb unknown Yb2+ unknown Yb3+ unknown Lu unknown Lu3+ unknown Hf unknown Hf4+ unknown Ta unknown Ta5+ unknown W unknown W6+ unknown Re unknown Os unknown Os4+ unknown Ir unknown Ir3+ unknown Ir4+ unknown Pt magenta Pt2+ magenta Pt4+ magenta Au magenta Au1+ magenta Au3+ magenta Hg magenta Hg1+ magenta Hg2+ magenta Tl unknown TL1+ unknown Tl3+ unknown Pb magenta Pb2+ magenta Pb4+ magenta Bi magenta Bi3+ magenta Bi5+ magenta Po unknown At unknown Rn unknown Fr unknown Ra unknown Ra2+ unknown Ac unknown Ac3+ unknown Th unknown Th4+ unknown Pa unknown U unknown U3+ unknown U4+ unknown U6+ unknown Np unknown Np3+ unknown Np4+ unknown Np6+ unknown Pu unknown Pu3+ unknown Pu4+ unknown Pu6+ unknown Am unknown Cm unknown Bk unknown Cf unknown _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type.electron_count _definition.id '_atom_type.electron_count' _definition.update 2006-12-14 _description.text ; Number of electrons in this atom type. ; _description.common 'AtomTypeElectrons' _name.category_id atom_type _name.object_id electron_count _type.purpose Observed _type.container Single _type.contents Index loop_ _enumeration_default.index _enumeration_default.value H 01 D 01 H1- 02 He 02 Li 03 Li1+ 02 Be 04 Be2+ 02 B 05 C 06 N 07 O 08 O1- 09 F 09 F1- 10 Ne 10 Na 11 Na1+ 10 Mg 12 Mg2+ 10 Al 13 Al3+ 10 Si 14 Si4+ 10 P 15 S 16 Cl 17 Cl1- 18 Ar 18 K 19 K1+ 18 Ca 20 Ca2+ 18 Sc 21 Sc3+ 18 Ti 22 Ti2+ 20 Ti3+ 19 Ti4+ 18 V 23 V2+ 21 V3+ 20 V5+ 18 Cr 24 Cr2+ 22 Cr3+ 21 Mn 25 Mn2+ 23 Mn3+ 22 Mn4+ 21 Fe 26 Fe2+ 24 Fe3+ 23 Co 27 Co2+ 25 Co3+ 24 Ni 28 Ni2+ 26 Ni3+ 25 Cu 29 Cu1+ 28 Cu2+ 27 Zn 30 Zn2+ 28 Ga 31 Ga3+ 28 Ge 32 Ge4+ 28 As 33 Se 34 Br 35 Br1- 36 Kr 36 Rb 37 Rb1+ 36 Sr 38 Sr2+ 36 Y 39 Y3+ 36 Zr 40 Zr4+ 36 Nb 41 Nb3+ 38 Nb5+ 36 Mo 42 Mo3+ 39 Mo5+ 37 Mo6+ 36 Tc 43 Ru 44 Ru3+ 41 Ru4+ 40 Rh 45 Rh3+ 42 Rh4+ 41 Pd 46 Pd2+ 44 Pd4+ 42 Ag 47 Ag1+ 46 Ag2+ 45 Cd 48 Cd2+ 46 In 49 In3+ 46 Sn 50 Sn2+ 48 Sn4+ 46 Sb 51 Sb3+ 48 Sb5+ 46 Te 52 I 53 I1- 54 Xe 54 Cs 55 Cs1+ 54 Ba 56 Ba2+ 54 La 57 La3+ 54 Ce 58 Ce3+ 55 Ce4+ 54 Pr 59 Pr3+ 56 Pr4+ 55 Nd 60 Nd3+ 57 Pm 61 Sm 62 Sm3+ 59 Eu 63 Eu2+ 61 Eu3+ 60 Gd 64 Gd3+ 61 Tb 65 Tb3+ 62 Dy 66 Dy3+ 63 Ho 67 Ho3+ 64 Er 68 Er3+ 65 Tm 69 Tm3+ 66 Yb 70 Yb2+ 68 Yb3+ 67 Lu 71 Lu3+ 68 Hf 72 Hf4+ 68 Ta 73 Ta5+ 68 W 74 W6+ 68 Re 75 Os 76 Os4+ 72 Ir 77 Ir3+ 74 Ir4+ 73 Pt 78 Pt2+ 76 Pt4+ 74 Au 79 Au1+ 78 Au3+ 76 Hg 80 Hg1+ 79 Hg2+ 78 Tl 81 TL1+ 80 Tl3+ 78 Pb 82 Pb2+ 80 Pb4+ 78 Bi 83 Bi3+ 80 Bi5+ 78 Po 84 At 85 Rn 86 Fr 87 Ra 88 Ra2+ 86 Ac 89 Ac3+ 86 Th 90 Th4+ 86 Pa 91 U 92 U3+ 89 U4+ 88 U6+ 84 Np 93 Np3+ 90 Np4+ 89 Np6+ 87 Pu 94 Pu3+ 91 Pu4+ 90 Pu6+ 88 Am 95 Cm 96 Bk 97 Cf 98 _enumeration.def_index_id '_atom_type.element_symbol' _enumeration.range 1: save_ save_atom_type.element_symbol _definition.id '_atom_type.element_symbol' _definition.update 2006-12-14 _description.text ; Element symbol for of this atom type. ; _description.common 'AtomTypeElement' _name.category_id atom_type _name.object_id element_symbol _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail Ac Actinium Ag Silver Al Aluminum Am Americium Ar Argon As Arsenic At Astatine Au Gold B Boron Ba Barium Be Beryllium Bh Bohrium Bi Bismuth Bk Berkelium Br Bromine C Carbon Ca Calcium Cd Cadmium Ce Cerium Cf Californium Cl Chlorine Cm Curium Co Cobalt Cr Chromium Cs Cesium Cu Copper Db Dubnium Ds Darmstadtium Dy Dysprosium Er Erbium Es Einsteinium Eu Europium F Fluorine Fe Iron Fm Fermium Fr Francium Ga Gallium Gd Gadolinium Ge Germanium H Hydrogen He Helium Hf Hafnium Hg Mercury Ho Holmium Hs Hassium I Iodine In Indium Ir Iridium K Potassium Kr Krypton La Lanthanum Li Lithium Lr Lawrencium Lu Lutetium Md Mendelevium Mg Magnesium Mn Manganese Mo Molybdenum Mt Meitnerium N Nitrogen Na Sodium Ne Neon Nb Niobium Nd Neodymium Ni Nickel No Nobelium Np Neptunium O Oxygen Os Osmium P Phosphorus Pd Palladium Po Polonium Pb Lead Pt Platinum Pr Praseodymium Pm Promethium Pu Plutonium Pa Protactinium Ra Radium Rb Rubidium Re Rhenium Rf Rutherfordium Rh Rhodium Rn Radon Ru Ruthenium S Sulfur Sb Antimony Sc Scandium Se Selenium Sg Seaborgium Si Silicon Sm Samarium Sn Tin Sr Strontium Ta Tantalum Tb Terbium Tc Technetium Te Tellurium Th Thorium Ti Titanium Tl Thallium Tm Thulium U Uranium Uub Ununbium Uun Ununnilium Uuu Ununumium V Vanadium W Tungsten Xe Xenon Y Yttrium Yb Ytterbium Zn Zinc Zr Zirconium loop_ _enumeration_default.index _enumeration_default.value H H D D H1- H He HE Li LI Li1+ LI Be BE Be2+ BE B B C C N N O O O1- O F F F1- F Ne NE Na NA Na1+ NA Mg MG Mg2+ MG Al AL Al3+ AL Si SI Si4+ SI P P S S Cl CL Cl1- CL Ar AR K K K1+ K Ca CA Ca2+ CA Sc SC Sc3+ SC Ti TI Ti2+ TI Ti3+ TI Ti4+ TI V V V2+ V V3+ V V5+ V Cr CR Cr2+ CR Cr3+ CR Mn MN Mn2+ MN Mn3+ MN Mn4+ MN Fe FE Fe2+ FE Fe3+ FE Co CO Co2+ CO Co3+ CO Ni NI Ni2+ NI Ni3+ NI Cu CU Cu1+ CU Cu2+ CU Zn ZN Zn2+ ZN Ga GA Ga3+ GA Ge GE Ge4+ GE As AS Se SE Br BR Br1- BR Kr KR Rb RB Rb1+ RB Sr SR Sr2+ SR Y Y Y3+ Y Zr ZR Zr4+ ZR Nb NB Nb3+ NB Nb5+ NB Mo MO Mo3+ MO Mo5+ MO Mo6+ MO Tc TC Ru RU Ru3+ RU Ru4+ RU Rh RH Rh3+ RH Rh4+ RH Pd PD Pd2+ PD Pd4+ PD Ag AG Ag1+ AG Ag2+ AG Cd CD Cd2+ CD In IN In3+ IN Sn SN Sn2+ SN Sn4+ SN Sb SB Sb3+ SB Sb5+ SB Te TE I I I1- I Xe XE Cs CS Cs1+ CS Ba BA Ba2+ BA La LA La3+ LA Ce CE Ce3+ CE Ce4+ CE Pr PR Pr3+ PR Pr4+ PR Nd ND Nd3+ ND Pm PM Sm SM Sm3+ SM Eu EU Eu2+ EU Eu3+ EU Gd GD Gd3+ GD Tb TB Tb3+ TB Dy DY Dy3+ DY Ho HO Ho3+ HO Er ER Er3+ ER Tm TM Tm3+ TM Yb YB Yb2+ YB Yb3+ YB Lu LU Lu3+ LU Hf HF Hf4+ HF Ta TA Ta5+ TA W W W6+ W Re RE Os OS Os4+ OS Ir IR Ir3+ IR Ir4+ IR Pt PT Pt2+ PT Pt4+ PT Au AU Au1+ AU Au3+ AU Hg HG Hg1+ HG Hg2+ HG Tl TL TL1+ TL Tl3+ TL Pb PB Pb2+ PB Pb4+ PB Bi BI Bi3+ BI Bi5+ BI Po PO At AT Rn RN Fr FR Ra RA Ra2+ RA Ac AC Ac3+ AC Th TH Th4+ TH Pa PA U U U3+ U U4+ U U6+ U Np NP Np3+ NP Np4+ NP Np6+ NP Pu PU Pu3+ PU Pu4+ PU Pu6+ PU Am AM Cm CM Bk BK Cf CF _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type.number_in_cell _definition.id '_atom_type.number_in_cell' _definition.update 2006-12-14 _description.text ; Total number of atoms of this atom type in the unit cell. ; _description.common 'AtomTypeCellCount' _name.category_id atom_type _name.object_id number_in_cell _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0: loop_ _method.purpose _method.expression Evaluation ; With t as atom_type cnt = 0. Loop a as atom_site { if ( a.type_symbol == t.symbol ) { cnt += a.occupancy * a.symmetry_multiplicity } } _atom_type.number_in_cell = cnt ; save_ save_atom_type.oxidation_number _definition.id '_atom_type.oxidation_number' _definition.update 2006-12-14 _description.text ; Formal oxidation state of this atom type in the structure. ; _description.common 'AtomTypeOxidation' _name.category_id atom_type _name.object_id oxidation_number _type.purpose Assigned _type.container Single _type.contents Integer _enumeration.range -8:8 _enumeration.default 0 save_ save_atom_type.radius_bond _definition.id '_atom_type.radius_bond' _definition.update 2006-12-14 _description.text ; The effective intra-molecular bonding radius of this atom type. ; _description.common 'AtomTypeBondRad' _name.category_id atom_type _name.object_id radius_bond _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 0.37 D 0.37 H1- 0.37 He 0.40 Li 1.23 Li1+ 1.23 Be 0.89 Be2+ 0.89 B 0.80 C 0.77 N 0.74 O 0.74 O1- 0.74 F 0.72 F1- 0.72 Ne 0.72 Na 1.57 Na1+ 1.57 Mg 1.36 Mg2+ 1.36 Al 1.25 Al3+ 1.25 Si 1.17 Si4+ 1.17 P 1.10 S 1.04 Cl 0.99 Cl1- 0.99 Ar 1.00 K 2.03 K1+ 2.03 Ca 1.74 Ca2+ 1.74 Sc 1.44 Sc3+ 1.44 Ti 1.35 Ti2+ 1.35 Ti3+ 1.35 Ti4+ 1.35 V 1.22 V2+ 1.22 V3+ 1.22 V5+ 1.22 Cr 1.17 Cr2+ 1.17 Cr3+ 1.17 Mn 1.17 Mn2+ 1.17 Mn3+ 1.17 Mn4+ 1.17 Fe 1.17 Fe2+ 1.17 Fe3+ 1.17 Co 1.16 Co2+ 1.16 Co3+ 1.16 Ni 1.15 Ni2+ 1.15 Ni3+ 1.15 Cu 1.17 Cu1+ 1.17 Cu2+ 1.17 Zn 1.25 Zn2+ 1.25 Ga 1.25 Ga3+ 1.25 Ge 1.22 Ge4+ 1.22 As 1.21 Se 1.17 Br 1.14 Br1- 1.14 Kr 1.14 Rb 2.16 Rb1+ 2.16 Sr 1.91 Sr2+ 1.91 Y 1.62 Y3+ 1.62 Zr 1.45 Zr4+ 1.45 Nb 1.34 Nb3+ 1.34 Nb5+ 1.34 Mo 1.29 Mo3+ 1.29 Mo5+ 1.29 Mo6+ 1.29 Tc 1.27 Ru 1.24 Ru3+ 1.24 Ru4+ 1.24 Rh 1.25 Rh3+ 1.25 Rh4+ 1.25 Pd 1.28 Pd2+ 1.28 Pd4+ 1.28 Ag 1.34 Ag1+ 1.34 Ag2+ 1.34 Cd 1.41 Cd2+ 1.41 In 1.50 In3+ 1.50 Sn 1.41 Sn2+ 1.41 Sn4+ 1.41 Sb 1.41 Sb3+ 1.41 Sb5+ 1.41 Te 1.37 I 1.33 I1- 1.33 Xe 1.33 Cs 2.35 Cs1+ 2.35 Ba 1.98 Ba2+ 1.98 La 1.69 La3+ 1.69 Ce 1.65 Ce3+ 1.65 Ce4+ 1.65 Pr 1.65 Pr3+ 1.65 Pr4+ 1.65 Nd 1.64 Nd3+ 1.64 Pm 1.63 Sm 1.66 Sm3+ 1.66 Eu 1.85 Eu2+ 1.85 Eu3+ 1.85 Gd 1.61 Gd3+ 1.61 Tb 1.59 Tb3+ 1.59 Dy 1.59 Dy3+ 1.59 Ho 1.58 Ho3+ 1.58 Er 1.57 Er3+ 1.57 Tm 1.56 Tm3+ 1.56 Yb 1.70 Yb2+ 1.70 Yb3+ 1.70 Lu 1.56 Lu3+ 1.56 Hf 1.44 Hf4+ 1.44 Ta 1.34 Ta5+ 1.34 W 1.30 W6+ 1.30 Re 1.28 Os 1.26 Os4+ 1.26 Ir 1.26 Ir3+ 1.26 Ir4+ 1.26 Pt 1.29 Pt2+ 1.29 Pt4+ 1.29 Au 1.34 Au1+ 1.34 Au3+ 1.34 Hg 1.44 Hg1+ 1.44 Hg2+ 1.44 Tl 1.55 TL1+ 1.55 Tl3+ 1.55 Pb 1.54 Pb2+ 1.54 Pb4+ 1.54 Bi 1.52 Bi3+ 1.52 Bi5+ 1.52 Po 1.53 At 1.53 Rn 1.53 Fr 1.53 Ra 1.53 Ra2+ 1.53 Ac 1.53 Ac3+ 1.53 Th 1.65 Th4+ 1.65 Pa 1.53 U 1.42 U3+ 1.42 U4+ 1.42 U6+ 1.42 Np 1.42 Np3+ 1.42 Np4+ 1.42 Np6+ 1.42 Pu 1.42 Pu3+ 1.42 Pu4+ 1.42 Pu6+ 1.42 Am 1.42 Cm 1.42 Bk 1.42 Cf 1.42 _enumeration.def_index_id '_atom_type.element_symbol' _enumeration.range 0.0:5.0 _units.code angstroms save_ save_atom_type.radius_contact _definition.id '_atom_type.radius_contact' _definition.update 2006-12-14 _description.text ; The effective inter-molecular bonding radius of this atom type. ; _description.common 'AtomTypeContactRad' _name.category_id atom_type _name.object_id radius_contact _type.purpose Assigned _type.container Single _type.contents Real _enumeration.range 0.0:5.0 _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; _atom_type.radius_contact = atom_type.radius_bond + 1.25 ; save_ save_atom_type.symbol _definition.id '_atom_type.symbol' _definition.update 2008-06-19 _description.text ; 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. ; _description.common 'AtomTypeSymbol' _name.category_id atom_type _name.object_id symbol _type.purpose Identify _type.container Single _type.contents Text loop_ _description_example.case Mg Cu2+ dummy FeNi save_ save_ATOM_TYPE_SCAT _definition.id atom_type_scat _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to describe atomic scattering information used in crystallographic structure studies. ; _category.parent_id atom_type _category.parent_join Yes _category_key.generic '_atom_type_scat.key' save_ save_atom_type_scat.key _definition.id '_atom_type_scat.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of ATOM_TYPE_SCAT items in a looped list. ; _description.common 'Key to atomic scattering list' _name.category_id atom_type_scat _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _atom_type_scat.key = _atom_type_scat.symbol ; save_ save_atom_type_scat.Cromer_Mann_coeffs _definition.id '_atom_type_scat.Cromer_Mann_coeffs' _definition.update 2006-12-14 _description.text ; The set of Cromer-Mann coefficients for generating X-ray scattering factors. [ a1, b1, a2, b2, a3, b3, a4, b4, c] Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.4 ; _description.common 'AtomTypeCMCoeffs' _name.category_id atom_type_scat _name.object_id Cromer_Mann_coeffs _type.purpose Observed _type.container Tuple _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With t as atom_type_scat _atom_type_scat.Cromer_Mann_coeffs = Tuple ( 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 ) ; save_ save_atom_type_scat.Cromer_Mann_a1 _definition.id '_atom_type_scat.Cromer_Mann_a1' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .493002 D .493002 H1- .897661 He 0.8734 Li 1.1282 Li1+ .6968 Be 1.5919 Be2+ 6.2603 B 2.0545 C 2.31 N 12.2126 O 3.0485 O1- 4.1916 F 3.5392 F1- 3.6322 Ne 3.9553 Na 4.7626 Na1+ 3.2565 Mg 5.4204 Mg2+ 3.4988 Al 6.4202 Al3+ 4.17448 Si 6.2915 Si4+ 4.43918 P 6.4345 S 6.9053 Cl 11.4604 Cl1- 18.2915 Ar 7.4845 K 8.2186 K1+ 7.9578 Ca 8.6266 Ca2+ 15.6348 Sc 9.189 Sc3+ 13.4008 Ti 9.7595 Ti2+ 9.11423 Ti3+ 17.7344 Ti4+ 19.5114 V 10.2971 V2+ 10.106 V3+ 9.43141 V5+ 15.6887 Cr 10.6406 Cr2+ 9.54034 Cr3+ 9.6809 Mn 11.2819 Mn2+ 10.8061 Mn3+ 9.84521 Mn4+ 9.96253 Fe 11.7695 Fe2+ 11.0424 Fe3+ 11.1764 Co 12.2841 Co2+ 11.2296 Co3+ 10.338 Ni 12.8376 Ni2+ 11.4166 Ni3+ 10.7806 Cu 13.338 Cu1+ 11.9475 Cu2+ 11.8168 Zn 14.0743 Zn2+ 11.9719 Ga 15.2354 Ga3+ 12.692 Ge 16.0816 Ge4+ 12.9172 As 16.6723 Se 17.0006 Br 17.1789 Br1- 17.1718 Kr 17.3555 Rb 17.1784 Rb1+ 17.5816 Sr 17.5663 Sr2+ 18.0874 Y 17.776 Y3+ 17.9268 Zr 17.8765 Zr4+ 18.1668 Nb 17.6142 Nb3+ 19.8812 Nb5+ 17.9163 Mo 3.7025 Mo3+ 21.1664 Mo5+ 21.0149 Mo6+ 17.8871 Tc 19.1301 Ru 19.2674 Ru3+ 18.5638 Ru4+ 18.5003 Rh 19.2957 Rh3+ 18.8785 Rh4+ 18.8545 Pd 19.3319 Pd2+ 19.1701 Pd4+ 19.2493 Ag 19.2808 Ag1+ 19.1812 Ag2+ 19.1643 Cd 19.2214 Cd2+ 19.1514 In 19.1624 In3+ 19.1045 Sn 19.1889 Sn2+ 19.1094 Sn4+ 18.9333 Sb 19.6418 Sb3+ 18.9755 Sb5+ 19.8685 Te 19.9644 I 20.1472 I1- 20.2332 Xe 20.2933 Cs 20.3892 Cs1+ 20.3524 Ba 20.3361 Ba2+ 20.1807 La 20.578 La3+ 20.2489 Ce 21.1671 Ce3+ 20.8036 Ce4+ 20.3235 Pr 22.044 Pr3+ 21.3727 Pr4+ 20.9413 Nd 22.6845 Nd3+ 21.961 Pm 23.3405 Sm 24.0042 Sm3+ 23.1504 Eu 24.6274 Eu2+ 24.0063 Eu3+ 23.7497 Gd 25.0709 Gd3+ 24.3466 Tb 25.8976 Tb3+ 24.9559 Dy 26.507 Dy3+ 25.5395 Ho 26.9049 Ho3+ 26.1296 Er 27.6563 Er3+ 26.722 Tm 28.1819 Tm3+ 27.3083 Yb 28.6641 Yb2+ 28.1209 Yb3+ 27.8917 Lu 28.9476 Lu3+ 28.4628 Hf 29.144 Hf4+ 28.8131 Ta 29.2024 Ta5+ 29.1587 W 29.0818 W6+ 29.4936 Re 28.7621 Os 28.1894 Os4+ 30.419 Ir 27.3049 Ir3+ 30.4156 Ir4+ 30.7058 Pt 27.0059 Pt2+ 29.8429 Pt4+ 30.9612 Au 16.8819 Au1+ 28.0109 Au3+ 30.6886 Hg 20.6809 Hg1+ 25.0853 Hg2+ 29.5641 Tl 27.5446 TL1+ 21.3985 Tl3+ 30.8695 Pb 31.0617 Pb2+ 21.7886 Pb4+ 32.1244 Bi 33.3689 Bi3+ 21.8053 Bi5+ 33.5364 Po 34.6726 At 35.3163 Rn 35.5631 Fr 35.9299 Ra 35.7630 Ra2+ 35.2150 Ac 35.6597 Ac3+ 35.1736 Th 35.5645 Th4+ 35.1007 Pa 35.8847 U 36.0228 U3+ 35.5747 U4+ 35.3715 U6+ 34.8509 Np 36.1874 Np3+ 35.7074 Np4+ 35.5103 Np6+ 35.0136 Pu 36.5254 Pu3+ 35.8400 Pu4+ 35.6493 Pu6+ 35.1736 Am 36.6706 Cm 36.6488 Bk 36.7881 Cf 36.9185 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_a1 save_ save_atom_type_scat.Cromer_Mann_a2 _definition.id '_atom_type_scat.Cromer_Mann_a2' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .322912 D .322912 H1- .565616 He 0.6309 Li .7508 Li1+ .7888 Be 1.1278 Be2+ .8849 B 1.3326 C 1.02 N 3.1322 O 2.2868 O1- 1.63969 F 2.6412 F1- 3.51057 Ne 3.1125 Na 3.1736 Na1+ 3.9362 Mg 2.1735 Mg2+ 3.8378 Al 1.9002 Al3+ 3.3876 Si 3.0353 Si4+ 3.20345 P 4.1791 S 5.2034 Cl 7.1964 Cl1- 7.2084 Ar 6.6623 K 7.4398 K1+ 7.4917 Ca 7.3873 Ca2+ 7.9518 Sc 7.3679 Sc3+ 8.0273 Ti 7.3558 Ti2+ 7.62174 Ti3+ 8.73816 Ti4+ 8.23473 V 7.3511 V2+ 7.3541 V3+ 7.7419 V5+ 8.14208 Cr 7.3537 Cr2+ 7.7509 Cr3+ 7.81136 Mn 7.3573 Mn2+ 7.362 Mn3+ 7.87194 Mn4+ 7.97057 Fe 7.3573 Fe2+ 7.374 Fe3+ 7.3863 Co 7.3409 Co2+ 7.3883 Co3+ 7.88173 Ni 7.292 Ni2+ 7.4005 Ni3+ 7.75868 Cu 7.1676 Cu1+ 7.3573 Cu2+ 7.11181 Zn 7.0318 Zn2+ 7.3862 Ga 6.7006 Ga3+ 6.69883 Ge 6.3747 Ge4+ 6.70003 As 6.0701 Se 5.8196 Br 5.2358 Br1- 6.3338 Kr 6.7286 Rb 9.6435 Rb1+ 7.6598 Sr 9.8184 Sr2+ 8.1373 Y 10.2946 Y3+ 9.1531 Zr 10.948 Zr4+ 10.0562 Nb 12.0144 Nb3+ 18.0653 Nb5+ 13.3417 Mo 17.2356 Mo3+ 18.2017 Mo5+ 18.0992 Mo6+ 11.175 Tc 11.0948 Ru 12.9182 Ru3+ 13.2885 Ru4+ 13.1787 Rh 14.3501 Rh3+ 14.1259 Rh4+ 13.9806 Pd 15.5017 Pd2+ 15.2096 Pd4+ 14.79 Ag 16.6885 Ag1+ 15.9719 Ag2+ 16.2456 Cd 17.6444 Cd2+ 17.2535 In 18.5596 In3+ 18.1108 Sn 19.1005 Sn2+ 19.0548 Sn4+ 19.7131 Sb 19.0455 Sb3+ 18.933 Sb5+ 19.0302 Te 19.0138 I 18.9949 I1- 18.997 Xe 19.0298 Cs 19.1062 Cs1+ 19.1278 Ba 19.297 Ba2+ 19.1136 La 19.599 La3+ 19.3763 Ce 19.7695 Ce3+ 19.559 Ce4+ 19.8186 Pr 19.6697 Pr3+ 19.7491 Pr4+ 20.0539 Nd 19.6847 Nd3+ 19.9339 Pm 19.6095 Sm 19.4258 Sm3+ 20.2599 Eu 19.0886 Eu2+ 19.9504 Eu3+ 20.3745 Gd 19.0798 Gd3+ 20.4208 Tb 18.2185 Tb3+ 20.3271 Dy 17.6383 Dy3+ 20.2861 Ho 17.294 Ho3+ 20.0994 Er 16.4285 Er3+ 19.7748 Tm 15.8851 Tm3+ 19.332 Yb 15.4345 Yb2+ 17.6817 Yb3+ 18.7614 Lu 15.2208 Lu3+ 18.121 Hf 15.1726 Hf4+ 18.4601 Ta 15.2293 Ta5+ 18.8407 W 15.43 W6+ 19.3763 Re 15.7189 Os 16.155 Os4+ 15.2637 Ir 16.7296 Ir3+ 15.862 Ir4+ 15.5512 Pt 17.7639 Pt2+ 16.7224 Pt4+ 15.9829 Au 18.5913 Au1+ 17.8204 Au3+ 16.9029 Hg 19.0417 Hg1+ 18.4973 Hg2+ 18.06 Tl 19.1584 TL1+ 20.4723 Tl3+ 18.3841 Pb 13.0637 Pb2+ 19.5682 Pb4+ 18.8003 Bi 12.951 Bi3+ 19.5026 Bi5+ 25.0946 Po 15.4733 At 19.0211 Rn 21.2816 Fr 23.0547 Ra 22.9064 Ra2+ 21.6700 Ac 23.1032 Ac3+ 22.1112 Th 23.4219 Th4+ 22.4418 Pa 23.2948 U 23.4128 U3+ 22.5259 U4+ 22.5326 U6+ 22.7584 Np 23.5964 Np3+ 22.6130 Np4+ 22.5787 Np6+ 22.7286 Pu 23.8083 Pu3+ 22.7169 Pu4+ 22.6460 Pu6+ 22.7181 Am 24.0992 Cm 24.4096 Bk 24.7736 Cf 25.1995 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_a2 save_ save_atom_type_scat.Cromer_Mann_a3 _definition.id '_atom_type_scat.Cromer_Mann_a3' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .140191 D .140191 H1- .415815 He 0.3112 Li .6175 Li1+ .3414 Be .5391 Be2+ .7993 B 1.0979 C 1.5886 N 2.0125 O 1.5463 O1- 1.52673 F 1.517 F1- 1.26064 Ne 1.4546 Na 1.2674 Na1+ 1.3998 Mg 1.2269 Mg2+ 1.3284 Al 1.5936 Al3+ 1.20296 Si 1.9891 Si4+ 1.19453 P 1.78 S 1.4379 Cl 6.2556 Cl1- 6.5337 Ar 0.6539 K 1.0519 K1+ 6.359 Ca 1.5899 Ca2+ 8.4372 Sc 1.6409 Sc3+ 1.65943 Ti 1.6991 Ti2+ 2.2793 Ti3+ 5.25691 Ti4+ 2.01341 V 2.0703 V2+ 2.2884 V3+ 2.15343 V5+ 2.03081 Cr 3.324 Cr2+ 3.58274 Cr3+ 2.87603 Mn 3.0193 Mn2+ 3.5268 Mn3+ 3.56531 Mn4+ 2.76067 Fe 3.5222 Fe2+ 4.1346 Fe3+ 3.3948 Co 4.0034 Co2+ 4.7393 Co3+ 4.76795 Ni 4.4438 Ni2+ 5.3442 Ni3+ 5.22746 Cu 5.6158 Cu1+ 6.2455 Cu2+ 5.78135 Zn 5.1652 Zn2+ 6.4668 Ga 4.3591 Ga3+ 6.06692 Ge 3.7068 Ge4+ 6.06791 As 3.4313 Se 3.9731 Br 5.6377 Br1- 5.5754 Kr 5.5493 Rb 5.1399 Rb1+ 5.8981 Sr 5.422 Sr2+ 2.5654 Y 5.72629 Y3+ 1.76795 Zr 5.41732 Zr4+ 1.01118 Nb 4.04183 Nb3+ 11.0177 Nb5+ 10.799 Mo 12.8876 Mo3+ 11.7423 Mo5+ 11.4632 Mo6+ 6.57891 Tc 4.64901 Ru 4.86337 Ru3+ 9.32602 Ru4+ 4.71304 Rh 4.73425 Rh3+ 3.32515 Rh4+ 2.53464 Pd 5.29537 Pd2+ 4.32234 Pd4+ 2.89289 Ag 4.8045 Ag1+ 5.27475 Ag2+ 4.3709 Cd 4.461 Cd2+ 4.47128 In 4.2948 In3+ 3.78897 Sn 4.4585 Sn2+ 4.5648 Sn4+ 3.4182 Sb 5.0371 Sb3+ 5.10789 Sb5+ 2.41253 Te 6.14487 I 7.5138 I1- 7.8069 Xe 8.9767 Cs 10.662 Cs1+ 10.2821 Ba 10.888 Ba2+ 10.9054 La 11.3727 La3+ 11.6323 Ce 11.8513 Ce3+ 11.9369 Ce4+ 12.1233 Pr 12.3856 Pr3+ 12.1329 Pr4+ 12.4668 Nd 12.774 Nd3+ 12.12 Pm 13.1235 Sm 13.4396 Sm3+ 11.9202 Eu 13.7603 Eu2+ 11.8034 Eu3+ 11.8509 Gd 13.8518 Gd3+ 11.8708 Tb 14.3167 Tb3+ 12.2471 Dy 14.5596 Dy3+ 11.9812 Ho 14.5583 Ho3+ 11.9788 Er 14.9779 Er3+ 12.1506 Tm 15.1542 Tm3+ 12.3339 Yb 15.3087 Yb2+ 13.3335 Yb3+ 12.6072 Lu 15.1 Lu3+ 12.8429 Hf 14.7586 Hf4+ 12.7285 Ta 14.5135 Ta5+ 12.8268 W 14.4327 W6+ 13.0544 Re 14.5564 Os 14.9305 Os4+ 14.7458 Ir 15.6115 Ir3+ 13.6145 Ir4+ 14.2326 Pt 15.7131 Pt2+ 13.2153 Pt4+ 13.7348 Au 25.5582 Au1+ 14.3359 Au3+ 12.7801 Hg 21.6575 Hg1+ 16.8883 Hg2+ 12.8374 Tl 15.538 TL1+ 18.7478 Tl3+ 11.9328 Pb 18.442 Pb2+ 19.1406 Pb4+ 12.0175 Bi 16.5877 Bi3+ 19.1053 Bi5+ 19.2497 Po 13.1138 At 9.49887 Rn 8.0037 Fr 12.1439 Ra 12.4739 Ra2+ 7.91342 Ac 12.5977 Ac3+ 8.19216 Th 12.7473 Th4+ 9.78554 Pa 14.1891 U 14.9491 U3+ 12.2165 U4+ 12.0291 U6+ 14.0099 Np 15.6402 Np3+ 12.9898 Np4+ 12.7766 Np6+ 14.3884 Pu 16.7707 Pu3+ 13.5807 Pu4+ 13.3595 Pu6+ 14.7635 Am 17.3415 Cm 17.3990 Bk 17.8919 Cf 18.3317 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_a3 save_ save_atom_type_scat.Cromer_Mann_a4 _definition.id '_atom_type_scat.Cromer_Mann_a4' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .04081 D .04081 H1- .116973 He 0.178 Li .4653 Li1+ .1563 Be .7029 Be2+ .1647 B .7068 C .865 N 1.1663 O .867 O1- -20.307 F 1.0243 F1- .940706 Ne 1.1251 Na 1.1128 Na1+ 1.0032 Mg 2.3073 Mg2+ .8497 Al 1.9646 Al3+ .528137 Si 1.541 Si4+ .41653 P 1.4908 S 1.5863 Cl 1.6455 Cl1- 2.3386 Ar 1.6442 K .8659 K1+ 1.1915 Ca 1.0211 Ca2+ .8537 Sc 1.468 Sc3+ 1.57936 Ti 1.9021 Ti2+ .087899 Ti3+ 1.92134 Ti4+ 1.5208 V 2.0571 V2+ .0223 V3+ .016865 V5+ -9.576 Cr 1.4922 Cr2+ .509107 Cr3+ .113575 Mn 2.2441 Mn2+ .2184 Mn3+ .323613 Mn4+ .054447 Fe 2.3045 Fe2+ .4399 Fe3+ .0724 Co 2.3488 Co2+ .7108 Co3+ .725591 Ni 2.38 Ni2+ .9773 Ni3+ .847114 Cu 1.6735 Cu1+ 1.5578 Cu+ 1.14523 Zn 2.41 Zn2+ 1.394 Ga 2.9623 Ga3+ 1.0066 Ge 3.683 Ge4+ .859041 As 4.2779 Se 4.3543 Br 3.9851 Br1- 3.7272 Kr 3.5375 Rb 1.5292 Rb1+ 2.7817 Sr 2.6694 Sr2+ -34.193 Y 3.26588 Y3+ -33.108 Zr 3.65721 Zr4+ -2.6479 Nb 3.53346 Nb3+ 1.94715 Nb5+ .337905 Mo 3.7429 Mo3+ 2.30951 Mo5+ .740625 Mo6+ 0. Tc 2.71263 Ru 1.56756 Ru3+ 3.00964 Ru4+ 2.18535 Rh 1.28918 Rh3+ -6.1989 Rh4+ -5.6526 Pd .605844 Pd2+ 0. Pd4+ -7.9492 Ag 1.0463 Ag1+ .357534 Ag2+ 0. Cd 1.6029 Cd2+ 0. In 2.0396 In3+ 0. Sn 2.4663 Sn2+ .487 Sn4+ .0193 Sb 2.6827 Sb3+ .288753 Sb5+ 0. Te 2.5239 I 2.2735 I1- 2.8868 Xe 1.99 Cs 1.4953 Cs1+ .9615 Ba 2.6959 Ba2+ .773634 La 3.28719 La3+ .336048 Ce 3.33049 Ce3+ .612376 Ce4+ .144583 Pr 2.82428 Pr3+ .97518 Pr4+ .296689 Nd 2.85137 Nd3+ 1.51031 Pm 2.87516 Sm 2.89604 Sm3+ 2.71488 Eu 2.9227 Eu2+ 3.87243 Eu3+ 3.26503 Gd 3.54545 Gd3+ 3.7149 Tb 2.95354 Tb3+ 3.773 Dy 2.96577 Dy3+ 4.50073 Ho 3.63837 Ho3+ 4.93676 Er 2.98233 Er3+ 5.17379 Tm 2.98706 Tm3+ 5.38348 Yb 2.98963 Yb2+ 5.14657 Yb3+ 5.47647 Lu 3.71601 Lu3+ 5.59415 Hf 4.30013 Hf4+ 5.59927 Ta 4.76492 Ta5+ 5.38695 W 5.11982 W6+ 5.06412 Re 5.44174 Os 5.67589 Os4+ 5.06795 Ir 5.83377 Ir3+ 5.82008 Ir4+ 5.53672 Pt 5.7837 Pt2+ 6.35234 Pt4+ 5.92034 Au 5.86 Au1+ 6.58077 Au3+ 6.52354 Hg 5.9676 Hg1+ 6.48216 Hg2+ 6.89912 Tl 5.52593 TL1+ 6.82847 Tl3+ 7.00574 Pb 5.9696 Pb2+ 7.01107 Pb4+ 6.96886 Bi 6.4692 Bi3+ 7.10295 Bi5+ 6.91555 Po 7.02588 At 7.42518 Rn 7.4433 Fr 2.11253 Ra 3.21097 Ra2+ 7.65078 Ac 4.08655 Ac3+ 7.05545 Th 4.80703 Th4+ 5.29444 Pa 4.17287 U 4.1880 U3+ 5.37073 U4+ 4.79840 U6+ 1.21457 Np 4.18550 Np3+ 5.43227 Np4+ 4.92159 Np6+ 1.75669 Pu 3.47947 Pu3+ 5.66016 Pu4+ 5.18831 Pu6+ 2.28678 Am 3.49331 Cm 4.21665 Bk 4.23284 Cf 4.24391 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_a4 save_ save_atom_type_scat.Cromer_Mann_b1 _definition.id '_atom_type_scat.Cromer_Mann_b1' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 10.5109 D 10.5109 H1- 53.1368 He 9.1037 Li 3.9546 Li1+ 4.6237 Be 43.6427 Be2+ .0027 B 23.2185 C 20.8439 N .0057 O 13.2771 O1- 12.8573 F 10.2825 F1- 5.27756 Ne 8.4042 Na 3.285 Na1+ 2.6671 Mg 2.8275 Mg2+ 2.1676 Al 3.0387 Al3+ 1.93816 Si 2.4386 Si4+ 1.64167 P 1.9067 S 1.4679 Cl .0104 Cl1- .0066 Ar 0.9072 K 12.7949 K1+ 12.6331 Ca 10.4421 Ca2+ -.0074 Sc 9.0213 Sc3+ .29854 Ti 7.8508 Ti2+ 7.5243 Ti3+ .22061 Ti4+ .178847 V 6.8657 V2+ 6.8818 V3+ 6.39535 V5+ .679003 Cr 6.1038 Cr2+ 5.66078 Cr3+ 5.59463 Mn 5.3409 Mn2+ 5.2796 Mn3+ 4.91797 Mn4+ 4.8485 Fe 4.7611 Fe2+ 4.6538 Fe3+ 4.6147 Co 4.2791 Co2+ 4.1231 Co3+ 3.90969 Ni 3.8785 Ni2+ 3.6766 Ni3+ 3.5477 Cu 3.5828 Cu1+ 3.3669 Cu2+ 3.37484 Zn 3.2655 Zn2+ 2.9946 Ga 3.0669 Ga3+ 2.81262 Ge 2.8509 Ge4+ 2.53718 As 2.6345 Se 2.4098 Br 2.1723 Br1- 2.2059 Kr 1.9384 Rb 1.7888 Rb1+ 1.7139 Sr 1.5564 Sr2+ 1.4907 Y 1.4029 Y3+ 1.35417 Zr 1.27618 Zr4+ 1.2148 Nb 1.18865 Nb3+ .019175 Nb5+ 1.12446 Mo .2772 Mo3+ .014734 Mo5+ .014345 Mo6+ 1.03649 Tc .864132 Ru .80852 Ru3+ .847329 Ru4+ .844582 Rh .751536 Rh3+ .764252 Rh4+ .760825 Pd .698655 Pd2+ .696219 Pd4+ .683839 Ag .6446 Ag1+ .646179 Ag2+ .645643 Cd .5946 Cd2+ .597922 In .5476 In3+ .551522 Sn 5.8303 Sn2+ .5036 Sn4+ 5.764 Sb 5.3034 Sb3+ .467196 Sb5+ 5.44853 Te 4.81742 I 4.347 I1- 4.3579 Xe 3.9282 Cs 3.569 Cs1+ 3.552 Ba 3.216 Ba2+ 3.21367 La 2.94817 La3+ 2.9207 Ce 2.81219 Ce3+ 2.77691 Ce4+ 2.65941 Pr 2.77393 Pr3+ 2.6452 Pr4+ 2.54467 Nd 2.66248 Nd3+ 2.52722 Pm 2.5627 Sm 2.47274 Sm3+ 2.31641 Eu 2.3879 Eu2+ 2.27783 Eu3+ 2.22258 Gd 2.25341 Gd3+ 2.13553 Tb 2.24256 Tb3+ 2.05601 Dy 2.1802 Dy3+ 1.9804 Ho 2.07051 Ho3+ 1.91072 Er 2.07356 Er3+ 1.84659 Tm 2.02859 Tm3+ 1.78711 Yb 1.9889 Yb2+ 1.78503 Yb3+ 1.73272 Lu 1.90182 Lu3+ 1.68216 Hf 1.83262 Hf4+ 1.59136 Ta 1.77333 Ta5+ 1.50711 W 1.72029 W6+ 1.42755 Re 1.67191 Os 1.62903 Os4+ 1.37113 Ir 1.59279 Ir3+ 1.34323 Ir4+ 1.30923 Pt 1.51293 Pt2+ 1.32927 Pt4+ 1.24813 Au .4611 Au1+ 1.35321 Au3+ 1.2199 Hg .545 Hg1+ 1.39507 Hg2+ 1.21152 Tl .65515 TL1+ 1.4711 Tl3+ 1.1008 Pb .6902 Pb2+ 1.3366 Pb4+ 1.00566 Bi .704 Bi3+ 1.2356 Bi5+ .91654 Po .700999 At .685870 Rn .6631 Fr .646453 Ra .616341 Ra2+ .604909 Ac .589092 Ac3+ .579689 Th .563359 Th4+ .555054 Pa .547751 U .5293 U3+ .520480 U4+ .516598 U6+ .507079 Np .511929 Np3+ .502322 Np4+ .498626 Np6+ .489810 Pu .499384 Pu3+ .484938 Pu4+ .481422 Pu6+ .473204 Am .483629 Cm .465154 Bk .451018 Cf .437533 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_b1 save_ save_atom_type_scat.Cromer_Mann_b2 _definition.id '_atom_type_scat.Cromer_Mann_b2' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 26.1257 D 26.1257 H1- 15.187 He 3.3568 Li 1.0524 Li1+ 1.9557 Be 1.8623 Be2+ .8313 B 1.021 C 10.2075 N 9.8933 O 5.7011 O1- 4.17236 F 4.2944 F1- 14.7353 Ne 3.4262 Na 8.8422 Na1+ 6.1153 Mg 79.2611 Mg2+ 4.7542 Al .7426 Al3+ 4.14553 Si 32.3337 Si4+ 3.43757 P 27.157 S 22.2151 Cl 1.1662 Cl1- 1.1717 Ar 14.8407 K .7748 K1+ .7674 Ca .6599 Ca2+ .6089 Sc .5729 Sc3+ 7.9629 Ti .5 Ti2+ .457585 Ti3+ 7.04716 Ti4+ 6.67018 V .4385 V2+ .4409 V3+ .383349 V5+ 5.40135 Cr .392 Cr2+ .344261 Cr3+ .334393 Mn .3432 Mn2+ .3435 Mn3+ .294393 Mn4+ .283303 Fe .3072 Fe2+ .3053 Fe3+ .3005 Co .2784 Co2+ .2726 Co3+ .238668 Ni .2565 Ni2+ .2449 Ni3+ .22314 Cu .247 Cu1+ .2274 Cu2+ .244078 Zn .2333 Zn2+ .2031 Ga .2412 Ga3+ .22789 Ge .2516 Ge4+ .205855 As .2647 Se .2726 Br 16.5796 Br1- 19.3345 Kr 16.5623 Rb 17.3151 Rb1+ 14.7957 Sr 14.0988 Sr2+ 12.6963 Y 12.8006 Y3+ 11.2145 Zr 11.916 Zr4+ 10.1483 Nb 11.766 Nb3+ 1.13305 Nb5+ .028781 Mo 1.0958 Mo3+ 1.03031 Mo5+ 1.02238 Mo6+ 8.48061 Tc 8.14487 Ru 8.43467 Ru3+ 8.37164 Ru4+ 8.12534 Rh 8.21758 Rh3+ 7.84438 Rh4+ 7.62436 Pd 7.98929 Pd2+ 7.55573 Pd4+ 7.14833 Ag 7.4726 Ag1+ 7.19123 Ag2+ 7.18544 Cd 6.9089 Cd2+ 6.80639 In 6.3776 In3+ 6.3247 Sn .5031 Sn2+ 5.8378 Sn4+ .4655 Sb .4607 Sb3+ 5.22126 Sb5+ .467973 Te .420885 I .3814 I1- .3815 Xe 0.344 Cs .3107 Cs1+ .3086 Ba .2756 Ba2+ .28331 La .244475 La3+ .250698 Ce .226836 Ce3+ .23154 Ce4+ .21885 Pr .222087 Pr3+ .214299 Pr4+ .202481 Nd .210628 Nd3+ .199237 Pm 0.202088 Sm .196451 Sm3+ .174081 Eu .1942 Eu2+ .17353 Eu3+ .16394 Gd .181951 Gd3+ .155525 Tb .196143 Tb3+ .149525 Dy .202172 Dy3+ .143384 Ho .19794 Ho3+ .139358 Er .223545 Er3+ .13729 Tm .238849 Tm3+ .136974 Yb .25711 Yb2+ .15997 Yb3+ .13879 Lu 9.98519 Lu3+ .142292 Hf 9.5999 Hf4+ .128903 Ta 9.37046 Ta5+ .116741 W 9.2259 W6+ .104621 Re 9.09227 Os 8.97948 Os4+ 6.84706 Ir 8.86553 Ir3+ 7.10909 Ir4+ 6.71983 Pt 8.81174 Pt2+ 7.38979 Pt4+ 6.60834 Au 8.6216 Au1+ 7.7395 Au3+ 6.82872 Hg 8.4484 Hg1+ 7.65105 Hg2+ 7.05639 Tl 8.70751 TL1+ .517394 Tl3+ 6.53852 Pb 2.3576 Pb2+ .488383 Pb4+ 6.10926 Bi 2.9238 Bi3+ 6.24149 Bi5+ .039042 Po 3.55078 At 3.97458 Rn 4.0691 Fr 4.17619 Ra 3.87135 Ra2+ 3.57670 Ac 3.65155 Ac3+ 3.41437 Th 3.46204 Th4+ 3.24498 Pa 3.41519 U 3.3253 U3+ 3.12293 U4+ 3.05053 U6+ 2.89030 Np 3.25396 Np3+ 3.03807 Np4+ 2.96627 Np6+ 2.81099 Pu 3.26371 Pu3+ 2.96118 Pu4+ 2.89020 Pu6+ 2.73848 Am 3.20647 Cm 3.08997 Bk 3.04619 Cf 3.00775 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_b2 save_ save_atom_type_scat.Cromer_Mann_b3 _definition.id '_atom_type_scat.Cromer_Mann_b3' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 3.14236 D 3.14236 H1- 186.576 He 22.9276 Li 85.3905 Li1+ .6316 Be 103.483 Be2+ 2.2758 B 60.3498 C .5687 N 28.9975 O .3239 O1- 47.0179 F .2615 F1- .442258 Ne 0.2306 Na .3136 Na1+ .2001 Mg .3808 Mg2+ .185 Al 31.5472 Al3+ .228753 Si .6785 Si4+ .2149 P .526 S .2536 Cl 18.5194 Cl1- 19.5424 Ar 43.8983 K 213.187 K1+ -.002 Ca 85.7484 Ca2+ 10.3116 Sc 136.108 Sc3+ -.28604 Ti 35.6338 Ti2+ 19.5361 Ti3+ -.15762 Ti4+ -.29263 V 26.8938 V2+ 20.3004 V3+ 15.1908 V5+ 9.97278 Cr 20.2626 Cr2+ 13.3075 Cr3+ 12.8288 Mn 17.8674 Mn2+ 14.343 Mn3+ 10.8171 Mn4+ 10.4852 Fe 15.3535 Fe2+ 12.0546 Fe3+ 11.6729 Co 13.5359 Co2+ 10.2443 Co3+ 8.35583 Ni 12.1763 Ni2+ 8.873 Ni3+ 7.64468 Cu 11.3966 Cu1+ 8.6625 Cu2+ 7.9876 Zn 10.3163 Zn2+ 7.0826 Ga 10.7805 Ga3+ 6.36441 Ge 11.4468 Ge4+ 5.47913 As 12.9479 Se 15.2372 Br .2609 Br1- .2871 Kr 0.2261 Rb .2748 Rb1+ .1603 Sr .1664 Sr2+ 24.5651 Y .125599 Y3+ 22.6599 Zr .117622 Zr4+ 21.6054 Nb .204785 Nb3+ 10.1621 Nb5+ 9.28206 Mo 11.004 Mo3+ 9.53659 Mo5+ 8.78809 Mo6+ .058881 Tc 21.5707 Ru 24.7997 Ru3+ .017662 Ru4+ .036495 Rh 25.8749 Rh3+ 21.2487 Rh4+ 19.3317 Pd 25.2052 Pd2+ 22.5057 Pd4+ 17.9144 Ag 24.6605 Ag1+ 21.7326 Ag2+ 21.4072 Cd 24.7008 Cd2+ 20.2521 In 25.8499 In3+ 17.3595 Sn 26.8909 Sn2+ 23.3752 Sn4+ 14.0049 Sb 27.9074 Sb3+ 19.5902 Sb5+ 14.1259 Te 28.5284 I 27.766 I1- 29.5259 Xe 26.4659 Cs 24.3879 Cs1+ 23.7128 Ba 20.2073 Ba2+ 20.0558 La 18.7726 La3+ 17.8211 Ce 17.6083 Ce3+ 16.5408 Ce4+ 15.7992 Pr 16.7669 Pr3+ 15.323 Pr4+ 14.8137 Nd 15.885 Nd3+ 14.1783 Pm 15.1009 Sm 14.3996 Sm3+ 12.1571 Eu 13.7546 Eu2+ 11.6096 Eu3+ 11.311 Gd 12.9331 Gd3+ 10.5782 Tb 12.6648 Tb3+ 10.0499 Dy 12.1899 Dy3+ 9.34972 Ho 11.4407 Ho3+ 8.80018 Er 11.3604 Er3+ 8.36225 Tm 10.9975 Tm3+ 7.96778 Yb 10.6647 Yb2+ 8.18304 Yb3+ 7.64412 Lu .261033 Lu3+ 7.33727 Hf .275116 Hf4+ 6.76232 Ta .295977 Ta5+ 6.31524 W .321703 W6+ 5.93667 Re .3505 Os .382661 Os4+ .165191 Ir .417916 Ir3+ .204633 Ir4+ .167252 Pt .424593 Pt2+ .263297 Pt4+ .16864 Au 1.4826 Au1+ .356752 Au3+ .212867 Hg 1.5729 Hg1+ .443378 Hg2+ .284738 Tl 1.96347 TL1+ 7.43463 Tl3+ .219074 Pb 8.618 Pb2+ 6.7727 Pb4+ .147041 Bi 8.7937 Bi3+ .469999 Bi5+ 5.71414 Po 9.55642 At 11.3824 Rn 14.0422 Fr 23.1052 Ra 19.9887 Ra2+ 12.6010 Ac 18.5990 Ac3+ 12.9187 Th 17.8309 Th4+ 13.4661 Pa 16.9235 U 16.0927 U3+ 12.7148 U4+ 12.5723 U6+ 13.1767 Np 15.3622 Np3+ 12.1449 Np4+ 11.9484 Np6+ 12.3300 Pu 14.9455 Pu3+ 11.5331 Pu4+ 11.3160 Pu6+ 11.5530 Am 14.3136 Cm 13.4346 Bk 12.8946 Cf 12.4044 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_b3 save_ save_atom_type_scat.Cromer_Mann_b4 _definition.id '_atom_type_scat.Cromer_Mann_b4' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H 57.7997 D 57.7997 H1- 3.56709 He 0.9821 Li 168.261 Li1+ 10.0953 Be .542 Be2+ 5.1146 B .1403 C 51.6512 N .5826 O 32.9089 O1- -.01404 F 26.1476 F1- 47.3437 Ne 21.7814 Na 129.424 Na1+ 14.039 Mg 7.1937 Mg2+ 10.1411 Al 85.0886 Al3+ 8.28524 Si 81.6937 Si4+ 6.65365 P 68.1645 S 56.172 Cl 47.7784 Cl1- 60.4486 Ar 33.3929 K 41.6841 K1+ 31.9128 Ca 178.437 Ca2+ 25.9905 Sc 51.3531 Sc3+ 16.0662 Ti 116.105 Ti2+ 61.6558 Ti3+ 15.9768 Ti4+ 12.9464 V 102.478 V2+ 115.122 V3+ 63.969 V5+ .940464 Cr 98.7399 Cr2+ 32.4224 Cr3+ 32.8761 Mn 83.7543 Mn2+ 41.3235 Mn3+ 24.1281 Mn4+ 27.573 Fe 76.8805 Fe2+ 31.2809 Fe3+ 38.5566 Co 71.1692 Co2+ 25.6466 Co3+ 18.3491 Ni 66.3421 Ni2+ 22.1626 Ni3+ 16.9673 Cu 64.8126 Cu1+ 25.8487 Cu2+ 19.897 Zn 58.7097 Zn2+ 18.0995 Ga 61.4135 Ga3+ 14.4122 Ge 54.7625 Ge4+ 11.603 As 47.7972 Se 43.8163 Br 41.4328 Br1- 58.1535 Kr 39.3972 Rb 164.934 Rb1+ 31.2087 Sr 132.376 Sr2+ -.0138 Y 104.354 Y3+ -.01319 Zr 87.6627 Zr4+ -.10276 Nb 69.7957 Nb3+ 28.3389 Nb5+ 25.7228 Mo 61.6584 Mo3+ 26.6307 Mo5+ 23.3452 Mo6+ 0. Tc 86.8472 Ru 94.2928 Ru3+ 22.887 Ru4+ 20.8504 Rh 98.6062 Rh3+ -.01036 Rh4+ -.0102 Pd 76.8986 Pd2+ 0. Pd4+ .005127 Ag 99.8156 Ag1+ 66.1147 Ag2+ 0. Cd 87.4825 Cd2+ 0. In 92.8029 In3+ 0. Sn 83.9571 Sn2+ 62.2061 Sn4+ -.7583 Sb 75.2825 Sb3+ 55.5113 Sb5+ 0. Te 70.8403 I 66.8776 I1- 84.9304 Xe 64.2658 Cs 213.904 Cs1+ 59.4565 Ba 167.202 Ba2+ 51.746 La 133.124 La3+ 54.9453 Ce 127.113 Ce3+ 43.1692 Ce4+ 62.2355 Pr 143.644 Pr3+ 36.4065 Pr4+ 45.4643 Nd 137.903 Nd3+ 30.8717 Pm 132.721 Sm 128.007 Sm3+ 24.8242 Eu 123.174 Eu2+ 26.5156 Eu3+ 22.9966 Gd 101.398 Gd3+ 21.7029 Tb 115.362 Tb3+ 21.2773 Dy 111.874 Dy3+ 19.581 Ho 92.6566 Ho3+ 18.5908 Er 105.703 Er3+ 17.8974 Tm 102.961 Tm3+ 17.2922 Yb 100.417 Yb2+ 20.39 Yb3+ 16.8153 Lu 84.3298 Lu3+ 16.3535 Hf 72.029 Hf4+ 14.0366 Ta 63.3644 Ta5+ 12.4244 W 57.056 W6+ 11.1972 Re 52.0861 Os 48.1647 Os4+ 18.003 Ir 45.0011 Ir3+ 20.3254 Ir4+ 17.4911 Pt 38.6103 Pt2+ 22.9426 Pt4+ 16.9392 Au 36.3956 Au1+ 26.4043 Au3+ 18.659 Hg 38.3246 Hg1+ 28.2262 Hg2+ 20.7482 Tl 45.8149 TL1+ 28.8482 Tl3+ 17.2114 Pb 47.2579 Pb2+ 23.8132 Pb4+ 14.714 Bi 48.0093 Bi3+ 20.3185 Bi5+ 12.8285 Po 47.0045 At 45.4715 Rn 44.2473 Fr 150.645 Ra 142.325 Ra2+ 29.8436 Ac 117.020 Ac3+ 25.9443 Th 99.1722 Th4+ 23.9533 Pa 105.251 U 100.613 U3+ 26.3394 U4+ 23.4582 U6+ 25.2017 Np 97.4908 Np3+ 25.4928 Np4+ 22.7502 Np6+ 22.6581 Pu 105.980 Pu3+ 24.3992 Pu4+ 21.8301 Pu6+ 20.9303 Am 102.273 Cm 88.4834 Bk 86.0030 Cf 83.7881 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_b4 save_ save_atom_type_scat.Cromer_Mann_c _definition.id '_atom_type_scat.Cromer_Mann_c' _definition.update 2006-06-29 _description.text ; The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .003038 D .003038 H1- .002389 He 0.0064 Li .0377 Li1+ .0167 Be .0385 Be2+ -6.1092 B -.1932 C .2156 N -11.529 O .2508 O1- 21.9412 F .2776 F1- .653396 Ne 0.3515 Na .6760 Na1+ .4040 Mg .8584 Mg2+ .4853 Al 1.1151 Al3+ .706786 Si 1.1407 Si4+ .746297 P 1.1149 S .8669 Cl -9.5574 Cl1- -16.378 Ar 1.44450 K 1.4228 K1+ -4.9978 Ca 1.3751 Ca2+ -14.875 Sc 1.3329 Sc3+ -6.6667 Ti 1.2807 Ti2+ .897155 Ti3+ -14.652 Ti4+ -13.280 V 1.2199 V2+ 1.2298 V3+ .656565 V5+ 1.71430 Cr 1.1832 Cr2+ .616898 Cr3+ .518275 Mn 1.0896 Mn2+ 1.0874 Mn3+ .393974 Mn4+ .251877 Fe 1.0369 Fe2+ 1.0097 Fe3+ .9707 Co 1.0118 Co2+ .9324 Co3+ .286667 Ni 1.0341 Ni2+ .8614 Ni3+ .386044 Cu 1.1910 Cu1+ .8900 Cu2+ 1.14431 Zn 1.3041 Zn2+ .7807 Ga 1.7189 Ga3+ 1.53545 Ge 2.1313 Ge4+ 1.45572 As 2.5310 Se 2.8409 Br 2.9557 Br1- 3.1776 Kr 2.825 Rb 3.4873 Rb1+ 2.0782 Sr 2.5064 Sr2+ 41.4025 Y 1.91213 Y3+ 40.2602 Zr 2.06929 Zr4+ 9.41454 Nb 3.75591 Nb3+ -12.912 Nb5+ -6.3934 Mo 4.3875 Mo3+ -14.421 Mo5+ -14.316 Mo6+ .344941 Tc 5.40428 Ru 5.37874 Ru3+ -3.1892 Ru4+ 1.42357 Rh 5.32800 Rh3+ 11.8678 Rh4+ 11.2835 Pd 5.26593 Pd2+ 5.29160 Pd4+ 13.0174 Ag 5.1790 Ag1+ 5.21572 Ag2+ 5.21404 Cd 5.0694 Cd2+ 5.11937 In 4.9391 In3+ 4.99635 Sn 4.7821 Sn2+ 4.7861 Sn4+ 3.9182 Sb 4.5909 Sb3+ 4.69626 Sb5+ 4.69263 Te 4.35200 I 4.0712 I1- 4.0714 Xe 3.7118 Cs 3.3352 Cs1+ 3.2791 Ba 2.7731 Ba2+ 3.02902 La 2.14678 La3+ 2.40860 Ce 1.86264 Ce3+ 2.09013 Ce4+ 1.59180 Pr 2.05830 Pr3+ 1.77132 Pr4+ 1.24285 Nd 1.98486 Nd3+ 1.47588 Pm 2.02876 Sm 2.20963 Sm3+ .954586 Eu 2.5745 Eu2+ 1.36389 Eu3+ .759344 Gd 2.41960 Gd3+ .645089 Tb 3.58324 Tb3+ .691967 Dy 4.29728 Dy3+ .689690 Ho 4.56796 Ho3+ .852795 Er 5.92046 Er3+ 1.17613 Tm 6.75621 Tm3+ 1.63929 Yb 7.56672 Yb2+ 3.70983 Yb3+ 2.26001 Lu 7.97628 Lu3+ 2.97573 Hf 8.58154 Hf4+ 2.39699 Ta 9.24354 Ta5+ 1.78555 W 9.88750 W6+ 1.01074 Re 10.4720 Os 11.0005 Os4+ 6.49804 Ir 11.4722 Ir3+ 8.27903 Ir4+ 6.96824 Pt 11.6883 Pt2+ 9.85329 Pt4+ 7.39534 Au 12.0658 Au1+ 11.2299 Au3+ 9.09680 Hg 12.6089 Hg1+ 12.0205 Hg2+ 10.6268 Tl 13.1746 TL1+ 12.5258 Tl3+ 9.80270 Pb 13.4118 Pb2+ 12.4734 Pb4+ 8.08428 Bi 13.5782 Bi3+ 12.4711 Bi5+ -6.7994 Po 13.6770 At 13.7108 Rn 13.6905 Fr 13.7247 Ra 13.6211 Ra2+ 13.5431 Ac 13.5266 Ac3+ 13.4637 Th 13.4314 Th4+ 13.3760 Pa 13.4287 U 13.3966 U3+ 13.3092 U4+ 13.2671 U6+ 13.1665 Np 13.3573 Np3+ 13.2544 Np4+ 13.2116 Np6+ 13.1130 Pu 13.3812 Pu3+ 13.1991 Pu4+ 13.1555 Pu6+ 13.0582 Am 13.3592 Cm 13.2887 Bk 13.2754 Cf 13.2674 _enumeration.def_index_id '_atom_type.element_symbol' _name.category_id atom_type_scat _name.object_id Cromer_Mann_c save_ save_atom_type_scat.dispersion_imag _definition.id '_atom_type_scat.dispersion_imag' _definition.update 2006-12-14 _description.text ; The imaginary component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value ; _description.common 'AnomDispImag' _name.category_id atom_type_scat _name.object_id dispersion_imag _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.0 loop_ _method.purpose _method.expression Evaluation ; With q as atom_type_scat If ( _diffrn_radiation.type == 'Cu' ) a = q.dispersion_imag_cu If ( _diffrn_radiation.type == 'Mo' ) a = q.dispersion_imag_mo _atom_type_scat.dispersion_imag = a ; save_ save_atom_type_scat.dispersion_imag_cu _definition.id '_atom_type_scat.dispersion_imag_cu' _definition.update 2006-12-14 _description.text ; The imaginary component of the anomalous dispersion scattering factors for this atom type and Cu K alpha radiation ; _description.common 'AnomDispImagCu' _name.category_id atom_type_scat _name.object_id dispersion_imag_cu _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He .0 Li .0 Li1+ .0 Be .001 Be2+ .001 B .004 C .009 N .018 O .032 O1- .032 F .053 F1- .053 Ne .083 Na .124 Na1+ .124 Mg .177 Mg2+ .177 Al .246 Al3+ .246 Si .33 Si4+ .33 P .434 S .557 Cl .702 Cl1- .702 Ar .872 K 1.066 K1+ 1.066 Ca 1.286 Ca2+ 1.286 Sc 1.533 Sc3+ 1.533 Ti 1.807 Ti2+ 1.807 Ti3+ 1.807 Ti4+ 1.807 V 2.11 V2+ 2.11 V3+ 2.11 V5+ 2.11 Cr 2.443 Cr2+ 2.443 Cr3+ 2.443 Mn 2.808 Mn2+ 2.808 Mn3+ 2.808 Mn4+ 2.808 Fe 3.204 Fe2+ 3.204 Fe3+ 3.204 Co 3.608 Co2+ 3.608 Co3+ 3.608 Ni .509 Ni2+ .509 Ni3+ .509 Cu .589 Cu1+ .589 Cu2+ .589 Zn .678 Zn2+ .678 Ga 0.777 Ga3+ 0.777 Ge .886 Ge4+ .886 As 1.006 Se 1.139 Br 1.283 Br1- 1.283 Kr 1.439 Rb 1.608 Rb1+ 1.608 Sr 1.82 Sr2+ 1.82 Y 2.025 Y3+ 2.025 Zr 2.245 Zr4+ 2.245 Nb 2.482 Nb3+ 2.482 Nb5+ 2.482 Mo 2.735 Mo3+ 2.735 Mo5+ 2.735 Mo6+ 2.735 Tc 3.005 Ru 3.296 Ru3+ 3.296 Ru4+ 3.296 Rh 3.605 Rh3+ 3.605 Rh4+ 3.605 Pd 3.934 Pd2+ 3.934 Pd4+ 3.934 Ag 4.282 Ag1+ 4.282 Ag2+ 4.282 Cd 4.653 Cd2+ 4.653 In 5.045 In3+ 5.045 Sn 5.459 Sn2+ 5.459 Sn4+ 5.459 Sb 5.894 Sb3+ 5.894 Sb5+ 5.894 Te 6.352 I 6.835 I1- 6.835 Xe 7.348 Cs 7.904 Cs1+ 7.904 Ba 8.46 Ba2+ 8.46 La 9.036 La3+ 9.036 Ce 9.648 Ce3+ 9.648 Ce4+ 9.648 Pr 10.535 Pr3+ 10.535 Pr4+ 10.535 Nd 10.933 Nd3+ 10.933 Pm 11.614 Sm 12.32 Sm3+ 12.32 Eu 11.276 Eu2+ 11.276 Eu3+ 11.276 Gd 11.946 Gd3+ 11.946 Tb 9.242 Tb3+ 9.242 Dy 9.748 Dy3+ 9.748 Ho 3.704 Ho3+ 3.704 Er 3.937 Er3+ 3.937 Tm 4.181 Tm3+ 4.181 Yb 4.432 Yb2+ 4.432 Yb3+ 4.432 Lu 4.693 Lu3+ 4.693 Hf 4.977 Hf4+ 4.977 Ta 5.271 Ta5+ 5.271 W 5.577 W6+ 5.577 Re 5.891 Os 6.221 Os4+ 6.221 Ir 6.566 Ir3+ 6.566 Ir4+ 6.566 Pt 6.925 Pt2+ 6.925 Pt4+ 6.925 Au 7.297 Au1+ 7.297 Au3+ 7.297 Hg 7.686 Hg1+ 7.686 Hg2+ 7.686 Tl 8.089 TL1+ 8.089 Tl3+ 8.089 Pb 8.505 Pb2+ 8.505 Pb4+ 8.505 Bi 8.93 Bi3+ 8.93 Bi5+ 8.93 Po 9.383 At 9.843 Rn 10.317 Fr 10.803 Ra 11.296 Ra2+ 11.296 Ac 11.799 Ac3+ 11.799 Th 12.33 Th4+ 12.33 Pa 12.868 U 13.409 U3+ 13.409 U4+ 13.409 U6+ 13.409 Np 13.967 Np3+ 13.967 Np4+ 13.967 Np6+ 13.967 Pu 14.536 Pu3+ 14.536 Pu4+ 14.536 Pu6+ 14.536 Am 15.087 Cm 15.634 Bk 16.317 Cf 16.93 _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type_scat.dispersion_imag_mo _definition.id '_atom_type_scat.dispersion_imag_mo' _definition.update 2006-12-14 _description.text ; The imaginary component of the anomalous dispersion scattering factors for this atom type and Mo K alpha radiation ; _description.common 'AnomDispImagMo' _name.category_id atom_type_scat _name.object_id dispersion_imag_mo _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He .0 Li .0 Li1+ .0 Be .0 Be2+ .0 B .001 C .002 N .003 O .006 O1- .006 F .01 F1- .01 Ne .016 Na .025 Na1+ .025 Mg .036 Mg2+ .036 Al .052 Al3+ .052 Si .071 Si4+ .071 P .095 S .124 Cl .159 Cl1- .159 Ar .201 K .25 K1+ .25 Ca .306 Ca2+ .306 Sc 0.372 Sc3+ 0.372 Ti .446 Ti2+ .446 Ti3+ .446 Ti4+ .446 V .53 V2+ .53 V3+ .53 V5+ .53 Cr .624 Cr2+ .624 Cr3+ .624 Mn .729 Mn2+ .729 Mn3+ .729 Mn4+ .729 Fe .845 Fe2+ .845 Fe3+ .845 Co .973 Co2+ .973 Co3+ .973 Ni 1.113 Ni2+ 1.113 Ni3+ 1.113 Cu 1.266 Cu1+ 1.266 Cu2+ 1.266 Zn 1.431 Zn2+ 1.431 Ga 1.609 Ga3+ 1.609 Ge 1.801 Ge4+ 1.801 As 2.007 Se 2.223 Br 2.456 Br1- 2.456 Kr 2.713 Rb 2.973 Rb1+ 2.973 Sr 3.264 Sr2+ 3.264 Y 3.542 Y3+ 3.542 Zr .56 Zr4+ .56 Nb 0.621 Nb3+ 0.621 Nb5+ 0.621 Mo .688 Mo3+ .688 Mo5+ .688 Mo6+ .688 Tc .759 Ru .836 Ru3+ .836 Ru4+ .836 Rh .919 Rh3+ .919 Rh4+ .919 Pd 1.007 Pd2+ 1.007 Pd4+ 1.007 Ag 1.101 Ag1+ 1.101 Ag2+ 1.101 Cd 1.202 Cd2+ 1.202 In 1.31 In3+ 1.31 Sn 1.424 Sn2+ 1.424 Sn4+ 1.424 Sb 1.546 Sb3+ 1.546 Sb5+ 1.546 Te 1.675 I 1.812 I1- 1.812 Xe 1.958 Cs 2.119 Cs1+ 2.119 Ba 2.282 Ba2+ 2.282 La 2.452 La3+ 2.452 Ce 2.632 Ce3+ 2.632 Ce4+ 2.632 Pr 2.845 Pr3+ 2.845 Pr4+ 2.845 Nd 3.018 Nd3+ 3.018 Pm 3.225 Sm 3.442 Sm3+ 3.442 Eu 3.669 Eu2+ 3.669 Eu3+ 3.669 Gd 3.904 Gd3+ 3.904 Tb 4.151 Tb3+ 4.151 Dy 4.41 Dy3+ 4.41 Ho 4.678 Ho3+ 4.678 Er 4.958 Er3+ 4.958 Tm 5.248 Tm3+ 5.248 Yb 5.548 Yb2+ 5.548 Yb3+ 5.548 Lu 5.858 Lu3+ 5.858 Hf 6.185 Hf4+ 6.185 Ta 6.523 Ta5+ 6.523 W 6.872 W6+ 6.872 Re 7.232 Os 7.605 Os4+ 7.605 Ir 7.99 Ir3+ 7.99 Ir4+ 7.99 Pt 8.388 Pt2+ 8.388 Pt4+ 8.388 Au 8.798 Au1+ 8.798 Au3+ 8.798 Hg 9.223 Hg1+ 9.223 Hg2+ 9.223 Tl 9.659 TL1+ 9.659 Tl3+ 9.659 Pb 10.102 Pb2+ 10.102 Pb4+ 10.102 Bi 10.559 Bi3+ 10.559 Bi5+ 10.559 Po 11.042 At 9.961 Rn 10.403 Fr 7.754 Ra 8.105 Ra2+ 8.105 Ac 8.472 Ac3+ 8.472 Th 8.87 Th4+ 8.87 Pa 9.284 U 9.654 U3+ 9.654 U4+ 9.654 U6+ 9.654 Np 4.148 Np3+ 4.148 Np4+ 4.148 Np6+ 4.148 Pu 4.33 Pu3+ 4.33 Pu4+ 4.33 Pu6+ 4.33 Am 4.511 Cm 4.697 Bk 4.908 Cf 5.107 _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type_scat.dispersion_real _definition.id '_atom_type_scat.dispersion_real' _definition.update 2006-12-14 _description.text ; The real component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value ; _description.common 'AtomTypeAnomDispReal' _name.category_id atom_type_scat _name.object_id dispersion_real _type.purpose Assigned _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With q as atom_type_scat If ( _diffrn_radiation.type == 'Cu' ) a = q.dispersion_real_cu If ( _diffrn_radiation.type == 'Mo' ) a = q.dispersion_real_mo _atom_type_scat.dispersion_real = a ; _enumeration.default 0.0 save_ save_atom_type_scat.dispersion_real_cu _definition.id '_atom_type_scat.dispersion_real_cu' _definition.update 2006-12-14 _description.text ; The real component of the anomalous dispersion scattering factors for this atom type and Cu K alpha radiation ; _description.common 'AnomDispRealCu' _name.category_id atom_type_scat _name.object_id dispersion_real_cu _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He .0 Li .001 Li1+ .001 Be .003 Be2+ .003 B .008 C .017 N .029 O .047 O1- .047 F .069 F1- .069 Ne .097 Na 0.129 Na1+ 0.129 Mg .165 Mg2+ .165 Al .204 Al3+ .204 Si .244 Si4+ .244 P .283 S .319 Cl .348 Cl1- .348 Ar .366 K .365 K1+ .365 Ca .341 Ca2+ .341 Sc 0.285 Sc3+ 0.285 Ti .189 Ti2+ .189 Ti3+ .189 Ti4+ .189 V .035 V2+ .035 V3+ .035 V5+ .035 Cr -.198 Cr2+ -.198 Cr3+ -.198 Mn -.568 Mn2+ -.568 Mn3+ -.568 Mn4+ -.568 Fe -1.179 Fe2+ -1.179 Fe3+ -1.179 Co -2.464 Co2+ -2.464 Co3+ -2.464 Ni -2.956 Ni2+ -2.956 Ni3+ -2.956 Cu -2.019 Cu1+ -2.019 Cu2+ -2.019 Zn -1.612 Zn2+ -1.612 Ga -1.354 Ga3+ -1.354 Ge -1.163 Ge4+ -1.163 As -1.011 Se -.879 Br -.767 Br1- -.767 Kr -.665 Rb -.574 Rb1+ -.574 Sr -.465 Sr2+ -.465 Y -.386 Y3+ -.386 Zr -.314 Zr4+ -.314 Nb -.248 Nb3+ -.248 Nb5+ -.248 Mo -.191 Mo3+ -.191 Mo5+ -.191 Mo6+ -.191 Tc -.145 Ru -.105 Ru3+ -.105 Ru4+ -.105 Rh -.077 Rh3+ -.077 Rh4+ -.077 Pd -.059 Pd2+ -.059 Pd4+ -.059 Ag -.06 Ag1+ -.06 Ag2+ -.06 Cd -.079 Cd2+ -.079 In -.126 In3+ -.126 Sn -.194 Sn2+ -.194 Sn4+ -.194 Sb -.287 Sb3+ -.287 Sb5+ -.287 Te -.418 I -.579 I1- -.579 Xe -.783 Cs -1.022 Cs1+ -1.022 Ba -1.334 Ba2+ -1.334 La -1.716 La3+ -1.716 Ce -2.17 Ce3+ -2.17 Ce4+ -2.17 Pr -2.939 Pr3+ -2.939 Pr4+ -2.939 Nd -3.431 Nd3+ -3.431 Pm -4.357 Sm -5.696 Sm3+ -5.696 Eu -7.718 Eu2+ -7.718 Eu3+ -7.718 Gd -9.242 Gd3+ -9.242 Tb -9.498 Tb3+ -9.498 Dy -10.423 Dy3+ -10.423 Ho -12.255 Ho3+ -12.255 Er -9.733 Er3+ -9.733 Tm -8.488 Tm3+ -8.488 Yb -7.701 Yb2+ -7.701 Yb3+ -7.701 Lu -7.133 Lu3+ -7.133 Hf -6.715 Hf4+ -6.715 Ta -6.351 Ta5+ -6.351 W -6.048 W6+ -6.048 Re -5.79 Os -5.581 Os4+ -5.581 Ir -5.391 Ir3+ -5.391 Ir4+ -5.391 Pt -5.233 Pt2+ -5.233 Pt4+ -5.233 Au -5.096 Au1+ -5.096 Au3+ -5.096 Hg -4.99 Hg1+ -4.99 Hg2+ -4.99 Tl -4.883 TL1+ -4.883 Tl3+ -4.883 Pb -4.818 Pb2+ -4.818 Pb4+ -4.818 Bi -4.776 Bi3+ -4.776 Bi5+ -4.776 Po -4.756 At -4.772 Rn -4.787 Fr -4.833 Ra -4.898 Ra2+ -4.898 Ac -4.994 Ac3+ -4.994 Th -5.091 Th4+ -5.091 Pa -5.216 U -5.359 U3+ -5.359 U4+ -5.359 U6+ -5.359 Np -5.529 Np3+ -5.529 Np4+ -5.529 Np6+ -5.529 Pu -5.712 Pu3+ -5.712 Pu4+ -5.712 Pu6+ -5.712 Am -5.93 Cm -6.176 Bk -6.498 Cf -6.798 _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type_scat.dispersion_real_mo _definition.id '_atom_type_scat.dispersion_real_mo' _definition.update 2006-12-14 _description.text ; The real component of the anomalous dispersion scattering factors for this atom type and Mo K alpha radiation ; _description.common 'AnomDispRealMo' _name.category_id atom_type_scat _name.object_id dispersion_real_mo _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He .0 Li .0 Li1+ .0 Be .0 Be2+ .0 B .0 C .002 N .004 O .008 O1- .008 F .014 F1- .014 Ne .021 Na 0.03 Na1+ 0.03 Mg .042 Mg2+ .042 Al .056 Al3+ .056 Si .072 Si4+ .072 P .09 S .11 Cl .132 Cl1- .132 Ar .155 K .179 K1+ .179 Ca .203 Ca2+ .203 Sc 0.226 Sc3+ 0.226 Ti .248 Ti2+ .248 Ti3+ .248 Ti4+ .248 V .267 V2+ .267 V3+ .267 V5+ .267 Cr .284 Cr2+ .284 Cr3+ .284 Mn .295 Mn2+ .295 Mn3+ .295 Mn4+ .295 Fe .301 Fe2+ .301 Fe3+ .301 Co .299 Co2+ .299 Co3+ .299 Ni .285 Ni2+ .285 Ni3+ .285 Cu .263 Cu1+ .263 Cu2+ .263 Zn .222 Zn2+ .222 Ga 0.163 Ga3+ 0.163 Ge .081 Ge4+ .081 As -.03 Se -.178 Br -.374 Br1- -.374 Kr -.652 Rb -1.044 Rb1+ -1.044 Sr -1.657 Sr2+ -1.657 Y -2.951 Y3+ -2.951 Zr -2.965 Zr4+ -2.965 Nb -2.197 Nb3+ -2.197 Nb5+ -2.197 Mo -1.825 Mo3+ -1.825 Mo5+ -1.825 Mo6+ -1.825 Tc -1.59 Ru -1.42 Ru3+ -1.42 Ru4+ -1.42 Rh -1.287 Rh3+ -1.287 Rh4+ -1.287 Pd -1.177 Pd2+ -1.177 Pd4+ -1.177 Ag -1.085 Ag1+ -1.085 Ag2+ -1.085 Cd -1.005 Cd2+ -1.005 In -.936 In3+ -.936 Sn -.873 Sn2+ -.873 Sn4+ -.873 Sb -.816 Sb3+ -.816 Sb5+ -.816 Te -.772 I -.726 I1- -.726 Xe -.684 Cs -.644 Cs1+ -.644 Ba -.613 Ba2+ -.613 La -.588 La3+ -.588 Ce -.564 Ce3+ -.564 Ce4+ -.564 Pr -.53 Pr3+ -.53 Pr4+ -.53 Nd -.535 Nd3+ -.535 Pm -.53 Sm -.533 Sm3+ -.533 Eu -.542 Eu2+ -.542 Eu3+ -.542 Gd -.564 Gd3+ -.564 Tb -.591 Tb3+ -.591 Dy -.619 Dy3+ -.619 Ho -.666 Ho3+ -.666 Er -.723 Er3+ -.723 Tm -.795 Tm3+ -.795 Yb -.884 Yb2+ -.884 Yb3+ -.884 Lu -.988 Lu3+ -.988 Hf -1.118 Hf4+ -1.118 Ta -1.258 Ta5+ -1.258 W -1.421 W6+ -1.421 Re -1.598 Os -1.816 Os4+ -1.816 Ir -2.066 Ir3+ -2.066 Ir4+ -2.066 Pt -2.352 Pt2+ -2.352 Pt4+ -2.352 Au -2.688 Au1+ -2.688 Au3+ -2.688 Hg -3.084 Hg1+ -3.084 Hg2+ -3.084 Tl -3.556 TL1+ -3.556 Tl3+ -3.556 Pb -4.133 Pb2+ -4.133 Pb4+ -4.133 Bi -4.861 Bi3+ -4.861 Bi5+ -4.861 Po -5.924 At -7.444 Rn -8.862 Fr -7.912 Ra -7.62 Ra2+ -7.62 Ac -7.725 Ac3+ -7.725 Th -8.127 Th4+ -8.127 Pa -8.96 U -10.673 U3+ -10.673 U4+ -10.673 U6+ -10.673 Np -11.158 Np3+ -11.158 Np4+ -11.158 Np6+ -11.158 Pu -9.725 Pu3+ -9.725 Pu4+ -9.725 Pu6+ -9.725 Am -8.926 Cm -8.416 Bk -7.99 Cf -7.683 _enumeration.def_index_id '_atom_type.element_symbol' save_ save_atom_type_scat.dispersion_source _definition.id '_atom_type_scat.dispersion_source' _definition.update 2006-12-14 _description.text ; Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type. ; _description.common 'AtomTypeAnomDispDetails' _name.category_id atom_type_scat _name.object_id dispersion_source _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'International Tables Vol. IV Table 2.3.1' save_ save_atom_type_scat.hi_ang_Fox_coeffs _definition.id '_atom_type_scat.hi_ang_Fox_coeffs' _definition.update 2006-12-14 _description.text ; 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 ; _description.common 'AtomTypeFoxCoeffs' _name.category_id atom_type_scat _name.object_id hi_ang_Fox_coeffs _type.purpose Measured _type.container Tuple _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With t as atom_type_scat _atom_type_scat.hi_ang_Fox_coeffs = Tuple( t.hi_ang_Fox_c0, t.hi_ang_Fox_c1, t.hi_ang_Fox_c2, t.hi_ang_Fox_c3 ) ; save_ save_atom_type_scat.hi_ang_Fox_c0 _definition.id '_atom_type_scat.hi_ang_Fox_c0' _definition.update 2006-06-29 _description.text ; The set of data items used to define Fox et al. coefficients for generation of high angle (s >2.0) X-ray scattering factors. Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H -4.8 D -4.8 H1- -4.8 He 0.52543 Li 0.89463 Li1+ 0.89463 Be 1.2584 Be2+ 1.2584 B 1.6672 C 1.70560 N 1.54940 O 1.30530 O1- 1.30530 F 1.16710 F1- 1.16710 Ne 1.09310 Na 0.84558 Na1+ 0.84558 Mg 0.71877 Mg2+ 0.71877 Al 0.67975 Al3+ 0.67975 Si 0.70683 Si4+ 0.70683 P 0.85532 S 1.10400 Cl 1.42320 Cl1- 1.42320 Ar 1.82020 K 2.26550 K1+ 2.26550 Ca 2.71740 Ca2+ 2.71740 Sc 3.11730 Sc3+ 3.11730 Ti 3.45360 Ti2+ 3.45360 Ti3+ 3.45360 Ti4+ 3.45360 V 3.71270 V2+ 3.71270 V3+ 3.71270 V5+ 3.71270 Cr 3.87870 Cr2+ 3.87870 Cr3+ 3.87870 Mn 3.98550 Mn2+ 3.98550 Mn3+ 3.98550 Mn4+ 3.98550 Fe 3.99790 Fe2+ 3.99790 Fe3+ 3.99790 Co 3.95900 Co2+ 3.95900 Co3+ 3.95900 Ni 3.86070 Ni2+ 3.86070 Ni3+ 3.86070 Cu 3.72510 Cu1+ 3.72510 Cu2+ 3.72510 Zn 3.55950 Zn2+ 3.55950 Ga 3.37560 Ga3+ 3.37560 Ge 3.17800 Ge4+ 3.17800 As 2.97740 Se 2.78340 Br 2.60610 Br1- 2.60610 Kr 2.44280 Rb 2.30990 Rb1+ 2.30990 Sr 2.21070 Sr2+ 2.21070 Y 2.14220 Y3+ 2.14220 Zr 2.12690 Zr4+ 2.12690 Nb 2.12120 Nb3+ 2.12120 Nb5+ 2.12120 Mo 2.18870 Mo3+ 2.18870 Mo5+ 2.18870 Mo6+ 2.18870 Tc 2.25730 Ru 2.37300 Ru3+ 2.37300 Ru4+ 2.37300 Rh 2.50990 Rh3+ 2.50990 Rh4+ 2.50990 Pd 2.67520 Pd2+ 2.67520 Pd4+ 2.67520 Ag 2.88690 Ag1+ 2.88690 Ag2+ 2.88690 Cd 3.08430 Cd2+ 3.08430 In 3.31400 In3+ 3.31400 Sn 3.49840 Sn2+ 3.49840 Sn4+ 3.49840 Sb 3.70410 Sb3+ 3.70410 Sb5+ 3.70410 Te 3.88240 I 4.08010 I1- 4.08010 Xe 4.24610 Cs 4.38910 Cs1+ 4.38910 Ba 4.51070 Ba2+ 4.51070 La 4.60250 La3+ 4.60250 Ce 4.69060 Ce3+ 4.69060 Ce4+ 4.69060 Pr 4.72150 Pr3+ 4.72150 Pr4+ 4.72150 Nd 4.75090 Nd3+ 4.75090 Pm 4.74070 Sm 4.71700 Sm3+ 4.71700 Eu 4.66940 Eu2+ 4.66940 Eu3+ 4.66940 Gd 4.61010 Gd3+ 4.61010 Tb 4.52550 Tb3+ 4.52550 Dy 4.45230 Dy3+ 4.45230 Ho 4.37660 Ho3+ 4.37660 Er 4.29460 Er3+ 4.29460 Tm 4.21330 Tm3+ 4.21330 Yb 4.13430 Yb2+ 4.13430 Yb3+ 4.13430 Lu 4.04230 Lu3+ 4.04230 Hf 3.95160 Hf4+ 3.95160 Ta 3.85000 Ta5+ 3.85000 W 3.76510 W6+ 3.76510 Re 3.67600 Os 3.60530 Os4+ 3.60530 Ir 3.53130 Ir3+ 3.53130 Ir4+ 3.53130 Pt 3.47070 Pt2+ 3.47070 Pt4+ 3.47070 Au 3.41630 Au1+ 3.41630 Au3+ 3.41630 Hg 3.37350 Hg1+ 3.37350 Hg2+ 3.37350 Tl 3.34590 TL1+ 3.34590 Tl3+ 3.34590 Pb 3.32330 Pb2+ 3.32330 Pb4+ 3.32330 Bi 3.31880 Bi3+ 3.31880 Bi5+ 3.31880 Po 3.32030 At 3.34250 Rn 3.37780 Fr 3.41990 Ra 3.47530 Ra2+ 3.47530 Ac 3.49020 Ac3+ 3.49020 Th 3.61060 Th4+ 3.61060 Pa 3.68630 U 3.76650 U3+ 3.76650 U4+ 3.76650 U6+ 3.76650 Np 3.82870 Np3+ 3.82870 Np4+ 3.82870 Np6+ 3.82870 Pu 3.88970 Pu3+ 3.88970 Pu4+ 3.88970 Pu6+ 3.88970 Am 3.95060 Cm 4.01470 Bk 4.07780 Cf 4.14210 _name.category_id atom_type_scat _name.object_id hi_ang_Fox_c0 save_ save_atom_type_scat.hi_ang_Fox_c1 _definition.id '_atom_type_scat.hi_ang_Fox_c1' _definition.update 2006-06-29 _description.text ; The set of data items used to define Fox et al. coefficients for generation of high angle (s >2.0) X-ray scattering factors. Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H -.5 D -.5 H1- -.5 He -3.433 Li -2.4366 Li1+ -2.4366 Be -1.9459 Be2+ -1.9459 B -1.8556 C -1.56760 N -1.20190 O -0.83742 O1- -0.83742 F -0.63203 F1- -0.63203 Ne -0.50221 Na -0.26294 Na1+ -0.26294 Mg -0.13144 Mg2+ -0.13144 Al -0.08756 Al3+ -0.08756 Si -0.09888 Si4+ -0.09888 P -0.21262 S -0.40325 Cl -0.63936 Cl1- -0.63936 Ar -0.92776 K -1.24530 K1+ -1.24530 Ca -1.55670 Ca2+ -1.55670 Sc -1.81380 Sc3+ -1.81380 Ti -2.01150 Ti2+ -2.01150 Ti3+ -2.01150 Ti4+ -2.01150 V -2.13920 V2+ -2.13920 V3+ -2.13920 V5+ -2.13920 Cr -2.19000 Cr2+ -2.19000 Cr3+ -2.19000 Mn -2.18850 Mn2+ -2.18850 Mn3+ -2.18850 Mn4+ -2.18850 Fe -2.11080 Fe2+ -2.11080 Fe3+ -2.11080 Co -1.99650 Co2+ -1.99650 Co3+ -1.99650 Ni -1.88690 Ni2+ -1.88690 Ni3+ -1.88690 Cu -1.65500 Cu1+ -1.65500 Cu2+ -1.65500 Zn -1.45100 Zn2+ -1.45100 Ga -1.23910 Ga3+ -1.23910 Ge -1.02230 Ge4+ -1.02230 As -0.81038 Se -0.61110 Br -0.43308 Br1- -0.43308 Kr -0.27244 Rb -0.14328 Rb1+ -0.14328 Sr -0.04770 Sr2+ -0.04770 Y 0.01935 Y3+ 0.01935 Zr 0.08618 Zr4+ 0.08618 Nb 0.05381 Nb3+ 0.05381 Nb5+ 0.05381 Mo -0.00655 Mo3+ -0.00655 Mo5+ -0.00655 Mo6+ -0.00655 Tc -0.05737 Ru -0.15040 Ru3+ -0.15040 Ru4+ -0.15040 Rh -0.25906 Rh3+ -0.25906 Rh4+ -0.25906 Pd -0.39137 Pd2+ -0.39137 Pd4+ -0.39137 Ag -0.56119 Ag1+ -0.56119 Ag2+ -0.56119 Cd -0.71450 Cd2+ -0.71450 In -0.89697 In3+ -0.89697 Sn -1.02990 Sn2+ -1.02990 Sn4+ -1.02990 Sb -1.18270 Sb3+ -1.18270 Sb5+ -1.18270 Te -1.30980 I -1.45080 I1- -1.45080 Xe -1.56330 Cs -1.65420 Cs1+ -1.65420 Ba -1.72570 Ba2+ -1.72570 La -1.77070 La3+ -1.77070 Ce -1.81790 Ce3+ -1.81790 Ce4+ -1.81790 Pr -1.81390 Pr3+ -1.81390 Pr4+ -1.81390 Nd -1.80800 Nd3+ -1.80800 Pm -1.76600 Sm -1.71410 Sm3+ -1.71410 Eu -1.64140 Eu2+ -1.64140 Eu3+ -1.64140 Gd -1.55750 Gd3+ -1.55750 Tb -1.45520 Tb3+ -1.45520 Dy -1.36440 Dy3+ -1.36440 Ho -1.27460 Ho3+ -1.27460 Er -1.18170 Er3+ -1.18170 Tm -1.09060 Tm3+ -1.09060 Yb -1.00310 Yb2+ -1.00310 Yb3+ -1.00310 Lu -0.90518 Lu3+ -0.90518 Hf -0.80978 Hf4+ -0.80978 Ta -0.70599 Ta5+ -0.70599 W -0.61807 W6+ -0.61807 Re -0.52688 Os -0.45420 Os4+ -0.45420 Ir -0.37856 Ir3+ -0.37856 Ir4+ -0.37856 Pt -0.31534 Pt2+ -0.31534 Pt4+ -0.31534 Au -0.25987 Au1+ -0.25987 Au3+ -0.25987 Hg -0.21428 Hg1+ -0.21428 Hg2+ -0.21428 Tl -0.18322 TL1+ -0.18322 Tl3+ -0.18322 Pb -0.15596 Pb2+ -0.15596 Pb4+ -0.15596 Bi -0.14554 Bi3+ -0.14554 Bi5+ -0.14554 Po -0.13999 At -0.15317 Rn -0.17800 Fr -0.20823 Ra -0.25005 Ra2+ -0.25005 Ac -0.25109 Ac3+ -0.25109 Th -0.35409 Th4+ -0.35409 Pa -0.41329 U -0.47542 U3+ -0.47542 U4+ -0.47542 U6+ -0.47542 Np -0.51955 Np3+ -0.51955 Np4+ -0.51955 Np6+ -0.51955 Pu -0.56296 Pu3+ -0.56296 Pu4+ -0.56296 Pu6+ -0.56296 Am -0.60554 Cm -0.65062 Bk -0.69476 Cf -0.73977 _name.category_id atom_type_scat _name.object_id hi_ang_Fox_c1 save_ save_atom_type_scat.hi_ang_Fox_c2 _definition.id '_atom_type_scat.hi_ang_Fox_c2' _definition.update 2006-06-29 _description.text ; The set of data items used to define Fox et al. coefficients for generation of high angle (s >2.0) X-ray scattering factors. Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He 4.8007 Li 2.325 Li1+ 2.325 Be 1.3046 Be2+ 1.3046 B 1.6044 C 1.18930 N 0.51064 O -0.16738 O1- -0.16738 F -0.40207 F1- -0.40207 Ne -0.53648 Na -0.87884 Na1+ -0.87884 Mg -1.20900 Mg2+ -1.20900 Al -0.95431 Al3+ -0.95431 Si -0.98356 Si4+ -0.98356 P -0.37390 S 0.20094 Cl 0.84722 Cl1- 0.84722 Ar 1.59220 K 2.38330 K1+ 2.38330 Ca 3.13170 Ca2+ 3.13170 Sc 3.71390 Sc3+ 3.71390 Ti 4.13170 Ti2+ 4.13170 Ti3+ 4.13170 Ti4+ 4.13170 V 4.35610 V2+ 4.35610 V3+ 4.35610 V5+ 4.35610 Cr 4.38670 Cr2+ 4.38670 Cr3+ 4.38670 Mn 4.27960 Mn2+ 4.27960 Mn3+ 4.27960 Mn4+ 4.27960 Fe 3.98170 Fe2+ 3.98170 Fe3+ 3.98170 Co 3.60630 Co2+ 3.60630 Co3+ 3.60630 Ni 3.12390 Ni2+ 3.12390 Ni3+ 3.12390 Cu 2.60290 Cu1+ 2.60290 Cu2+ 2.60290 Zn 2.03390 Zn2+ 2.03390 Ga 1.46160 Ga3+ 1.46160 Ge 0.89119 Ge4+ 0.89119 As 0.34861 Se -0.14731 Br -0.57381 Br1- -0.57381 Kr -0.95570 Rb -1.22600 Rb1+ -1.22600 Sr -1.41100 Sr2+ -1.41100 Y -1.52240 Y3+ -1.52240 Zr -1.49190 Zr4+ -1.49190 Nb -1.50070 Nb3+ -1.50070 Nb5+ -1.50070 Mo -1.25340 Mo3+ -1.25340 Mo5+ -1.25340 Mo6+ -1.25340 Tc -1.07450 Ru -0.77694 Ru3+ -0.77694 Ru4+ -0.77694 Rh -0.44719 Rh3+ -0.44719 Rh4+ -0.44719 Pd -0.05894 Pd2+ -0.05894 Pd4+ -0.05894 Ag 0.42189 Ag1+ 0.42189 Ag2+ 0.42189 Cd 0.84482 Cd2+ 0.84482 In 1.35030 In3+ 1.35030 Sn 1.68990 Sn2+ 1.68990 Sn4+ 1.68990 Sb 2.08920 Sb3+ 2.08920 Sb5+ 2.08920 Te 2.41170 I 2.76730 I1- 2.76730 Xe 3.04200 Cs 3.25450 Cs1+ 3.25450 Ba 3.41320 Ba2+ 3.41320 La 3.49970 La3+ 3.49970 Ce 3.60280 Ce3+ 3.60280 Ce4+ 3.60280 Pr 3.56480 Pr3+ 3.56480 Pr4+ 3.56480 Nd 3.51970 Nd3+ 3.51970 Pm 3.37430 Sm 3.20800 Sm3+ 3.20800 Eu 2.98580 Eu2+ 2.98580 Eu3+ 2.98580 Gd 2.73190 Gd3+ 2.73190 Tb 2.43770 Tb3+ 2.43770 Dy 2.17540 Dy3+ 2.17540 Ho 1.92540 Ho3+ 1.92540 Er 1.67060 Er3+ 1.67060 Tm 1.42390 Tm3+ 1.42390 Yb 1.18810 Yb2+ 1.18810 Yb3+ 1.18810 Lu 0.92889 Lu3+ 0.92889 Hf 0.67951 Hf4+ 0.67951 Ta 0.41103 Ta5+ 0.41103 W 0.18568 W6+ 0.18568 Re -0.04706 Os -0.22529 Os4+ -0.22529 Ir -0.41174 Ir3+ -0.41174 Ir4+ -0.41174 Pt -0.56487 Pt2+ -0.56487 Pt4+ -0.56487 Au -0.69030 Au1+ -0.69030 Au3+ -0.69030 Hg -0.79013 Hg1+ -0.79013 Hg2+ -0.79013 Tl -0.84911 TL1+ -0.84911 Tl3+ -0.84911 Pb -0.89878 Pb2+ -0.89878 Pb4+ -0.89878 Bi -0.90198 Bi3+ -0.90198 Bi5+ -0.90198 Po -0.89333 At -0.83350 Rn -0.74320 Fr -0.64000 Ra -0.50660 Ra2+ -0.50660 Ac -0.49651 Ac3+ -0.49651 Th -0.18926 Th4+ -0.18926 Pa -0.01192 U 0.16850 U3+ 0.16850 U4+ 0.16850 U6+ 0.16850 Np 0.29804 Np3+ 0.29804 Np4+ 0.29804 Np6+ 0.29804 Pu 0.42597 Pu3+ 0.42597 Pu4+ 0.42597 Pu6+ 0.42597 Am 0.54967 Cm 0.67922 Bk 0.80547 Cf 0.93342 _name.category_id atom_type_scat _name.object_id hi_ang_Fox_c2 save_ save_atom_type_scat.hi_ang_Fox_c3 _definition.id '_atom_type_scat.hi_ang_Fox_c3' _definition.update 2006-06-29 _description.text ; The set of data items used to define Fox et al. coefficients for generation of high angle (s >2.0) X-ray scattering factors. Ref: International Tables for Crystallography, Vol. C (1991) Table 6.1.1.5 ; _type.purpose Assigned _type.container Single _type.contents Real loop_ _enumeration_default.index _enumeration_default.value H .0 D .0 H1- .0 He -2.5476 Li -.71949 Li1+ -.71949 Be -0.04297 Be2+ -0.04297 B -0.65981 C -0.42715 N 0.02472 O 0.47500 O1- 0.47500 F 0.54352 F1- 0.54352 Ne 0.60957 Na 0.76974 Na1+ 0.76974 Mg 0.82738 Mg2+ 0.82738 Al 0.72294 Al3+ 0.72294 Si 0.55631 Si4+ 0.55631 P 0.20731 S -0.26058 Cl -0.76135 Cl1- -0.76135 Ar -1.32510 K -1.91290 K1+ -1.91290 Ca -2.45670 Ca2+ -2.45670 Sc -2.85330 Sc3+ -2.85330 Ti -3.11710 Ti2+ -3.11710 Ti3+ -3.11710 Ti4+ -3.11710 V -3.22040 V2+ -3.22040 V3+ -3.22040 V5+ -3.22040 Cr -3.17520 Cr2+ -3.17520 Cr3+ -3.17520 Mn -3.02150 Mn2+ -3.02150 Mn3+ -3.02150 Mn4+ -3.02150 Fe -2.71990 Fe2+ -2.71990 Fe3+ -2.71990 Co -2.37050 Co2+ -2.37050 Co3+ -2.37050 Ni -1.94290 Ni2+ -1.94290 Ni3+ -1.94290 Cu -1.49760 Cu1+ -1.49760 Cu2+ -1.49760 Zn -1.02160 Zn2+ -1.02160 Ga -0.55471 Ga3+ -0.55471 Ge -0.09984 Ge4+ -0.09984 As 0.32231 Se 0.69837 Br 1.00950 Br1- 1.00950 Kr 1.27070 Rb 1.45320 Rb1+ 1.45320 Sr 1.55410 Sr2+ 1.55410 Y 1.59630 Y3+ 1.59630 Zr 1.51820 Zr4+ 1.51820 Nb 1.50150 Nb3+ 1.50150 Nb5+ 1.50150 Mo 1.24010 Mo3+ 1.24010 Mo5+ 1.24010 Mo6+ 1.24010 Tc 1.06630 Ru 0.79060 Ru3+ 0.79060 Ru4+ 0.79060 Rh 0.49443 Rh3+ 0.49443 Rh4+ 0.49443 Pd 0.15404 Pd2+ 0.15404 Pd4+ 0.15404 Ag -0.25659 Ag1+ -0.25659 Ag2+ -0.25659 Cd -0.60990 Cd2+ -0.60990 In -1.03910 In3+ -1.03910 Sn -1.29860 Sn2+ -1.29860 Sn4+ -1.29860 Sb -1.61640 Sb3+ -1.61640 Sb5+ -1.61640 Te -1.86420 I -2.13920 I1- -2.13920 Xe -2.34290 Cs -2.49220 Cs1+ -2.49220 Ba -2.59590 Ba2+ -2.59590 La -2.64050 La3+ -2.64050 Ce -2.70670 Ce3+ -2.70670 Ce4+ -2.70670 Pr -2.65180 Pr3+ -2.65180 Pr4+ -2.65180 Nd -2.59010 Nd3+ -2.59010 Pm -2.44210 Sm -2.28170 Sm3+ -2.28170 Eu -2.07460 Eu2+ -2.07460 Eu3+ -2.07460 Gd -1.84040 Gd3+ -1.84040 Tb -1.57950 Tb3+ -1.57950 Dy -1.34550 Dy3+ -1.34550 Ho -1.13090 Ho3+ -1.13090 Er -0.91467 Er3+ -0.91467 Tm -0.70804 Tm3+ -0.70804 Yb -0.51120 Yb2+ -0.51120 Yb3+ -0.51120 Lu -0.29820 Lu3+ -0.29820 Hf -0.09620 Hf4+ -0.09620 Ta 0.11842 Ta5+ 0.11842 W 0.29787 W6+ 0.29787 Re 0.48180 Os 0.61700 Os4+ 0.61700 Ir 0.75967 Ir3+ 0.75967 Ir4+ 0.75967 Pt 0.87492 Pt2+ 0.87492 Pt4+ 0.87492 Au 0.96224 Au1+ 0.96224 Au3+ 0.96224 Hg 1.02850 Hg1+ 1.02850 Hg2+ 1.02850 Tl 1.05970 TL1+ 1.05970 Tl3+ 1.05970 Pb 1.08380 Pb2+ 1.08380 Pb4+ 1.08380 Bi 1.06850 Bi3+ 1.06850 Bi5+ 1.06850 Po 1.04380 At 0.97641 Rn 0.88510 Fr 0.78354 Ra 0.65836 Ra2+ 0.65836 Ac 0.64340 Ac3+ 0.64340 Th 0.36849 Th4+ 0.36849 Pa 0.20878 U 0.05060 U3+ 0.05060 U4+ 0.05060 U6+ 0.05060 Np -0.06566 Np3+ -0.06566 Np4+ -0.06566 Np6+ -0.06566 Pu -0.18080 Pu3+ -0.18080 Pu4+ -0.18080 Pu6+ -0.18080 Am -0.29112 Cm -0.40588 Bk -0.51729 Cf -0.62981 _name.category_id atom_type_scat _name.object_id hi_ang_Fox_c3 save_ save_atom_type_scat.length_neutron _definition.id '_atom_type_scat.length_neutron' _definition.update 2006-12-14 _description.text ; The bound coherent scattering length for the atom type at the isotopic composition used for the diffraction experiment. ; _description.common 'AtomTypeScatNeutronB' _name.category_id atom_type_scat _name.object_id length_neutron _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.0 _units.code femtometres save_ save_atom_type_scat.source _definition.id '_atom_type_scat.source' _definition.update 2006-12-14 _description.text ; Reference to source of scattering factors used for this atom type. ; _description.common 'AtomTypeScatDetails' _name.category_id atom_type_scat _name.object_id source _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'International Tables Vol. IV Table 2.4.6B' save_ save_atom_type_scat.symbol _definition.id '_atom_type_scat.symbol' _definition.update 2008-06-19 _description.text ; The identity of the atom specie(s) representing this atom type. See _atom_type.symbol for further details. ; _description.common 'AtomTypeScatSymbol' _name.category_id atom_type_scat _name.object_id symbol _type.purpose Identify _type.container Single _type.contents Text save_ save_atom_type_scat.versus_stol_list _definition.id '_atom_type_scat.versus_stol_list' _definition.update 2006-12-14 _description.text ; Table of scattering factors as a function of sin theta on lambda in increments of 0.01, increasing from 0.0. ; _description.common 'AtomTypeScatTable' _name.category_id atom_type_scat _name.object_id versus_stol_list _type.purpose Assigned _type.container Table _type.contents Real save_ save_REFINE _definition.id refine _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to specify information about the refinement of the structural model. ; _category.parent_id core_structure save_ save_refine.special_details _definition.id '_refine.special_details' _definition.update 2006-12-14 _description.text ; Details of the refinement not specified by other data items. ; _description.common 'RefinementDetails' _name.category_id refine _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text save_ save_REFINE_DIFF _definition.id refine_diff _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items which specify the electron 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. ; _category.parent_id refine save_ save_refine_diff.density_max _definition.id '_refine_diff.density_max' _definition.update 2006-12-14 _description.text ; Maximum density value in a difference Fourier map. ; _description.common 'RefineDiffDensMax' _name.category_id refine_diff _name.object_id density_max _type.purpose Measured _type.container Single _type.contents Real save_ save_refine_diff.density_min _definition.id '_refine_diff.density_min' _definition.update 2006-12-14 _description.text ; Miniumum density value in a difference Fourier map. ; _description.common 'RefineDiffDensMin' _name.category_id refine_diff _name.object_id density_min _type.purpose Measured _type.container Single _type.contents Real save_ save_refine_diff.density_rms _definition.id '_refine_diff.density_rms' _definition.update 2006-12-14 _description.text ; Root mean square density value in a difference Fourier map. ; _description.common 'RefineDiffDensRms' _name.category_id refine_diff _name.object_id density_rms _type.purpose Measured _type.container Single _type.contents Real save_ save_REFINE_LS _definition.id refine_ls _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to specify information about the refinement of the structural model. ; _category.parent_id refine save_ save_refine_ls.abs_structure_details _definition.id '_refine_ls.abs_structure_details' _definition.update 2006-12-14 _description.text ; Details on the absolute structure and how it was determined. ; _description.common 'RefineAbsStructDetails' _name.category_id refine_ls _name.object_id abs_structure_details _type.purpose Describe _type.container Single _type.contents Text save_ save_refine_ls.abs_structure_Flack _definition.id '_refine_ls.abs_structure_Flack' _definition.update 2006-12-14 _description.text ; Measured of absolute structure as defined by Flack (Acta Cryst. A39, 876-881). For non-centrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty u must be supplied. If the listed atom site coordinates correspond to the absolute structure expected from the Friedel differences, the Flack value will be within 3u of 0.0; if the atom site coordinates correspond to the inverse of the absolute structure the value will close to 1.0. The value is not applicable for centrosymmetric structures. ; _description.common 'RefineAbsStructFlack' _name.category_id refine_ls _name.object_id abs_structure_Flack _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0:1.0 save_ save_refine_ls.abs_structure_Rogers _definition.id '_refine_ls.abs_structure_Rogers' _definition.update 2006-12-14 _description.text ; Measured of absolute structure as defined by Rogers (Acta Cryst. A37, 734-741). For non-centrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty u must be supplied. If the atom site coordinates correspond to the absolute structure expected from the Friedel differences, the Rogers value will be within 3u of 1.0; if the atom site coordinates correspond to the inverse of the absolute structure the value will close to -1.0. The value is not applicable for centrosymmetric structures. ^^ **** check values ; _description.common 'RefineAbsStructRogers' _name.category_id refine_ls _name.object_id abs_structure_Rogers _type.purpose Measured _type.container Single _type.contents Real _enumeration.range -1.0:1.0 save_ save_refine_ls.d_res_high _definition.id '_refine_ls.d_res_high' _definition.update 2006-12-14 _description.text ; Highest resolution for the reflections used in refinement. This corresponds to the smallest interpanar d value. ; _description.common 'RefineResolutionHigh' _name.category_id refine_ls _name.object_id d_res_high _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_refine_ls.d_res_low _definition.id '_refine_ls.d_res_low' _definition.update 2006-12-14 _description.text ; Lowest resolution for the reflections used in refinement. This corresponds to the largest interpanar d value. ; _description.common 'RefineResolutionLow' _name.category_id refine_ls _name.object_id d_res_low _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_refine_ls.extinction_coef _definition.id '_refine_ls.extinction_coef' _definition.update 2006-12-14 _description.text ; Extinction coefficient used to calculate the correction factor applied to the structure-factor data. How the extinction coefficient is estimated and applied is specified in the definitions of _refine_ls.extinction_expression and _refine_ls.extinction_method. For the 'Zachariasen' method it is the r* value (Zachariasen (1967) Acta Cryst. 23, 558-564; Larson (1967) Acta Cryst. 23, 664-665) For the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' method it is the 'rho' value (Becker & Coppens (1974) Acta Cryst. A30, 129-153). Note the magnitude of these values is usually about 10000. ; _description.common 'RefineExtinctionCoeff' _name.category_id refine_ls _name.object_id extinction_coef _type.purpose Measured _type.container Single _type.contents Real loop_ _description_example.case _description_example.detail 3472(52) 'Zachariasen coefficient r* = 0.347(5) E04' save_ save_refine_ls.extinction_expression _definition.id '_refine_ls.extinction_expression' _definition.update 2006-12-14 _description.text ; Description or reference of the extinction correction equation used to apply the _refine_ls.extinction_coef. This information should be sufficient to reproduce the extinction correction factors applied. ; _description.common 'RefineExtinctionExpression' _name.category_id refine_ls _name.object_id extinction_expression _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case _description_example.detail 'Larson approach' ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard. ; save_ save_refine_ls.extinction_method _definition.id '_refine_ls.extinction_method' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'RefineExtinctionMethod' _name.category_id refine_ls _name.object_id extinction_method _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case 'Becker-Coppens type 2 Gaussian isotropic' save_ save_refine_ls.goodness_of_fit_all _definition.id '_refine_ls.goodness_of_fit_all' _definition.update 2006-12-14 _description.text ; 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(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see @refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see @refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; _description.common 'RefineLsGofAllReflns' _name.category_id refine_ls _name.object_id goodness_of_fit_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.goodness_of_fit_gt _definition.id '_refine_ls.goodness_of_fit_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.goodness_of_fit_obs' _description.text ; Least-squares goodness-of-fit parameter S for significantly intense reflections, (see _reflns.threshold_expression), after the final cycle of refinement. Account should be taken of parameters restrained in the least squares. See _refine_ls.goodness_of_fit_all for the S expression. ; _description.common 'RefineLsGofGtReflns' _name.category_id refine_ls _name.object_id goodness_of_fit_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.goodness_of_fit_ref _definition.id '_refine_ls.goodness_of_fit_ref' _definition.update 2006-12-14 _description.text ; Least-squares goodness-of-fit parameter S for those reflections included in the final cycle of refinement. Account should be taken of restrained parameters. See _refine_ls.goodness_of_fit_all for the S expression. ; _description.common 'RefineLsGofRefineReflns' _name.category_id refine_ls _name.object_id goodness_of_fit_ref _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.hydrogen_treatment _definition.id '_refine_ls.hydrogen_treatment' _definition.update 2006-12-14 _description.text ; Code identifying how hydrogen atoms were treated in the refinement. ; _description.common 'RefineLsHatomTreatment' _name.category_id refine_ls _name.object_id hydrogen_treatment _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail refall 'refined all H parameters' refxyz 'refined H coordinates only' refU 'refined H U only' noref 'no refinement of H parameters' constr 'H parameters constrained' mixed 'some constrained, some independent' undef 'H-atom parameters not defined' _enumeration.default undef save_ save_refine_ls.matrix_type _definition.id '_refine_ls.matrix_type' _definition.update 2006-12-14 _description.text ; Code identifying the matrix type used for least-squares derivatives. ; _description.common 'RefineLsMatrixType' _name.category_id refine_ls _name.object_id matrix_type _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only' _enumeration.default full save_ save_refine_ls.number_constraints _definition.id '_refine_ls.number_constraints' _definition.update 2006-12-14 _description.text ; Count of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any 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. ; _description.common 'RefineLsConstraintsCount' _name.category_id refine_ls _name.object_id number_constraints _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: _enumeration.default 0 save_ save_refine_ls.number_parameters _definition.id '_refine_ls.number_parameters' _definition.update 2007-02-09 _description.text ; Count 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. ; _description.common 'RefineLsParametersCount' _name.category_id refine_ls _name.object_id number_parameters _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 0: save_ save_refine_ls.number_reflns _definition.id '_refine_ls.number_reflns' _definition.update 2007-02-09 _description.text ; Number of unique reflections used in the least-squares refinement. ; _description.common 'RefineLsReflectionsCount' _name.category_id refine_ls _name.object_id number_reflns _type.purpose Assigned _type.container Single _type.contents Count _enumeration.range 1: save_ save_refine_ls.number_restraints _definition.id '_refine_ls.number_restraints' _definition.update 2006-12-14 _description.text ; 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. ; _description.common 'RefineLsConstraintsCount' _name.category_id refine_ls _name.object_id number_restraints _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0: save_ save_refine_ls.R_factor_all _definition.id '_refine_ls.R_factor_all' _definition.update 2006-12-14 _description.text ; 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 ; _description.common 'RefineLsResid(F)AllReflns' _name.category_id refine_ls _name.object_id R_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.R_factor_gt _definition.id '_refine_ls.R_factor_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.R_factor_obs' _description.text ; 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 (expressed in _refine_ls.R_factor_all). ; _description.common 'RefineLsResid(F)GtReflns' _name.category_id refine_ls _name.object_id R_factor_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.R_Fsqd_factor _definition.id '_refine_ls.R_Fsqd_factor' _definition.update 2006-12-14 _description.text ; 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)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(meas)^2^ F(meas)^2^ = squares of the measured structure-factor F(calc)^2^ = squares of the calculated structure-factor and the sum is taken over the specified reflections ; _description.common 'RefineLsResid(Fsqd)GtReflns' _name.category_id refine_ls _name.object_id R_Fsqd_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.R_I_factor _definition.id '_refine_ls.R_I_factor' _definition.update 2006-12-14 _description.text ; 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) - I(calc) | R(I) = ------------------------ sum | I(meas) | I(meas) = the net measured intensities I(calc) = the net calculated intensities and the sum is taken over the specified reflections ; _description.common 'RefineLsResid(I)GtReflns' _name.category_id refine_ls _name.object_id R_I_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.restrained_S_all _definition.id '_refine_ls.restrained_S_all' _definition.update 2006-12-14 _description.text ; 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 observed 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 ; _description.common 'RefineLsGofRestrainedAllReflns' _name.category_id refine_ls _name.object_id restrained_S_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.restrained_S_gt _definition.id '_refine_ls.restrained_S_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.restrained_S_obs' _description.text ; 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. See also _refine_ls.goodness_of_fit_all definition. ; _description.common 'RefineLsGofRestrainedGtReflns' _name.category_id refine_ls _name.object_id restrained_S_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.shift_over_su_max _definition.id '_refine_ls.shift_over_su_max' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.shift/esd_max' _description.text ; Largest l-s parameter-shift (unsigned) to standard-uncertainty RATIO. ; _description.common 'RefineLsMaxShift/Su' _name.category_id refine_ls _name.object_id shift_over_su_max _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.shift_over_su_mean _definition.id '_refine_ls.shift_over_su_mean' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.shift/esd_mean' _description.text ; Mean l-s parameter-shift (unsigned) to standard-uncertainty RATIO. ; _description.common 'RefineLsMeanShift/Su' _name.category_id refine_ls _name.object_id shift_over_su_mean _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.structure_factor_coef _definition.id '_refine_ls.structure_factor_coef' _definition.update 2006-12-14 _description.text ; Structure-factor coefficient used in the least-squares refinement process. ; _description.common 'RefineLsStructFactorCoeff' _name.category_id refine_ls _name.object_id structure_factor_coef _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail F 'structure factor magnitude' Fsqd 'structure factor squared' Inet 'net intensity' _enumeration.default F save_ save_refine_ls.weighting_details _definition.id '_refine_ls.weighting_details' _definition.update 2006-12-14 _description.text ; 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'. ; _description.common 'RefineLsWeightDetails' _name.category_id refine_ls _name.object_id weighting_details _type.purpose Describe _type.container Single _type.contents Text loop_ _description_example.case ; Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. ; save_ save_refine_ls.weighting_scheme _definition.id '_refine_ls.weighting_scheme' _definition.update 2006-12-14 _description.text ; General description of the weighting scheme used in the least-squares. An enumerated code should be contained in this description. ; _description.common 'RefineLsWeightCode' _name.category_id refine_ls _name.object_id weighting_scheme _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail sigma "based on measured s.u.'s" unit 'unit or no weights applied' calc 'calculated weights applied' _enumeration.default sigma save_ save_refine_ls.wR_factor_all _definition.id '_refine_ls.wR_factor_all' _definition.update 2006-12-14 _description.text ; 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 ; _description.common 'RefineLsWResidAllReflns' _name.category_id refine_ls _name.object_id wR_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.wR_factor_gt _definition.id '_refine_ls.wR_factor_gt' _definition.update 2006-12-14 loop_ _alias.definition_id '_refine_ls.wR_factor_obs' _description.text ; 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. The expression is given in the _refine_ls.wR_factor_all definition. ; _description.common 'RefineLsWResidGtReflns' _name.category_id refine_ls _name.object_id wR_factor_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls.wR_factor_ref _definition.id '_refine_ls.wR_factor_ref' _definition.update 2006-12-14 _description.text ; 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. See expression in _refine_ls.wR_factor_gt ; _description.common 'RefineLsWResidRefineReflns' _name.category_id refine_ls _name.object_id wR_factor_ref _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_REFINE_LS_CLASS _definition.id refine_ls_class _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify information about the refinement of the structural model. ; _category.parent_id refine_ls _category_key.generic '_refine_ls_class.key' save_ save_refine_ls_class.key _definition.id '_refine_ls_class.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of REFINE_LS_CLASS items in a looped list. ; _description.common 'Key to ls refinement data' _name.category_id refine_ls_class _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _refine_ls_class.key = _refine_ls_class.code ; save_ save_refine_ls_class.code _definition.id '_refine_ls_class.code' _definition.update 2008-06-19 _description.text ; Name identifying a certain reflection class. ; _description.common 'LsShellCode' _name.category_id refine_ls_class _name.object_id code _name.linked_item_id '_reflns_class.code' _type.purpose Link _type.container Single _type.contents Text loop_ _description_example.case 'c1' save_ save_refine_ls_class.d_res_high _definition.id '_refine_ls_class.d_res_high' _definition.update 2006-12-14 _description.text ; Highest resolution for the reflections in this class. This corresponds to the smallest interpanar d value. ; _description.common 'LsShellResolHigh' _name.category_id refine_ls_class _name.object_id d_res_high _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_refine_ls_class.d_res_low _definition.id '_refine_ls_class.d_res_low' _definition.update 2006-12-14 _description.text ; Lowest resolution for the reflections in this class. This corresponds to the largest interpanar d value. ; _description.common 'LsShellResolLow' _name.category_id refine_ls_class _name.object_id d_res_low _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms save_ save_refine_ls_class.R_factor_all _definition.id '_refine_ls_class.R_factor_all' _definition.update 2006-12-14 _description.text ; Residual factor for reflections in this class included in the refinement. See _refine_ls.R_factor_all definition for details. ; _description.common 'LsShellResid(F)AllReflns' _name.category_id refine_ls_class _name.object_id R_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls_class.R_factor_gt _definition.id '_refine_ls_class.R_factor_gt' _definition.update 2006-12-14 _description.text ; Residual factor for the reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_factor_all definition for details. ; _description.common 'LsShellResid(F)GtReflns' _name.category_id refine_ls_class _name.object_id R_factor_gt _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls_class.R_Fsqd_factor _definition.id '_refine_ls_class.R_Fsqd_factor' _definition.update 2006-12-14 _description.text ; Residual factor R(F^2^) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_Fsqd_factor definition for details. ; _description.common 'LsShellResid(Fsqd)GtReflns' _name.category_id refine_ls_class _name.object_id R_Fsqd_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls_class.R_I_factor _definition.id '_refine_ls_class.R_I_factor' _definition.update 2006-12-14 _description.text ; Residual factor R(I) for reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.R_I_factor definition for details. ; _description.common 'LsShellResid(I)GtReflns' _name.category_id refine_ls_class _name.object_id R_I_factor _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_refine_ls_class.wR_factor_all _definition.id '_refine_ls_class.wR_factor_all' _definition.update 2006-12-14 _description.text ; Weight residual for all reflections in this class judged significantly intense (see _reflns.threshold_expression) and included in the refinement. See _refine_ls.wR_factor_all definition for details. ; _description.common 'LsShellWResid(F)GtReflns' _name.category_id refine_ls_class _name.object_id wR_factor_all _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: save_ save_CORE_MODEL _definition.id core_model _definition.scope Category _definition.class Head _definition.update 2006-12-14 _description.text ; The DICTIONARY group encompassing the CORE MODEL data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_core save_ save_GEOM _definition.id geom _definition.scope Category _definition.class Set _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to specify the geometry of the structural model as derived from the atomic sites. ; _description.common 'Structural geometry' _category.parent_id core_model save_ save_geom.bond_distance_incr _definition.id '_geom.bond_distance_incr' _definition.update 2006-12-14 _description.text ; Increment added to the bond radii for the atomic species to specify the maximum permitted "bonded" distance between two atom sites. ; _description.common 'GeomBondDistIncr' _name.category_id geom _name.object_id bond_distance_incr _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.2 _units.code angstroms save_ save_geom.bond_distance_min _definition.id '_geom.bond_distance_min' _definition.update 2008-03-28 _description.text ; Minimum permitted "bonded" distance between two atom sites. ; _description.common 'GeomBondDistMin' _name.category_id geom _name.object_id bond_distance_min _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.2 _units.code angstroms save_ save_geom.contact_distance_incr _definition.id '_geom.contact_distance_incr' _definition.update 2008-03-28 _description.text ; Increment added to the bond radii for the atomic species to specify the maximum permitted "contact" distance between two "non-bonded" atom sites. ; _description.common 'GeomContactDistIncr' _name.category_id geom _name.object_id contact_distance_incr _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.2 _units.code angstroms save_ save_geom.contact_distance_min _definition.id '_geom.contact_distance_min' _definition.update 2008-03-28 _description.text ; Minimum permitted "contact" distance between two "non-bonded" atom sites. ; _description.common 'GeomContactDistMin' _name.category_id geom _name.object_id contact_distance_min _type.purpose Assigned _type.container Single _type.contents Real _enumeration.default 0.2 _units.code angstroms save_ save_geom.special_details _definition.id '_geom.special_details' _definition.update 2006-12-14 _description.text ; Description of geometry information not covered by the existing data names in the geometry categories, such as least-squares planes. ; _description.common 'GeomSpecialDetails' _name.category_id geom _name.object_id special_details _type.purpose Describe _type.container Single _type.contents Text save_ save_GEOM_ANGLE _definition.id geom_angle _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the geometry angles in the structural model as derived from the atomic sites. ; _description.common 'BondAngleList' _category.parent_id geom _category_key.generic '_geom_angle.key' loop_ _method.purpose _method.expression Evaluation ; 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(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(rad2+m3.radius_bond)) Next angle = Acosd ( v1*v2 / (d1*d2) ) geom_angle( .id = Tuple ( m2.id, m1.id, m3.id ), .distances = Tuple ( d1, d2 ), .value = angle ) } } } ; save_ save_geom_angle.key _definition.id '_geom_angle.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of GEOM_ANGLE items in a looped list. ; _description.common 'Key to geometry angles' _name.category_id geom_angle _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _geom_angle.key = _geom_angle.id ; save_ save_geom_angle.atom_site_label_1 _definition.id '_geom_angle.atom_site_label_1' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_angle _name.object_id atom_site_label_1 save_ save_geom_angle.atom_site_label_2 _definition.id '_geom_angle.atom_site_label_2' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_angle _name.object_id atom_site_label_2 save_ save_geom_angle.atom_site_label_3 _definition.id '_geom_angle.atom_site_label_3' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_angle _name.object_id atom_site_label_3 save_ save_geom_angle.distances _definition.id '_geom_angle.distances' _definition.update 2006-12-14 _description.text ; The pair of distances between sites 1 - 2 and 2 - 3. ; _name.category_id geom_angle _name.object_id distances _type.purpose Measured _type.container Tuple _type.contents Real _units.code angstroms save_ save_geom_angle.id _definition.id '_geom_angle.id' _definition.update 2008-06-24 _description.text ; Atom site labels and symmetry operators as pairs for each of the three atom sites which identify the angle. The second label-symop pair in the list identifies the site at the apex of the angle. ; _description.common 'BondAngleId' _name.category_id geom_angle _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Tuple[Label,Symop] loop_ _method.purpose _method.expression Evaluation ; With a as geom_angle _geom_angle.id = Tuple ( Tuple ( a.atom_site_label_1, a.site_symmetry_1 ), Tuple ( a.atom_site_label_2, a.site_symmetry_2 ), Tuple ( a.atom_site_label_3, a.site_symmetry_3 ) ) ; save_ save_geom_angle.publ_flag _definition.id '_geom_angle.publ_flag' _definition.update 2008-03-28 _description.text ; Code signals if the angle is required for publication. ; _description.common 'BondAnglePublFlag' _name.category_id geom_angle _name.object_id publ_flag _type.purpose Assigned _type.container Single _type.contents YesorNo _enumeration.default no save_ save_geom_angle.site_symmetry_1 _definition.id '_geom_angle.site_symmetry_1' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_angle _name.object_id site_symmetry_1 save_ save_geom_angle.site_symmetry_2 _definition.id '_geom_angle.site_symmetry_2' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_angle _name.object_id site_symmetry_2 save_ save_geom_angle.site_symmetry_3 _definition.id '_geom_angle.site_symmetry_3' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_angle _name.object_id site_symmetry_3 save_ save_geom_angle.value _definition.id '_geom_angle.value' _definition.update 2006-12-14 # _alias.definition_id '_geom_angle' # Now a category!! _description.text ; Angle defined by the sites identified by _geom_angle.id ; _description.common 'BondAngle' _name.category_id geom_angle _name.object_id value _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; xc = List() For [label,symop] in _geom_angle.id { xf = SymEquiv(symop, symmetry_equiv, _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) ) ) ; save_ save_GEOM_BOND _definition.id geom_bond _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the geometry bonds in the structural model as derived from the atomic sites. ; _description.common 'BondDistList' _category.parent_id geom _category_key.generic '_geom_bond.key' loop_ _method.purpose _method.expression Evaluation ; 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(rad+m2.radius_bond)) Next geom_bond( .id = Tuple ( m1.id, m2.id ), .distance = d ) } } ; save_ save_geom_bond.key _definition.id '_geom_bond.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of GEOM_BOND items in a looped list. ; _description.common 'Key to geometry distances' _name.category_id geom_bond _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _geom_bond.key = _geom_bond.id ; save_ save_geom_bond.atom_site_label_1 _definition.id '_geom_bond.atom_site_label_1' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_bond _name.object_id atom_site_label_1 save_ save_geom_bond.atom_site_label_2 _definition.id '_geom_bond.atom_site_label_2' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_bond _name.object_id atom_site_label_2 save_ save_geom_bond.distance _definition.id '_geom_bond.distance' _definition.update 2006-12-14 _description.text ; Distance between the sites identified by _geom_bond.id ; _description.common 'BondDist' _name.category_id geom_bond _name.object_id distance _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; xc = List() For [label,symop] in _geom_bond.id { xf = SymEquiv(symop, symmetry_equiv, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_bond.distance = Norm ( xc[0] - xc[1] ) ; save_ save_geom_bond.id _definition.id '_geom_bond.id' _definition.update 2008-06-24 _description.text ; Identity of bond distance in terms of the atom site labels and symmetry operators as pairs for each of the two "bonded" atom sites. ; _description.common 'BondDistId' _name.category_id geom_bond _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Tuple[Label,Symop] loop_ _method.purpose _method.expression Evaluation ; With a as geom_bond _geom_bond.id = Tuple ( Tuple ( a.atom_site_label_1, a.site_symmetry_1 ), Tuple ( a.atom_site_label_2, a.site_symmetry_2 ) ) ; save_ save_geom_bond.publ_flag _definition.id '_geom_bond.publ_flag' _definition.update 2008-03-28 _description.text ; Code signals if the bond is required for publication. ; _description.common 'BondDistPublFlag' _name.category_id geom_bond _name.object_id publ_flag _type.purpose Assigned _type.container Single _type.contents YesorNo _enumeration.default no save_ save_geom_bond.site_symmetry_1 _definition.id '_geom_bond.site_symmetry_1' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_bond _name.object_id site_symmetry_1 save_ save_geom_bond.site_symmetry_2 _definition.id '_geom_bond.site_symmetry_2' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_bond _name.object_id site_symmetry_2 save_ save_GEOM_CONTACT _definition.id geom_contact _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the contact distances in the structural model as derived from the atomic sites. ; _description.common 'Bond contact list' _category.parent_id geom _category_key.generic '_geom_contact.key' loop_ _method.purpose _method.expression Evaluation ; 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.id[1] != '1_555') Next radb = rb + m2.radius_bond radc = rc + m2.radius_contact label = m2.id[0] Loop s as symmetry_equiv :ns { axyz = s.R * m2.fract_xyz + s.T Do i = -2,2 { Do j = -2,2 { Do k = -2,2 { # cell translations tran = Array ([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 id = Tuple( m1.id, Tuple( label, Symop(ns+1,tran) ) ) geom_contact( .id = id, .distance = d ) } } } } } } ; save_ save_geom_contact.key _definition.id '_geom_contact.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of GEOM_CONTACT items in a looped list. ; _description.common 'Key to geometry contact data' _name.category_id geom_contact _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _geom_contact.key = _geom_contact.id ; save_ save_geom_contact.atom_site_label_1 _definition.id '_geom_contact.atom_site_label_1' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_contact _name.object_id atom_site_label_1 save_ save_geom_contact.atom_site_label_2 _definition.id '_geom_contact.atom_site_label_2' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_contact _name.object_id atom_site_label_2 save_ save_geom_contact.distance _definition.id '_geom_contact.distance' _definition.update 2006-12-14 _description.text ; Distance between the sites identifyed in _geom_contact.id ; _description.common 'BondContactDist' _name.category_id geom_contact _name.object_id distance _type.purpose Measured _type.container Single _type.contents Real _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; xc = List() For [label,symop] in _geom_contact.id { xf = SymEquiv(symop, symmetry_equiv, _atom_site[label].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_contact.distance = Norm ( xc[0] - xc[1] ) ; save_ save_geom_contact.id _definition.id '_geom_contact.id' _definition.update 2008-06-24 _description.text ; Atom site labels and symmetry operators as pairs for each of the two atom sites which define the contact bond. ; _description.common 'BondContactId' _name.category_id geom_contact _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Tuple[Label,Symop] loop_ _method.purpose _method.expression Evaluation ; With a as geom_contact _geom_contact.id = Tuple ( Tuple ( a.atom_site_label_1, a.site_symmetry_1 ), Tuple ( a.atom_site_label_2, a.site_symmetry_2 ) ) ; save_ save_geom_contact.publ_flag _definition.id '_geom_contact.publ_flag' _definition.update 2008-02-28 _description.text ; Code signals if the contact is required for publication. ; _description.common 'BondContactPublFlag' _name.category_id geom_contact _name.object_id publ_flag _type.purpose Assigned _type.container Single _type.contents YesorNo _enumeration.default no save_ save_geom_contact.site_symmetry_1 _definition.id '_geom_contact.site_symmetry_1' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_contact _name.object_id site_symmetry_1 save_ save_geom_contact.site_symmetry_2 _definition.id '_geom_contact.site_symmetry_2' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_contact _name.object_id site_symmetry_2 save_ save_GEOM_HBOND _definition.id geom_hbond _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the hydrogen bond distances in the structural model as derived from the atomic sites. ; _description.common 'HbondList' _category.parent_id geom _category_key.generic '_geom_hbond.key' save_ save_geom_hbond.key _definition.id '_geom_hbond.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of GEOM_HBOND items in a looped list. ; _description.common 'Key to hydrogen bond data' _name.category_id geom_hbond _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _geom_hbond.key = _geom_hbond.id ; save_ save_geom_hbond.angle_DHA _definition.id '_geom_hbond.angle_DHA' _definition.update 2006-12-14 _description.text ; Angle subtended by the sites identifyed in _geom_hbond.id. The hydrogen at site H is at the apex of the angle. ; _description.common 'HbondAngleDHA' _name.category_id geom_hbond _name.object_id angle_DHA _type.purpose Measured _type.container Single _type.contents Real _units.code degrees loop_ _method.purpose _method.expression Evaluation ; xc = List() For [label,symop] in _geom_hbond.id { xf = SymEquiv(symop, symmetry_equiv, _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) ) ) ; save_ save_geom_hbond.atom_site_label_A _definition.id '_geom_hbond.atom_site_label_A' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_hbond _name.object_id atom_site_label_A save_ save_geom_hbond.atom_site_label_D _definition.id '_geom_hbond.atom_site_label_D' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_hbond _name.object_id atom_site_label_D save_ save_geom_hbond.atom_site_label_H _definition.id '_geom_hbond.atom_site_label_H' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_hbond _name.object_id atom_site_label_H save_ save_geom_hbond.distance_DH _definition.id '_geom_hbond.distance_DH' _definition.update 2006-12-14 _description.text ; The set of data items which specify the distance between the three atom sites identified by _geom_hbond.id. ; _name.category_id geom_hbond _name.object_id distance_DH _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; xc = List() Do i=0,1 { l,s = _geom_hbond.id [i] xf = SymEquiv(s, symmetry_equiv, _atom_site[l].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_hbond.distance_DH = Norm ( xc[0] - xc[1] ) ; save_ save_geom_hbond.distance_HA _definition.id '_geom_hbond.distance_HA' _definition.update 2006-12-14 _description.text ; The set of data items which specify the distance between the three atom sites identified by _geom_hbond.id. ; _name.category_id geom_hbond _name.object_id distance_HA _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; xc = List() Do i=1,2 { l,s = _geom_hbond.id [i] xf = SymEquiv(s, symmetry_equiv, _atom_site[l].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_hbond.distance_HA = Norm ( xc[0] - xc[1] ) ; save_ save_geom_hbond.distance_DA _definition.id '_geom_hbond.distance_DA' _definition.update 2006-12-14 _description.text ; The set of data items which specify the distance between the three atom sites identified by _geom_hbond.id. ; _name.category_id geom_hbond _name.object_id distance_DA _type.purpose Measured _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms loop_ _method.purpose _method.expression Evaluation ; xc = List() Do i=0,2,2 { l,s = _geom_hbond.id [i] xf = SymEquiv(s, symmetry_equiv, _atom_site[l].fract_xyz) xc ++= _atom_sites_Cartn_transform.matrix * xf } _geom_hbond.distance_DA = Norm ( xc[0] - xc[1] ) ; save_ save_geom_hbond.id _definition.id '_geom_hbond.id' _definition.update 2008-06-24 _description.text ; Atom site labels and symmetry operators as pairs for each of the three atom sites which define the hydrogen angle and distances. Site H is at the apex of the angle. ; _description.common 'HbondId' _name.category_id geom_hbond _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Tuple[Label,Symop] loop_ _method.purpose _method.expression Evaluation ; With a as geom_hbond _geom_hbond.id = Tuple ( Tuple ( a.atom_site_label_D, a.site_symmetry_D ), Tuple ( a.atom_site_label_H, a.site_symmetry_H ), Tuple ( a.atom_site_label_A, a.site_symmetry_A ) ) ; save_ save_geom_hbond.publ_flag _definition.id '_geom_hbond.publ_flag' _definition.update 2008-03-28 _description.text ; Code signals if the angle and distances are required for publication. ; _description.common 'HbondPublFlag' _name.category_id geom_hbond _name.object_id publ_flag _type.purpose Assigned _type.container Single _type.contents YesorNo _enumeration.default no save_ save_geom_hbond.site_symmetry_A _definition.id '_geom_hbond.site_symmetry_A' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_hbond _name.object_id site_symmetry_A save_ save_geom_hbond.site_symmetry_D _definition.id '_geom_hbond.site_symmetry_D' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_hbond _name.object_id site_symmetry_D save_ save_geom_hbond.site_symmetry_H _definition.id '_geom_hbond.site_symmetry_H' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_hbond _name.object_id site_symmetry_H save_ save_GEOM_TORSION _definition.id geom_torsion _definition.scope Category _definition.class List _definition.update 2007-02-07 _description.text ; The CATEGORY of data items used to specify the torsion angles in the structural model as derived from the atomic sites. ; _description.common 'Torsion angle list' _category.parent_id geom _category_key.generic '_geom_torsion.key' loop_ _method.purpose _method.expression Evaluation ; 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( .id = Tuple ( m1.id,m2.id,m3.id,m4.id ), .distances = Tuple ( d21,d23,d34 ), .angle = angle ) } } } } ; save_ save_geom_torsion.key _definition.id '_geom_torsion.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of GEOM_TORSION items in a looped list. ; _description.common 'Key to geometry torsion data' _name.category_id geom_torsion _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _geom_torsion.key = _geom_torsion.id ; save_ save_geom_torsion.atom_site_label_1 _definition.id '_geom_torsion.atom_site_label_1' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_torsion _name.object_id atom_site_label_1 save_ save_geom_torsion.atom_site_label_2 _definition.id '_geom_torsion.atom_site_label_2' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_torsion _name.object_id atom_site_label_2 save_ save_geom_torsion.atom_site_label_3 _definition.id '_geom_torsion.atom_site_label_3' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_torsion _name.object_id atom_site_label_3 save_ save_geom_torsion.atom_site_label_4 _definition.id '_geom_torsion.atom_site_label_4' _definition.update 2006-06-29 _description.text ; This label is a unique identifier for a particular site in the asymmetric unit of the crystal unit cell. It is made up of components, _atom_site.label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type.symbol codes. This is not mandatory if an _atom_site.type_symbol item is included in the atom site list. The _atom_site.type_symbol always takes precedence over an _atom_site.label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underline character. Underline separators are only used if higher-order components exist. If an intermediate component is not used it may be omitted provided the underline separators are inserted. For example the label 'C233__ggg' is acceptable and represents the components C, 233, '', and ggg. Each label may have a different number of components. ; _description.common 'Atom Site Label' _name.linked_item_id '_atom_site.label' _type.purpose Assigned _type.container Single _type.contents Label loop_ _description_example.case C12 Ca3g28 Fe3+17 H*251 C_a_phe_83_a_0 Zn_Zn_301_A_0 _name.category_id geom_torsion _name.object_id atom_site_label_4 save_ save_geom_torsion.distances _definition.id '_geom_torsion.distances' _definition.update 2006-12-14 _description.text ; Distances between sites 1 - 2, 2 - 3 and 3 - 4. ; _name.category_id geom_torsion _name.object_id distances _type.purpose Measured _type.container Tuple _type.contents Real _units.code angstroms save_ save_geom_torsion.id _definition.id '_geom_torsion.id' _definition.update 2008-06-24 _description.text ; Atom site labels and symmetry operators as pairs for each of the four atom sites which define the torsion angle. ; _description.common 'TorsionAngleId' _name.category_id geom_torsion _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Tuple[Label,Symop] loop_ _method.purpose _method.expression Evaluation ; With a as geom_torsion _geom_torsion.id = Tuple ( Tuple ( a.atom_site_label_1, a.site_symmetry_1 ), Tuple ( a.atom_site_label_2, a.site_symmetry_2 ), Tuple ( a.atom_site_label_3, a.site_symmetry_3 ), Tuple ( a.atom_site_label_4, a.site_symmetry_4 )) ; save_ save_geom_torsion.publ_flag _definition.id '_geom_torsion.publ_flag' _definition.update 2008-03-28 _description.text ; Code signals if the torsion angle is required for publication. ; _description.common 'TorsionAnglePublFlag' _name.category_id geom_torsion _name.object_id publ_flag _type.purpose Assigned _type.container Single _type.contents YesorNo _enumeration.default no save_ save_geom_torsion.angle _definition.id '_geom_torsion.angle' _definition.update 2006-12-14 _description.text ; Angle defined by the sites identifyed in _geom_torsion.id. ; _description.common 'TorsionAngle' _name.category_id geom_torsion _name.object_id angle _type.purpose Measured _type.container Single _type.contents Real _units.code degrees save_ save_geom_torsion.site_symmetry_1 _definition.id '_geom_torsion.site_symmetry_1' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_torsion _name.object_id site_symmetry_1 save_ save_geom_torsion.site_symmetry_2 _definition.id '_geom_torsion.site_symmetry_2' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_torsion _name.object_id site_symmetry_2 save_ save_geom_torsion.site_symmetry_3 _definition.id '_geom_torsion.site_symmetry_3' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_torsion _name.object_id site_symmetry_3 save_ save_geom_torsion.site_symmetry_4 _definition.id '_geom_torsion.site_symmetry_4' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _name.category_id geom_torsion _name.object_id site_symmetry_4 save_ save_MODEL_SITE _definition.id model_site _definition.scope Category _definition.class List _definition.update 2008-08-14 _description.text ; The CATEGORY of data items used to describe atomic sites and connections in the proposed atomic model. ; _description.common 'ModelSiteList' _category.parent_id core_model _category_key.generic '_model_site.key' loop_ _method.purpose _method.expression Evaluation ; # Store unique sites as a local list 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 = Tuple ( a.label, "1_555" ) atomlist ++= [ls, axyz, cxyz, radb, radc, 0] } # Store closest connected sites as a list 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 symmetry_equiv :ns { axyz = s.R * a3 + s.T bxyz,tran = Closest (axyz, a2) cxyz = _atom_sites_Cartn_transform.matrix *bxyz d = Norm (cxyz - c2) If (d > dmin and d < dmax) { ls = Tuple ( 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 } } # Store connected molecular sites as MODEL_SITE list For [ls,ax,cx,rb,rc,n,m] in molelist { model_site( .id = ls, .fract_xyz = ax, .Cartn_xyz = cx, .radius_bond = rb, .radius_contact = rc, .index = n, .mole_index = m ) } ; save_ save_model_site.key _definition.id '_model_site.key' _definition.update 2008-06-18 _description.text ; Value is a unique key to a set of MODEL_SITE items in a looped list. ; _description.common 'Key to model atomic sites' _name.category_id model_site _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _model_site.key = _model_site.id ; save_ save_model_site.display_colour _definition.id '_model_site.display_colour' _definition.update 2008-01-22 _description.text ; The display colour assigned to this atom site. Note that the possible colours are enumerated in the display_colour list category of items. ; _description.common 'AtomTypeColour' _name.category_id model_site _name.object_id display_colour _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_default.index _enumeration_default.value H white D blue_light H1- white He unknown Li unknown Li1+ unknown Be unknown Be2+ unknown B unknown C steel_grey N blue O red O1- red F green F1- green Ne unknown Na magenta Na1+ magenta Mg magenta Mg2+ magenta Al magenta Al3+ magenta Si unknown Si4+ unknown P magenta S yellow Cl green Cl1- green Ar unknown K magenta K1+ magenta Ca magenta Ca2+ magenta Sc unknown Sc3+ unknown Ti magenta Ti2+ magenta Ti3+ magenta Ti4+ magenta V magenta V2+ magenta V3+ magenta V5+ magenta Cr magenta Cr2+ magenta Cr3+ magenta Mn magenta Mn2+ magenta Mn3+ magenta Mn4+ magenta Fe magenta Fe2+ magenta Fe3+ magenta Co magenta Co2+ magenta Co3+ magenta Ni magenta Ni2+ magenta Ni3+ magenta Cu magenta Cu1+ magenta Cu2+ magenta Zn magenta Zn2+ magenta Ga magenta Ga3+ magenta Ge magenta Ge4+ magenta As magenta Se yellow Br green Br1- green Kr unknown Rb unknown Rb1+ unknown Sr unknown Sr2+ unknown Y unknown Y3+ unknown Zr unknown Zr4+ unknown Nb unknown Nb3+ unknown Nb5+ unknown Mo unknown Mo3+ magenta Mo5+ magenta Mo6+ magenta Tc unknown Ru unknown Ru3+ unknown Ru4+ unknown Rh unknown Rh3+ unknown Rh4+ unknown Pd unknown Pd2+ unknown Pd4+ unknown Ag magenta Ag1+ magenta Ag2+ magenta Cd magenta Cd2+ magenta In unknown In3+ unknown Sn magenta Sn2+ magenta Sn4+ magenta Sb magenta Sb3+ magenta Sb5+ magenta Te unknown I green I1- green Xe unknown Cs unknown Cs1+ unknown Ba unknown Ba2+ unknown La unknown La3+ unknown Ce unknown Ce3+ unknown Ce4+ unknown Pr unknown Pr3+ unknown Pr4+ unknown Nd unknown Nd3+ unknown Pm unknown Sm unknown Sm3+ unknown Eu unknown Eu2+ unknown Eu3+ unknown Gd unknown Gd3+ unknown Tb unknown Tb3+ unknown Dy unknown Dy3+ unknown Ho unknown Ho3+ unknown Er unknown Er3+ unknown Tm unknown Tm3+ unknown Yb unknown Yb2+ unknown Yb3+ unknown Lu unknown Lu3+ unknown Hf unknown Hf4+ unknown Ta unknown Ta5+ unknown W unknown W6+ unknown Re unknown Os unknown Os4+ unknown Ir unknown Ir3+ unknown Ir4+ unknown Pt magenta Pt2+ magenta Pt4+ magenta Au magenta Au1+ magenta Au3+ magenta Hg magenta Hg1+ magenta Hg2+ magenta Tl unknown TL1+ unknown Tl3+ unknown Pb magenta Pb2+ magenta Pb4+ magenta Bi magenta Bi3+ magenta Bi5+ magenta Po unknown At unknown Rn unknown Fr unknown Ra unknown Ra2+ unknown Ac unknown Ac3+ unknown Th unknown Th4+ unknown Pa unknown U unknown U3+ unknown U4+ unknown U6+ unknown Np unknown Np3+ unknown Np4+ unknown Np6+ unknown Pu unknown Pu3+ unknown Pu4+ unknown Pu6+ unknown Am unknown Cm unknown Bk unknown Cf unknown _enumeration.def_index_id '_model_site.type_symbol' save_ save_model_site.radius_bond _definition.id '_model_site.radius_bond' _definition.update 2008-03-28 _description.text ; Atomic radius of atom specie located at this site. ; _description.common 'ModelSiteBondRadius' _name.category_id model_site _name.object_id radius_bond _type.purpose Assigned _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With m as model_site _model_site.radius_bond = _atom_type[m.type_symbol].radius_bond ; save_ save_model_site.adp_matrix_beta _definition.id '_model_site.adp_matrix_beta' _definition.update 2008-06-24 _description.text ; Matrix of dimensionless anisotropic atomic displacement parameters. ; _description.common 'ModelSiteAdpMatrixBeta' _name.category_id model_site _name.object_id adp_matrix_beta _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; [label,symop] = _model_site.id a = atom_site[label] s = symmetry_equiv[SymKey(symop)] _model_site.adp_matrix_beta = s.R * a.matrix_beta * s.RT ; save_ save_model_site.adp_eigen_system _definition.id '_model_site.adp_eigen_system' _definition.update 2008-06-24 _description.text ; The set of three adp eigenvales and associated eigenvectors in the form of 4 element Tuples. Each tuple has the form (val, vecX, vecY, vecZ) where the vector elements are direction cosines to the orthogonal axes X,Y,Z. The tuples are sorted in descending magnitude of val. That is, the tuple with the largest val is first, and the smallest val is last. ; _description.common 'ModelSiteAdpEigenSystem' _name.category_id model_site _name.object_id adp_eigen_system _type.purpose Measured _type.container Tuple _type.contents Tuple[Real,Real,Real,Real] loop_ _method.purpose _method.expression Evaluation ; A = _cell.orthogonal_matrix U = A * _model_site.adp_matrix_beta * Transpose(A) /(2*Pi**2) _model_site.adp_eigen_system = Eigen( U ) ; save_ save_model_site.radius_contact _definition.id '_model_site.radius_contact' _definition.update 2008-03-28 _description.text ; Atomic contact radius of atom specie located at this site. ; _description.common 'ModelSiteContactRadius' _name.category_id model_site _name.object_id radius_contact _type.purpose Assigned _type.container Single _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With m as model_site _model_site.radius_contact = _atom_type[m.type_symbol].radius_contact ; save_ save_model_site.Cartn_xyz _definition.id '_model_site.Cartn_xyz' _definition.update 2006-12-14 _description.text ; Vector of Cartesian (orthogonal angstrom) atom site coordinates. ; _description.common 'ModelCartCoords' _name.category_id model_site _name.object_id Cartn_xyz _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With m as model_site _model_site.Cartn_xyz = _atom_sites_Cartn_transform.matrix * m.fract_xyz ; save_ save_model_site.fract_xyz _definition.id '_model_site.fract_xyz' _definition.update 2006-12-14 _description.text ; Vector of fractional atom site coordinates. ; _description.common 'ModelFractCoords' _name.category_id model_site _name.object_id fract_xyz _type.purpose Measured _type.container Array _type.contents Real loop_ _method.purpose _method.expression Evaluation ; With m as model_site xyz = _atom_site[m.label].fract_xyz _model_site.fract_xyz = SymEquiv(m.symop, symmetry_equiv, xyz) ; save_ save_model_site.id _definition.id '_model_site.id' _definition.update 2008-06-18 _description.text ; Identifier of model site in terms of the atom site label and symmetry operator. ; _description.common 'ModelSiteId' _name.category_id model_site _name.object_id id _type.purpose Identify _type.container Tuple _type.contents Label,Symop loop_ _method.purpose _method.expression Evaluation ; With m as model_site _model_site.id = Tuple ( m.label, m.symop ) ; save_ save_model_site.index _definition.id '_model_site.index' _definition.update 2006-12-14 _description.text ; Index number of an atomic site in the connected molecule. ; _description.common 'ModelSiteIndex' _name.category_id model_site _name.object_id index _type.purpose Assigned _type.container Single _type.contents Index save_ save_model_site.label _definition.id '_model_site.label' _definition.update 2006-12-14 _description.text ; Label identifies a site in the atom_site category of data. ; _description.common 'ModelSiteLabel' _name.category_id model_site _name.object_id label _name.linked_item_id '_atom_site.label' _type.purpose Link _type.container Single _type.contents Label loop_ _method.purpose _method.expression Evaluation ; _model_site.label = _model_site.id [0] ; save_ save_model_site.mole_index _definition.id '_model_site.mole_index' _definition.update 2007-02-09 _description.text ; Index number of a distinct molecules in the cell, not related by symmetry. ; _description.common 'ModelSiteMoleIndex' _name.category_id model_site _name.object_id mole_index _type.purpose Assigned _type.container Single _type.contents Index save_ save_model_site.symop _definition.id '_model_site.symop' _definition.update 2006-06-29 _description.text ; The set of data items which specify the symmetry operation codes which must be applied to the atom sites involved in the geometry angle. The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site.fract_xyz. It must match a number given in _symmetry_equiv.pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z ; _type.purpose Assigned _type.container Single _type.contents Symop loop_ _description_example.case _description_example.detail 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _enumeration.default '1_555' _description.common 'ModelSiteSymop' _name.category_id model_site _name.object_id symop loop_ _method.purpose _method.expression Evaluation ; _model_site.symop = _model_site.id [1] ; save_ save_model_site.type_symbol _definition.id '_model_site.type_symbol' _definition.update 2006-12-14 _description.text ; A code to identify the atom specie(s) occupying this site. ; _description.common 'ModelSiteAtomType' _name.category_id model_site _name.object_id type_symbol _name.linked_item_id '_atom_type.symbol' _type.purpose Link _type.container Single _type.contents Element loop_ _method.purpose _method.expression Evaluation ; _model_site.type_symbol = AtomType ( _model_site.label ) ; save_ save_CORE_PUBLICATION _definition.id core_publication _definition.scope Category _definition.class Head _definition.update 2006-12-14 _description.text ; The DICTIONARY group encompassing the CORE PUBLICATION data items defined and used with in the Crystallographic Information Framework (CIF). ; _category.parent_id cif_core save_ save_DISPLAY_COLOUR _definition.id display_colour _definition.scope Category _definition.class List _definition.update 2006-12-14 _description.text ; The CATEGORY of data items used to enumerate the display colour codes used in the discipline. ; _category.parent_id core_publication _category_key.generic '_display_colour.key' save_ save_display_colour.key _definition.id '_display_colour.key' _definition.update 2008-05-18 _description.text ; Value is a unique key to a set of DISPLAY_COLOUR items in a looped list. ; _description.common 'Key to display colours' _name.category_id display_colour _name.object_id key _type.purpose Key _type.container Single _type.contents Inherited loop_ _method.purpose _method.expression Evaluation ; _display_colour.key = _display_colour.hue ; save_ save_display_colour.hue _definition.id '_display_colour.hue' _definition.update 2008-02-07 _description.text ; Colour hue as an enumerated code. ; _description.common 'DisplayHue' _name.category_id display_colour _name.object_id hue _type.purpose State _type.container Single _type.contents Code loop_ _enumeration_set.state _enumeration_set.detail black [ 000, 000, 000 ] white [ 255, 255, 255 ] grey [ 192, 192, 192 ] grey_light [ 211, 211, 211 ] grey_slate [ 112, 128, 144 ] blue [ 000, 000, 255 ] blue_light [ 176, 224, 230 ] blue_medium [ 000, 000, 205 ] blue_dark [ 025, 025, 112 ] blue_navy [ 000, 000, 128 ] blue_royal [ 065, 105, 225 ] blue_sky [ 135, 206, 235 ] blue_steel [ 070, 130, 180 ] turquoise [ 064, 224, 208 ] cyan [ 000, 255, 255 ] cyan_light [ 224, 255, 255 ] green [ 000, 255, 000 ] green_light [ 152, 251, 152 ] green_dark [ 000, 100, 000 ] green_sea [ 046, 139, 087 ] green_lime [ 050, 205, 050 ] green_olive [ 107, 142, 035 ] green_khaki [ 240, 230, 140 ] yellow [ 255, 255, 000 ] yellow_light [ 255, 255, 224 ] yellow_gold [ 255, 215, 000 ] brown [ 165, 042, 042 ] brown_sienna [ 160, 082, 045 ] brown_beige [ 245, 245, 220 ] brown_tan [ 210, 180, 140 ] salmon [ 250, 128, 114 ] salmon_light [ 255, 160, 122 ] salmon_dark [ 233, 150, 122 ] orange [ 255, 165, 000 ] orange_dark [ 255, 140, 000 ] red [ 255, 000, 000 ] red_coral [ 255, 127, 080 ] red_tomato [ 255, 099, 071 ] red_orange [ 255, 069, 000 ] red_violet [ 219, 112, 147 ] red_maroon [ 176, 048, 096 ] pink [ 255, 192, 203 ] pink_light [ 255, 182, 193 ] pink_deep [ 255, 020, 147 ] pink_hot [ 255, 105, 180 ] violet [ 238, 130, 238 ] violet_red [ 208, 032, 144 ] violet_magenta [ 255, 000, 255 ] violet_dark [ 148, 000, 211 ] violet_blue [ 138, 043, 226 ] _enumeration.default 'black' save_ save_display_colour.RGB _definition.id '_display_colour.RGB' _definition.update 2006-12-14 _description.text ; The red-green-blue intensities, bases 256, for each colour code. ; _description.common 'DisplayColourRGB' _name.category_id display_colour _name.object_id RGB _type.purpose Assigned _type.container Tuple _type.contents Index loop_ _method.purpose _method.expression Evaluation ; With c as display_colour _display_colour.RGB = Tuple( c.red, c.green, c.blue ) ; save_ save_display_colour.red _definition.id '_display_colour.red' _definition.update 2006-06-29 _description.text ; The set of data items which specify the intensity values of red, green and blue for display colour codes. ; _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0:255 _name.category_id display_colour _name.object_id red save_ save_display_colour.green _definition.id '_display_colour.green' _definition.update 2006-06-29 _description.text ; The set of data items which specify the intensity values of red, green and blue for display colour codes. ; _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0:255 _name.category_id display_colour _name.object_id green save_ save_display_colour.blue _definition.id '_display_colour.blue' _definition.update 2006-06-29 _description.text ; The set of data items which specify the intensity values of red, green and blue for display colour codes. ; _type.purpose Observed _type.container Single _type.contents Count _enumeration.range 0:255 _name.category_id display_colour _name.object_id blue save_ # {{'Dic','CIF_CORE', 'cif_core.dic', 'Exit', 'Exit'}} # common core # {'Dic','CIF_SMOL', 'cif_smol.dic', 'Exit', 'Exit'}, # small molecule # {'Dic','CIF_MMOL', 'cif_mmol.dic', 'Exit', 'Exit'}, # macromolecule # {'Dic','CIF_POWD', 'cif_powd.dic', 'Exit', 'Exit'}, # powder diffraction # {'Dic','CIF_RHOD', 'cif_rhod.dic', 'Exit', 'Exit'}, # charge density #============================================================================= # This dictionary's creation history. #============================================================================= loop_ _dictionary_audit.version _dictionary_audit.date _dictionary_audit.revision 1.0.0 2005-12-12 ; Initial version created from the CORE_3 version 3.5.02. ; 1.0.01 2006-02-06 ; Place import_dictionary.id values into a tuple. ; 1.1.01 2006-02-06 ; Remove dictionary attributes from a save frames. Add dictionary id to the import tuple. ; 1.1.02 2006-02-13 ; Change _import_dictionary.id from a loop_ to a tuple. ; 1.2.01 2006-02-21 ; Basic change in dictionary structure where the dictionary data block now contains a saveframe defining the category of the DICTIONRY to which contained data categories are linked. It differs from other CATEGORY definitions in that its name is NOT part of the child data tags. This change allows imported dictionaries to be inserted without their data block header or non-savedframed attributes. ; 1.2.02 2006-06-30 ; Apply the latest attribute changes as per DDL 3.6.06 ; 1.2.03 2006-11-13 ; Removed method and context imports ; 1.2.04 2008-02-12 ; Updated the IMPORT values as per ddl.dic 3.07.09 ; 1.2.05 2008-05-18 ; Changed looped list of imports to _import_list.id syntax. ; 1.2.06 2009-10-24 ; Changed list of imports for _import_list.id from () to {} for CIF 2 compliance. ;