diff --git a/cif_core.dic b/cif_core.dic index 8002658..5af2fa7 100644 --- a/cif_core.dic +++ b/cif_core.dic @@ -10,7 +10,7 @@ data_CORE_DIC _dictionary.title CORE_DIC _dictionary.class Instance _dictionary.version 3.2.0 - _dictionary.date 2023-02-06 + _dictionary.date 2023-03-02 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic _dictionary.ddl_conformance 4.1.0 @@ -497,1511 +497,1283 @@ save_diffrn.symmetry_description save_ -save_DIFFRN_ATTENUATOR +save_CELL - _definition.id DIFFRN_ATTENUATOR + _definition.id CELL _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.class Set + _definition.update 2023-03-02 _description.text ; - The CATEGORY of data items which specify the attenuators used in the - diffraction source. + The CATEGORY of data items used to describe the parameters of + the crystal unit cell. ; _name.category_id DIFFRN - _name.object_id DIFFRN_ATTENUATOR - _category_key.name '_diffrn_attenuator.code' + _name.object_id CELL + _category_key.name '_cell.diffrn_id' save_ -save_diffrn_attenuator.code - - _definition.id '_diffrn_attenuator.code' - _alias.definition_id '_diffrn_attenuator_code' - _definition.update 2012-11-26 - _description.text -; - Code identifying a particular attenuator setting; referenced by the - _diffrn_refln.attenuator_code which is stored with the intensities. -; - _name.category_id diffrn_attenuator - _name.object_id code - _type.purpose Encode - _type.source Assigned - _type.container Single - _type.contents Word - -save_ +save_cell.angle_alpha -save_diffrn_attenuator.material + _definition.id '_cell.angle_alpha' + _alias.definition_id '_cell_angle_alpha' + _name.category_id cell + _name.object_id angle_alpha - _definition.id '_diffrn_attenuator.material' - _alias.definition_id '_diffrn_attenuator_material' - _definition.update 2012-11-26 - _description.text -; - Description of the material from which the attenuator is made. -; - _name.category_id diffrn_attenuator - _name.object_id material - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _import.get [{'file':templ_attr.cif 'save':cell_angle}] save_ -save_diffrn_attenuator.scale +save_cell.angle_alpha_su - _definition.id '_diffrn_attenuator.scale' - _alias.definition_id '_diffrn_attenuator_scale' - _definition.update 2012-11-26 - _description.text -; - The scale factor applied to a measured intensity if it is reduced by - an attenuator identified by _diffrn_attenuator.code. -; - _name.category_id diffrn_attenuator - _name.object_id scale - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 1.0: - _units.code none + _definition.id '_cell.angle_alpha_su' -save_ + loop_ + _alias.definition_id + '_cell_angle_alpha_su' + '_cell.angle_alpha_esd' -save_DIFFRN_DETECTOR + _name.category_id cell + _name.object_id angle_alpha_su + _name.linked_item_id '_cell.angle_alpha' - _definition.id DIFFRN_DETECTOR - _definition.scope Category - _definition.class Set - _definition.update 2023-01-13 - _description.text -; - The CATEGORY of data items which specify the detectors used - in the measurement of diffraction intensities. -; - _name.category_id DIFFRN - _name.object_id DIFFRN_DETECTOR + _import.get + [{'file':templ_attr.cif 'save':cell_angle_su}] save_ -save_diffrn_detector.area_resol_mean +save_cell.angle_beta - _definition.id '_diffrn_detector.area_resol_mean' - _alias.definition_id '_diffrn_detector_area_resol_mean' - _definition.update 2012-11-26 - _description.text -; - The resolution limit of an area diffraction radiation detector. -; - _name.category_id diffrn_detector - _name.object_id area_resol_mean - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code pixels_per_millimetre + _definition.id '_cell.angle_beta' + _alias.definition_id '_cell_angle_beta' + _name.category_id cell + _name.object_id angle_beta + + _import.get [{'file':templ_attr.cif 'save':cell_angle}] save_ -save_diffrn_detector.description +save_cell.angle_beta_su - _definition.id '_diffrn_detector.description' + _definition.id '_cell.angle_beta_su' loop_ _alias.definition_id - '_diffrn_radiation_detector' - '_diffrn_detector' - '_diffrn_detector.detector' + '_cell_angle.beta_su' + '_cell_angle_beta_su' + '_cell.angle_beta_esd' - _definition.update 2012-11-26 - _description.text -; - Description of the type of diffraction radiation detector. -; - _name.category_id diffrn_detector - _name.object_id description - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _name.category_id cell + _name.object_id angle_beta_su + _name.linked_item_id '_cell.angle_beta' - loop_ - _description_example.case - 'photographic film' - 'scintillation counter' - 'CCD plate' - 'BF~3~ counter' + _import.get + [{'file':templ_attr.cif 'save':cell_angle_su}] save_ -save_diffrn_detector.details +save_cell.angle_gamma - _definition.id '_diffrn_detector.details' - _alias.definition_id '_diffrn_detector_details' - _definition.update 2012-11-26 - _description.text -; - Description of special aspects of the radiation detector. -; - _name.category_id diffrn_detector - _name.object_id details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _definition.id '_cell.angle_gamma' + _alias.definition_id '_cell_angle_gamma' + _name.category_id cell + _name.object_id angle_gamma + + _import.get [{'file':templ_attr.cif 'save':cell_angle}] save_ -save_diffrn_detector.dtime +save_cell.angle_gamma_su - _definition.id '_diffrn_detector.dtime' + _definition.id '_cell.angle_gamma_su' loop_ _alias.definition_id - '_diffrn_detector_dtime' - '_diffrn_radiation.detector_dtime' - '_diffrn_radiation_detector_dtime' + '_cell_angle.gamma_su' + '_cell_angle_gamma_su' + '_cell.angle_gamma_esd' - _definition.update 2012-11-26 + _name.category_id cell + _name.object_id angle_gamma_su + _name.linked_item_id '_cell.angle_gamma' + + _import.get + [{'file':templ_attr.cif 'save':cell_angle_su}] + +save_ + +save_cell.atomic_mass + + _definition.id '_cell.atomic_mass' + _definition.update 2012-11-22 _description.text ; - The maximum time between two detector signals that cannot be resolved. + 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. ; - _name.category_id diffrn_detector - _name.object_id dtime + _name.category_id cell + _name.object_id atomic_mass _type.purpose Number - _type.source Assigned + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code microseconds - -save_ - -save_diffrn_detector.make - - _definition.id '_diffrn_detector.make' + _enumeration.range 0.: + _units.code dalton + _method.purpose Evaluation + _method.expression +; + mass = 0. - loop_ - _alias.definition_id - '_diffrn_detector_type' - '_diffrn_detector.type' + Loop t as atom_type { - _definition.update 2012-11-26 - _description.text -; - The make, model or name of the diffraction radiation detector. + mass += t.number_in_cell * t.atomic_mass + } + _cell.atomic_mass = mass ; - _name.category_id diffrn_detector - _name.object_id make - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text save_ -save_DIFFRN_MEASUREMENT +save_cell.convert_uij_to_betaij - _definition.id DIFFRN_MEASUREMENT - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 + _definition.id '_cell.convert_Uij_to_betaij' + _definition.update 2021-09-24 _description.text ; - The CATEGORY of data items which specify the details of the - diffraction measurement. -; - _name.category_id DIFFRN - _name.object_id DIFFRN_MEASUREMENT + 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: -save_ + 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 ) -save_diffrn_measurement.details - - _definition.id '_diffrn_measurement.details' - - loop_ - _alias.definition_id - '_diffrn_measurement_details' - '_diffrn.measurement_details' - - _definition.update 2012-11-26 - _description.text -; - Description of special aspects of the diffraction measurement. -; - _name.category_id diffrn_measurement - _name.object_id details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case '440 frames of 0.25\%' - -save_ - -save_diffrn_measurement.device_class - - _definition.id '_diffrn_measurement.device_class' - - loop_ - _alias.definition_id - '_diffrn_measurement_device' - '_diffrn.measurement_device_class' - '_diffrn_measurement.device' - - _definition.update 2012-11-26 - _description.text -; - Type of goniometer device used to mount and orient the specimen. -; - _name.category_id diffrn_measurement - _name.object_id device_class - _type.purpose Describe - _type.source Recorded - _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' - - loop_ - _alias.definition_id - '_diffrn_measurement_device_details' - '_diffrn.measurement_device_details' - - _definition.update 2012-11-26 - _description.text -; - Details of the goniometer device used in the diffraction experiment. -; - _name.category_id diffrn_measurement - _name.object_id device_details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _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' + The conversion of the U or B matrices to the beta matrix - loop_ - _alias.definition_id - '_diffrn_measurement_device_type' - '_diffrn.measurement_device_make' - '_diffrn_measurement.device_type' + beta = C U C = C B C /8pi**2 - _definition.update 2013-03-07 - _description.text + where C is conversion matrix defined here. ; - The make, model or name of the goniometer device used. + _name.category_id cell + _name.object_id convert_Uij_to_betaij + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression ; - _name.category_id diffrn_measurement - _name.object_id device_make - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - - loop_ - _description_example.case - 'Supper model q' - 'Huber model r' - 'Enraf-Nonius model s' - 'home-made' - -save_ - -save_diffrn_measurement.method - - _definition.id '_diffrn_measurement.method' - - loop_ - _alias.definition_id - '_diffrn_measurement_method' - '_diffrn.measurement_method' + With c as cell - _definition.update 2012-11-26 - _description.text -; - Description of scan method used to measure diffraction intensities. + _cell.convert_Uij_to_betaij = 1.4142 * Pi * + Matrix([[ c.reciprocal_length_a, 0, 0 ], + [ 0, c.reciprocal_length_b, 0 ], + [ 0, 0, c.reciprocal_length_c ]]) ; - _name.category_id diffrn_measurement - _name.object_id method - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'profile data from \q/2\q scans' save_ -save_diffrn_measurement.specimen_attachment_type +save_cell.convert_uij_to_betaij_su - _definition.id '_diffrn_measurement.specimen_attachment_type' - _definition.update 2023-02-06 + _definition.id '_cell.convert_Uij_to_betaij_su' + _definition.update 2021-09-23 _description.text ; - The way in which the sample is attached to the sample holder, - including the type of adhesive material used if relevant. The sample - holder is usually wholly outside the beam, whereas the attachment - method may cause non-sample material to be illuminated. If the - attachment method is not included in the list below, 'other' should be - chosen and details provided in _diffrn_measurement.specimen_support. -; - _name.category_id diffrn_measurement - _name.object_id specimen_attachment_type - _type.purpose State - _type.source Recorded - _type.container Single - _type.contents Word - - loop_ - _enumeration_set.state - _enumeration_set.detail - epoxy -; - An epoxy glue. -; - oil -; - An oil. -; - grease -; - A type of grease, for example hydrocarbon or silicone grease. -; - frozen_liquid -; - A frozen liquid, not water or oil. -; - other -; - A method not listed here. -; - ice -; - The specimen is frozen in place using water ice. -; - mechanical -; - The specimen is held in place by mechanical forces, e.g. capillary or - pressure cell. + Standard uncertainty of _cell.convert_Uij_to_betaij. ; + _name.category_id cell + _name.object_id convert_Uij_to_betaij_su + _name.linked_item_id '_cell.convert_Uij_to_betaij' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstroms save_ -save_diffrn_measurement.specimen_support - - _definition.id '_diffrn_measurement.specimen_support' - - loop_ - _alias.definition_id - '_diffrn_measurement_specimen_support' - '_diffrn.measurement_specimen_support' +save_cell.convert_uiso_to_uij - _definition.update 2013-01-23 + _definition.id '_cell.convert_Uiso_to_Uij' + _definition.update 2021-07-07 _description.text ; - Mounting method for the crystal specimen during data collection. -; - _name.category_id diffrn_measurement - _name.object_id specimen_support - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - - loop_ - _description_example.case - 'glass capillary' - 'quartz capillary' - 'fiber' - 'metal loop' - -save_ - -save_DIFFRN_ORIENT + The reciprocal space matrix for converting the isotropic Uiso + atomic displacement parameter to the anisotropic matrix Uij. - _definition.id DIFFRN_ORIENT - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 - _description.text + | 1 cos(gamma*) cos(beta*) | + U[i,j] = Uiso * | cos(gamma*) 1 cos(alpha*) | + | cos(beta*) cos(alpha*) 1 | ; - The CATEGORY of data items which specify the orientation of the crystal - axes to the diffractometer goniometer. + _name.category_id cell + _name.object_id convert_Uiso_to_Uij + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code none + _method.purpose Evaluation + _method.expression ; - _name.category_id DIFFRN - _name.object_id DIFFRN_ORIENT - -save_ - -save_DIFFRN_ORIENT_MATRIX + With c as cell - _definition.id DIFFRN_ORIENT_MATRIX - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 - _description.text -; - The CATEGORY of data items which specify the matrix specifying the - orientation of the crystal axes to the diffractometer goniometer. + _cell.convert_Uiso_to_Uij = [[ 1., + Cosd(c.reciprocal_angle_gamma), Cosd(c.reciprocal_angle_beta) ], + [ Cosd(c.reciprocal_angle_gamma), 1., + Cosd(c.reciprocal_angle_alpha) ], [ + Cosd(c.reciprocal_angle_beta), Cosd(c.reciprocal_angle_alpha), 1. ]] ; - _name.category_id DIFFRN_ORIENT - _name.object_id DIFFRN_ORIENT_MATRIX save_ -save_diffrn_orient_matrix.type +save_cell.convert_uiso_to_uij_su - _definition.id '_diffrn_orient_matrix.type' - _alias.definition_id '_diffrn_orient_matrix_type' - _definition.update 2012-11-26 + _definition.id '_cell.convert_Uiso_to_Uij_su' + _definition.update 2021-09-23 _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. + Standard uncertainty of _cell.convert_Uiso_to_Uij. ; - _name.category_id diffrn_orient_matrix - _name.object_id type - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - -save_ - -save_diffrn_orient_matrix.ub_11 - - _definition.id '_diffrn_orient_matrix.UB_11' - - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_11' - '_diffrn_orient_matrix.UB[1][1]' - - _name.category_id diffrn_orient_matrix - _name.object_id UB_11 - - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] - -save_ - -save_diffrn_orient_matrix.ub_12 - - _definition.id '_diffrn_orient_matrix.UB_12' - - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_12' - '_diffrn_orient_matrix.UB[1][2]' - - _name.category_id diffrn_orient_matrix - _name.object_id UB_12 - - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + _name.category_id cell + _name.object_id convert_Uiso_to_Uij_su + _name.linked_item_id '_cell.convert_Uiso_to_Uij' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code none save_ -save_diffrn_orient_matrix.ub_13 +save_cell.diffrn_id - _definition.id '_diffrn_orient_matrix.UB_13' + _definition.id '_cell.diffrn_id' + _definition.update 2023-02-01 + _description.text +; + A pointer to the diffraction conditions to which this cell has been applied, + for example, to locate and extract diffraction peaks. These will normally be + the same conditions as those under which the cell was measured, but some + legacy data sets may have used a cell measured under differing conditions, + in which case those conditions should be indicated using + `_cell_measurement.condition_id` +; + _name.category_id cell + _name.object_id diffrn_id + _name.linked_item_id '_diffrn.id' + _type.purpose Link + _type.source Related + _type.container Single + _type.contents Word - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_13' - '_diffrn_orient_matrix.UB[1][3]' +save_ - _name.category_id diffrn_orient_matrix - _name.object_id UB_13 +save_cell.formula_units_z - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + _definition.id '_cell.formula_units_Z' + _alias.definition_id '_cell_formula_units_Z' + _definition.update 2021-03-01 + _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. +; + _name.category_id cell + _name.object_id formula_units_Z + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range 1: + _units.code none save_ -save_diffrn_orient_matrix.ub_21 - - _definition.id '_diffrn_orient_matrix.UB_21' - - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_21' - '_diffrn_orient_matrix.UB[2][1]' +save_cell.length_a - _name.category_id diffrn_orient_matrix - _name.object_id UB_21 + _definition.id '_cell.length_a' + _alias.definition_id '_cell_length_a' + _name.category_id cell + _name.object_id length_a - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + _import.get [{'file':templ_attr.cif 'save':cell_length}] save_ -save_diffrn_orient_matrix.ub_22 +save_cell.length_a_su - _definition.id '_diffrn_orient_matrix.UB_22' + _definition.id '_cell.length_a_su' loop_ _alias.definition_id - '_diffrn_orient_matrix_UB_22' - '_diffrn_orient_matrix.UB[2][2]' + '_cell_length_a_su' + '_cell.length_a_esd' - _name.category_id diffrn_orient_matrix - _name.object_id UB_22 + _name.category_id cell + _name.object_id length_a_su + _name.linked_item_id '_cell.length_a' _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + [{'file':templ_attr.cif 'save':cell_length_su}] save_ -save_diffrn_orient_matrix.ub_23 - - _definition.id '_diffrn_orient_matrix.UB_23' - - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_23' - '_diffrn_orient_matrix.UB[2][3]' +save_cell.length_b - _name.category_id diffrn_orient_matrix - _name.object_id UB_23 + _definition.id '_cell.length_b' + _alias.definition_id '_cell_length_b' + _name.category_id cell + _name.object_id length_b - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + _import.get [{'file':templ_attr.cif 'save':cell_length}] save_ -save_diffrn_orient_matrix.ub_31 +save_cell.length_b_su - _definition.id '_diffrn_orient_matrix.UB_31' + _definition.id '_cell.length_b_su' loop_ _alias.definition_id - '_diffrn_orient_matrix_UB_31' - '_diffrn_orient_matrix.UB[3][1]' + '_cell_length_b_su' + '_cell.length_b_esd' - _name.category_id diffrn_orient_matrix - _name.object_id UB_31 + _name.category_id cell + _name.object_id length_b_su + _name.linked_item_id '_cell.length_b' _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + [{'file':templ_attr.cif 'save':cell_length_su}] save_ -save_diffrn_orient_matrix.ub_32 - - _definition.id '_diffrn_orient_matrix.UB_32' - - loop_ - _alias.definition_id - '_diffrn_orient_matrix_UB_32' - '_diffrn_orient_matrix.UB[3][2]' +save_cell.length_c - _name.category_id diffrn_orient_matrix - _name.object_id UB_32 + _definition.id '_cell.length_c' + _alias.definition_id '_cell_length_c' + _name.category_id cell + _name.object_id length_c - _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + _import.get [{'file':templ_attr.cif 'save':cell_length}] save_ -save_diffrn_orient_matrix.ub_33 +save_cell.length_c_su - _definition.id '_diffrn_orient_matrix.UB_33' + _definition.id '_cell.length_c_su' loop_ _alias.definition_id - '_diffrn_orient_matrix_UB_33' - '_diffrn_orient_matrix.UB[3][3]' + '_cell_length_c_su' + '_cell.length_c_esd' - _name.category_id diffrn_orient_matrix - _name.object_id UB_33 + _name.category_id cell + _name.object_id length_c_su + _name.linked_item_id '_cell.length_c' _import.get - [{'file':templ_attr.cif 'save':orient_matrix}] + [{'file':templ_attr.cif 'save':cell_length_su}] save_ -save_diffrn_orient_matrix.ubij +save_cell.metric_tensor - _definition.id '_diffrn_orient_matrix.UBij' - _definition.update 2021-03-01 + _definition.id '_cell.metric_tensor' + _definition.update 2021-07-07 _description.text ; - The 3x3 matrix specifying the orientation of the crystal with - respect to the diffractometer axes. + The direct space (covariant) metric tensor used to transform + vectors and coordinates from real (direct) to reciprocal space. ; - _name.category_id diffrn_orient_matrix - _name.object_id UBij + _name.category_id cell + _name.object_id metric_tensor _type.purpose Number _type.source Derived _type.container Matrix _type.dimension '[3,3]' _type.contents Real - _units.code none + _units.code angstrom_squared _method.purpose Evaluation _method.expression ; - With o as diffrn_orient_matrix - - _diffrn_orient_matrix.UBIJ = [[ o.ub_11, o.ub_12, o.ub_13 ], - [ o.ub_21, o.ub_22, o.ub_23 ], - [ o.ub_31, o.ub_32, o.ub_33 ]] -; - -save_ - -save_DIFFRN_ORIENT_REFLN + with c as cell - _definition.id DIFFRN_ORIENT_REFLN - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 - _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. + _cell.metric_tensor = [[ c.vector_a*c.vector_a, + c.vector_a*c.vector_b, c.vector_a*c.vector_c ], + [ c.vector_b*c.vector_a, c.vector_b*c.vector_b, c.vector_b*c.vector_c ], + [ c.vector_c*c.vector_a, c.vector_c*c.vector_b, + c.vector_c*c.vector_c ]] ; - _name.category_id DIFFRN_ORIENT - _name.object_id DIFFRN_ORIENT_REFLN - - loop_ - _category_key.name - '_diffrn_orient_refln.index_h' - '_diffrn_orient_refln.index_k' - '_diffrn_orient_refln.index_l' save_ -save_diffrn_orient_refln.angle_chi - - _definition.id '_diffrn_orient_refln.angle_chi' - _alias.definition_id '_diffrn_orient_refln_angle_chi' - _name.category_id diffrn_orient_refln - _name.object_id angle_chi - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] - -save_ - -save_diffrn_orient_refln.angle_chi_su +save_cell.orthogonal_matrix - _definition.id '_diffrn_orient_refln.angle_chi_su' - _definition.update 2021-09-23 + _definition.id '_cell.orthogonal_matrix' + _definition.update 2021-07-07 _description.text ; - Standard uncertainty of _diffrn_orient_refln.angle_chi. + 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. ; - _name.category_id diffrn_orient_refln - _name.object_id angle_chi_su - _name.linked_item_id '_diffrn_orient_refln.angle_chi' - _units.code degrees - - _import.get [{'file':templ_attr.cif 'save':general_su}] - -save_ - -save_diffrn_orient_refln.angle_kappa - - _definition.id '_diffrn_orient_refln.angle_kappa' - _alias.definition_id '_diffrn_orient_refln_angle_kappa' - _name.category_id diffrn_orient_refln - _name.object_id angle_kappa - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] - -save_ - -save_diffrn_orient_refln.angle_kappa_su - - _definition.id '_diffrn_orient_refln.angle_kappa_su' - _definition.update 2021-09-23 - _description.text + _name.category_id cell + _name.object_id orthogonal_matrix + _type.purpose Number + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code angstroms + _method.purpose Evaluation + _method.expression ; - Standard uncertainty of _diffrn_orient_refln.angle_kappa. + With c as cell + _cell.orthogonal_matrix = [ + [ c.length_a*Sind(c.angle_beta)*Sind(c.reciprocal_angle_gamma), 0, + 0 ], [ + -c.length_a*Sind(c.angle_beta)*Cosd(c.reciprocal_angle_gamma), + c.length_b*Sind(c.angle_alpha), 0 ], [ + c.length_a*Cosd(c.angle_beta), + c.length_b*Cosd(c.angle_alpha), c.length_c ]] ; - _name.category_id diffrn_orient_refln - _name.object_id angle_kappa_su - _name.linked_item_id '_diffrn_orient_refln.angle_kappa' - _units.code degrees - - _import.get [{'file':templ_attr.cif 'save':general_su}] - -save_ - -save_diffrn_orient_refln.angle_omega - - _definition.id '_diffrn_orient_refln.angle_omega' - _alias.definition_id '_diffrn_orient_refln_angle_omega' - _name.category_id diffrn_orient_refln - _name.object_id angle_omega - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] save_ -save_diffrn_orient_refln.angle_omega_su +save_cell.reciprocal_angle_alpha - _definition.id '_diffrn_orient_refln.angle_omega_su' - _definition.update 2021-09-23 + _definition.id '_cell.reciprocal_angle_alpha' + _alias.definition_id '_cell_reciprocal_angle_alpha' + _definition.update 2013-01-18 _description.text ; - Standard uncertainty of _diffrn_orient_refln.angle_omega. + Reciprocal of the angle between _cell.length_b and _cell.length_c. + Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. + New York: John Wiley & Sons Inc. ; - _name.category_id diffrn_orient_refln - _name.object_id angle_omega_su - _name.linked_item_id '_diffrn_orient_refln.angle_omega' + _name.category_id cell + _name.object_id reciprocal_angle_alpha + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.:180. _units.code degrees + _method.purpose Evaluation + _method.expression +; + With c as cell - _import.get [{'file':templ_attr.cif 'save':general_su}] + _cell.reciprocal_angle_alpha = + Acosd((Cosd(c.angle_beta)*Cosd(c.angle_gamma)-Cosd(c.angle_alpha))/ + (Sind(c.angle_beta)*Sind(c.angle_gamma))) +; save_ -save_diffrn_orient_refln.angle_phi - - _definition.id '_diffrn_orient_refln.angle_phi' - _alias.definition_id '_diffrn_orient_refln_angle_phi' - _name.category_id diffrn_orient_refln - _name.object_id angle_phi - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] +save_cell.reciprocal_angle_alpha_su -save_ + _definition.id '_cell.reciprocal_angle_alpha_su' -save_diffrn_orient_refln.angle_phi_su + loop_ + _alias.definition_id + '_cell_reciprocal_angle_alpha_su' + '_cell.reciprocal_angle_alpha_esd' - _definition.id '_diffrn_orient_refln.angle_phi_su' - _definition.update 2021-09-23 + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _diffrn_orient_refln.angle_phi. + Standard uncertainty of the reciprocal of the angle + between _cell.length_b and _cell.length_c. ; - _name.category_id diffrn_orient_refln - _name.object_id angle_phi_su - _name.linked_item_id '_diffrn_orient_refln.angle_phi' + _name.category_id cell + _name.object_id reciprocal_angle_alpha_su + _name.linked_item_id '_cell.reciprocal_angle_alpha' + _type.purpose SU + _type.source Related + _type.container Single + _type.contents Real _units.code degrees - _import.get [{'file':templ_attr.cif 'save':general_su}] - -save_ - -save_diffrn_orient_refln.angle_psi - - _definition.id '_diffrn_orient_refln.angle_psi' - _alias.definition_id '_diffrn_orient_refln_angle_psi' - _name.category_id diffrn_orient_refln - _name.object_id angle_psi - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] - save_ -save_diffrn_orient_refln.angle_psi_su +save_cell.reciprocal_angle_beta - _definition.id '_diffrn_orient_refln.angle_psi_su' - _definition.update 2021-09-23 + _definition.id '_cell.reciprocal_angle_beta' + _alias.definition_id '_cell_reciprocal_angle_beta' + _definition.update 2013-01-18 _description.text ; - Standard uncertainty of _diffrn_orient_refln.angle_psi. + Reciprocal of the angle between _cell.length_a and _cell.length_c. + Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. + New York: John Wiley & Sons Inc. ; - _name.category_id diffrn_orient_refln - _name.object_id angle_psi_su - _name.linked_item_id '_diffrn_orient_refln.angle_psi' + _name.category_id cell + _name.object_id reciprocal_angle_beta + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.:180. _units.code degrees + _method.purpose Evaluation + _method.expression +; + With c as cell - _import.get [{'file':templ_attr.cif 'save':general_su}] + _cell.reciprocal_angle_beta = + Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_gamma)-Cosd(c.angle_beta))/ + (Sind(c.angle_alpha)*Sind(c.angle_gamma))) +; save_ -save_diffrn_orient_refln.angle_theta - - _definition.id '_diffrn_orient_refln.angle_theta' - _alias.definition_id '_diffrn_orient_refln_angle_theta' - _name.category_id diffrn_orient_refln - _name.object_id angle_theta - - _import.get [{'file':templ_attr.cif 'save':orient_angle}] +save_cell.reciprocal_angle_beta_su -save_ + _definition.id '_cell.reciprocal_angle_beta_su' -save_diffrn_orient_refln.angle_theta_su + loop_ + _alias.definition_id + '_cell_reciprocal_angle_beta_su' + '_cell.reciprocal_angle_beta_esd' - _definition.id '_diffrn_orient_refln.angle_theta_su' - _definition.update 2021-09-23 + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _diffrn_orient_refln.angle_theta. + Standard uncertainty of the reciprocal of the angle + between _cell.length_a and _cell.length_c. ; - _name.category_id diffrn_orient_refln - _name.object_id angle_theta_su - _name.linked_item_id '_diffrn_orient_refln.angle_theta' + _name.category_id cell + _name.object_id reciprocal_angle_beta_su + _name.linked_item_id '_cell.reciprocal_angle_beta' + _type.purpose SU + _type.source Related + _type.container Single + _type.contents Real _units.code degrees - _import.get [{'file':templ_attr.cif 'save':general_su}] - save_ -save_diffrn_orient_refln.hkl +save_cell.reciprocal_angle_gamma - _definition.id '_diffrn_orient_refln.hkl' - _definition.update 2021-03-01 + _definition.id '_cell.reciprocal_angle_gamma' + _alias.definition_id '_cell_reciprocal_angle_gamma' + _definition.update 2016-09-09 _description.text ; - Miller indices of a reflection used to define the orientation matrix. + Reciprocal of the angle between _cell.length_a and _cell.length_b. + Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. + New York: John Wiley & Sons Inc. ; - _name.category_id diffrn_orient_refln - _name.object_id hkl - _type.purpose Number + _name.category_id cell + _name.object_id reciprocal_angle_gamma + _type.purpose Measurand _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer - _units.code none + _type.container Single + _type.contents Real + _enumeration.range 0.:180. + _units.code degrees _method.purpose Evaluation _method.expression ; - With a as diffrn_orient_refln + With c as cell - _diffrn_orient_refln.hkl = [a.index_h, a.index_k, a.index_l] + _cell.reciprocal_angle_gamma = + Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_beta)-Cosd(c.angle_gamma))/ + (Sind(c.angle_alpha)*Sind(c.angle_beta))) ; save_ -save_diffrn_orient_refln.index_h - - _definition.id '_diffrn_orient_refln.index_h' - _alias.definition_id '_diffrn_orient_refln_index_h' - _name.category_id diffrn_orient_refln - _name.object_id index_h - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] - -save_ - -save_diffrn_orient_refln.index_k - - _definition.id '_diffrn_orient_refln.index_k' - _alias.definition_id '_diffrn_orient_refln_index_k' - _name.category_id diffrn_orient_refln - _name.object_id index_k - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] - -save_ +save_cell.reciprocal_angle_gamma_su -save_diffrn_orient_refln.index_l + _definition.id '_cell.reciprocal_angle_gamma_su' - _definition.id '_diffrn_orient_refln.index_l' - _alias.definition_id '_diffrn_orient_refln_index_l' - _name.category_id diffrn_orient_refln - _name.object_id index_l + loop_ + _alias.definition_id + '_cell_reciprocal_angle_gamma_su' + '_cell.reciprocal_angle_gamma_esd' - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _definition.update 2021-03-03 + _description.text +; + Standard uncertainty of the reciprocal of the angle + between _cell.length_a and _cell.length_b. +; + _name.category_id cell + _name.object_id reciprocal_angle_gamma_su + _name.linked_item_id '_cell.reciprocal_angle_gamma' + _type.purpose SU + _type.source Derived + _type.container Single + _type.contents Real + _units.code degrees save_ -save_DIFFRN_RADIATION +save_cell.reciprocal_length_a - _definition.id DIFFRN_RADIATION - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_length_a' + _alias.definition_id '_cell_reciprocal_length_a' + _definition.update 2012-11-22 _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. + Reciprocal of the _cell.length_a. +; + _name.category_id cell + _name.object_id reciprocal_length_a + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + _cell.reciprocal_length_a = Norm ( _cell.reciprocal_vector_a ) ; - _name.category_id DIFFRN - _name.object_id DIFFRN_RADIATION save_ -save_diffrn_radiation.collimation +save_cell.reciprocal_length_a_su - _definition.id '_diffrn_radiation.collimation' - _alias.definition_id '_diffrn_radiation_collimation' - _definition.update 2012-11-26 - _description.text -; - Description of the collimation or focusing applied to the radiation. -; - _name.category_id diffrn_radiation - _name.object_id collimation - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _definition.id '_cell.reciprocal_length_a_su' loop_ - _description_example.case - '0.3 mm double-pinhole' - '0.5 mm' - 'focusing mirrors' - -save_ - -save_diffrn_radiation.filter_edge + _alias.definition_id + '_cell_reciprocal_length_a_su' + '_cell.reciprocal_length_a_esd' - _definition.id '_diffrn_radiation.filter_edge' - _alias.definition_id '_diffrn_radiation_filter_edge' - _definition.update 2012-11-26 + _definition.update 2021-03-03 _description.text ; - Absorption edge of the radiation filter used. + Standard uncertainty of the reciprocal of the _cell.length_a. ; - _name.category_id diffrn_radiation - _name.object_id filter_edge - _type.purpose Number - _type.source Assigned + _name.category_id cell + _name.object_id reciprocal_length_a_su + _name.linked_item_id '_cell.reciprocal_length_a' + _type.purpose SU + _type.source Related _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _units.code reciprocal_angstroms save_ -save_diffrn_radiation.inhomogeneity +save_cell.reciprocal_length_b - _definition.id '_diffrn_radiation.inhomogeneity' - _alias.definition_id '_diffrn_radiation_inhomogeneity' - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_length_b' + _alias.definition_id '_cell_reciprocal_length_b' + _definition.update 2012-11-22 _description.text ; - Half-width of the incident beam perpendicular to the diffraction plane. + Reciprocal of the _cell.length_b. ; - _name.category_id diffrn_radiation - _name.object_id inhomogeneity - _type.purpose Number - _type.source Recorded + _name.category_id cell + _name.object_id reciprocal_length_b + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code millimetres + _enumeration.range 0.: + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + _cell.reciprocal_length_b = Norm ( _cell.reciprocal_vector_b ) +; save_ -save_diffrn_radiation.monochromator +save_cell.reciprocal_length_b_su - _definition.id '_diffrn_radiation.monochromator' - _alias.definition_id '_diffrn_radiation_monochromator' - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_length_b_su' + + loop_ + _alias.definition_id + '_cell_reciprocal_length_b_su' + '_cell.reciprocal_length_b_esd' + + _definition.update 2021-03-03 _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. + Standard uncertainty of the reciprocal of the _cell.length_b. ; - _name.category_id diffrn_radiation - _name.object_id monochromator - _type.purpose Describe - _type.source Recorded + _name.category_id cell + _name.object_id reciprocal_length_b_su + _name.linked_item_id '_cell.reciprocal_length_b' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Text - - loop_ - _description_example.case - 'Zr filter' - 'Ge 220' - 'none' - 'equatorial mounted graphite' + _type.contents Real + _units.code reciprocal_angstroms save_ -save_diffrn_radiation.polarisn_norm +save_cell.reciprocal_length_c - _definition.id '_diffrn_radiation.polarisn_norm' - _alias.definition_id '_diffrn_radiation_polarisn_norm' - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_length_c' + _alias.definition_id '_cell_reciprocal_length_c' + _definition.update 2012-11-22 _description.text ; - The angle, as viewed from the specimen, between the perpendicular - component of the polarisation and the diffraction plane. + Reciprocal of the _cell.length_c. ; - _name.category_id diffrn_radiation - _name.object_id polarisn_norm - _type.purpose Number - _type.source Assigned + _name.category_id cell + _name.object_id reciprocal_length_c + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real - _enumeration.range -180.0:180.0 - _units.code degrees + _enumeration.range 0.: + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + _cell.reciprocal_length_c = Norm ( _cell.reciprocal_vector_c ) +; save_ -save_diffrn_radiation.polarisn_ratio +save_cell.reciprocal_length_c_su - _definition.id '_diffrn_radiation.polarisn_ratio' - _alias.definition_id '_diffrn_radiation_polarisn_ratio' - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_length_c_su' + + loop_ + _alias.definition_id + '_cell_reciprocal_length_c_su' + '_cell.reciprocal_length_c_esd' + + _definition.update 2021-03-03 _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). + Standard uncertainty of the reciprocal of the _cell.length_c. ; - _name.category_id diffrn_radiation - _name.object_id polarisn_ratio - _type.purpose Number - _type.source Assigned + _name.category_id cell + _name.object_id reciprocal_length_c_su + _name.linked_item_id '_cell.reciprocal_length_c' + _type.purpose SU + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code none + _units.code reciprocal_angstroms save_ -save_diffrn_radiation.probe +save_cell.reciprocal_metric_tensor - _definition.id '_diffrn_radiation.probe' - _alias.definition_id '_diffrn_radiation_probe' - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_metric_tensor' + _definition.update 2021-07-07 _description.text ; - Enumerated code for the nature of radiation used (i.e. name of - subatomic particle or region of the electromagnetic spectrum). + The reciprocal (contravariant) metric tensor used to transform + vectors and coordinates from reciprocal space to real (direct) + space. +; + _name.category_id cell + _name.object_id reciprocal_metric_tensor + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstrom_squared + _method.purpose Evaluation + _method.expression +; + with c as cell + _cell.reciprocal_metric_tensor = [ + [ c.reciprocal_vector_a*c.reciprocal_vector_a, + c.reciprocal_vector_a*c.reciprocal_vector_b, + c.reciprocal_vector_a*c.reciprocal_vector_c ], [ + c.reciprocal_vector_b*c.reciprocal_vector_a, + c.reciprocal_vector_b*c.reciprocal_vector_b, + c.reciprocal_vector_b*c.reciprocal_vector_c ], [ + c.reciprocal_vector_c*c.reciprocal_vector_a, + c.reciprocal_vector_c*c.reciprocal_vector_b, + c.reciprocal_vector_c*c.reciprocal_vector_c ]] ; - _name.category_id diffrn_radiation - _name.object_id probe - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text - - loop_ - _enumeration_set.state - x-ray - neutron - electron - gamma save_ -save_diffrn_radiation.type +save_cell.reciprocal_metric_tensor_su - _definition.id '_diffrn_radiation.type' - _definition_replaced.id 1 - _definition_replaced.by '_diffrn_radiation_wavelength.type' - _alias.definition_id '_diffrn_radiation_type' - _definition.update 2022-10-04 + _definition.id '_cell.reciprocal_metric_tensor_su' + _definition.update 2021-09-23 _description.text ; - DEPRECATED. Use _diffrn_radiation_wavelength.type. Details of the - radiation source or energy spectrum. + Standard uncertainty of _cell.reciprocal_metric_tensor. ; - _name.category_id diffrn_radiation - _name.object_id type - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - - loop_ - _description_example.case - 'Mo K\a' - 'Cu K\a' - 'Cu K\a~1~' - 'Cu K-L~2,3~' - 'white-beam' + _name.category_id cell + _name.object_id reciprocal_metric_tensor_su + _name.linked_item_id '_cell.reciprocal_metric_tensor' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstrom_squared save_ -save_diffrn_radiation.xray_symbol +save_cell.reciprocal_orthogonal_matrix - _definition.id '_diffrn_radiation.xray_symbol' - _definition_replaced.id 1 - _definition_replaced.by '_diffrn_radiation_wavelength.xray_symbol' - _alias.definition_id '_diffrn_radiation_xray_symbol' - _definition.update 2022-10-04 + _definition.id '_cell.reciprocal_orthogonal_matrix' + _definition.update 2021-07-07 _description.text ; - DEPRECATED. Use _diffrn_radiation_wavelength.xray_symbol. IUPAC - symbol for the X-ray wavelength for probe radiation. + 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 ; - _name.category_id diffrn_radiation - _name.object_id xray_symbol - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text + _name.category_id cell + _name.object_id reciprocal_orthogonal_matrix + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + _cell.reciprocal_orthogonal_matrix = Inverse( - 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.' + Transpose( _cell.orthogonal_matrix )) +; save_ -save_DIFFRN_RADIATION_WAVELENGTH +save_cell.reciprocal_orthogonal_matrix_su - _definition.id DIFFRN_RADIATION_WAVELENGTH - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_cell.reciprocal_orthogonal_matrix_su' + _definition.update 2021-09-23 _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. + Standard uncertainty of _cell.reciprocal_orthogonal_matrix. ; - _name.category_id DIFFRN_RADIATION - _name.object_id DIFFRN_RADIATION_WAVELENGTH - _category_key.name '_diffrn_radiation_wavelength.id' + _name.category_id cell + _name.object_id reciprocal_orthogonal_matrix_su + _name.linked_item_id '_cell.reciprocal_orthogonal_matrix' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' + _type.contents Real + _units.code reciprocal_angstroms save_ -save_diffrn_radiation_wavelength.details - - _definition.id '_diffrn_radiation_wavelength.details' - - loop_ - _alias.definition_id - '_diffrn_radiation_wavelength_details' - '_diffrn_radiation.wavelength_details' +save_cell.reciprocal_vector_a - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_vector_a' + _definition.update 2021-07-07 _description.text ; - Information about the determination of the radiation - diffrn_radiation_wavelength that is not conveyed completely by an - enumerated value of _diffrn_radiation_wavelength.determination. + Reciprocal of the _cell.vector_a. +; + _name.category_id cell + _name.object_id reciprocal_vector_a + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + With c as cell + + _cell.reciprocal_vector_a = c.vector_b ^ c.vector_c / _cell.volume ; - _name.category_id diffrn_radiation_wavelength - _name.object_id details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text save_ -save_diffrn_radiation_wavelength.determination +save_cell.reciprocal_vector_a_su - _definition.id '_diffrn_radiation_wavelength.determination' + _definition.id '_cell.reciprocal_vector_a_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _cell.reciprocal_vector_a. +; + _name.category_id cell + _name.object_id reciprocal_vector_a_su + _name.linked_item_id '_cell.reciprocal_vector_a' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code reciprocal_angstroms - loop_ - _alias.definition_id - '_diffrn_radiation_wavelength_determination' - '_diffrn_radiation.wavelength_determination' +save_ - _definition.update 2023-01-13 +save_cell.reciprocal_vector_b + + _definition.id '_cell.reciprocal_vector_b' + _definition.update 2021-07-07 _description.text ; - Method by which the radiation wavelength was determined. + Reciprocal of the _cell.vector_b. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id determination - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text + _name.category_id cell + _name.object_id reciprocal_vector_b + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + With c as cell - loop_ - _enumeration_set.state - _enumeration_set.detail - fundamental - 'Fundamental property of matter, e.g. MoK\a.' - estimated - 'Estimated, e.g. from monochromator angle or time of flight.' - refined - 'Refined using a standard crystal with known cell parameters.' + _cell.reciprocal_vector_b = c.vector_c ^ c.vector_a / _cell.volume +; save_ -save_diffrn_radiation_wavelength.id - - _definition.id '_diffrn_radiation_wavelength.id' - - loop_ - _alias.definition_id - '_diffrn_radiation_wavelength_id' - '_diffrn_radiation.wavelength_id' +save_cell.reciprocal_vector_b_su - _definition.update 2021-10-27 + _definition.id '_cell.reciprocal_vector_b_su' + _definition.update 2021-09-23 _description.text ; - Code identifying a radiation used in the diffraction measurements. - This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id + Standard uncertainty of _cell.reciprocal_vector_b. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id id - _type.purpose Encode - _type.source Assigned - _type.container Single - _type.contents Word - _description_example.case x2 + _name.category_id cell + _name.object_id reciprocal_vector_b_su + _name.linked_item_id '_cell.reciprocal_vector_b' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code reciprocal_angstroms save_ -save_diffrn_radiation_wavelength.type +save_cell.reciprocal_vector_c - _definition.id '_diffrn_radiation_wavelength.type' - _definition.update 2022-10-04 + _definition.id '_cell.reciprocal_vector_c' + _definition.update 2021-07-07 _description.text ; - Details of the radiation source or energy spectrum. + Reciprocal of the _cell.vector_c. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id type - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _name.category_id cell + _name.object_id reciprocal_vector_c + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + With c as cell - loop_ - _description_example.case - 'Mo K\a' - 'Cu K\a' - 'Cu K\a~1~' - 'Cu K-L~2,3~' - 'white-beam' + _cell.reciprocal_vector_c = c.vector_a ^ c.vector_b / _cell.volume +; save_ -save_diffrn_radiation_wavelength.value - - _definition.id '_diffrn_radiation_wavelength.value' - - loop_ - _alias.definition_id - '_diffrn_radiation_wavelength' - '_diffrn_radiation_wavelength.wavelength' +save_cell.reciprocal_vector_c_su - _definition.update 2012-11-26 + _definition.id '_cell.reciprocal_vector_c_su' + _definition.update 2021-09-23 _description.text ; - Wavelength of radiation used in diffraction measurements. + Standard uncertainty of _cell.reciprocal_vector_c. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id value - _type.purpose Measurand - _type.source Assigned - _type.container Single + _name.category_id cell + _name.object_id reciprocal_vector_c_su + _name.linked_item_id '_cell.reciprocal_vector_c' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _units.code reciprocal_angstroms save_ -save_diffrn_radiation_wavelength.value_su +save_cell.special_details - _definition.id '_diffrn_radiation_wavelength.value_su' + _definition.id '_cell.special_details' loop_ _alias.definition_id - '_diffrn_radiation_wavelength_su' - '_diffrn_radiation_wavelength.wavelength_su' + '_cell_special_details' + '_cell.details' - _definition.update 2021-08-03 + _definition.update 2012-11-22 _description.text ; - Standard uncertainty of the wavelength of radiation used in diffraction - measurements. + Description of special aspects of the cell choice, noting + possible alternative settings. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id value_su - _name.linked_item_id '_diffrn_radiation_wavelength.value' - _type.purpose SU - _type.source Related + _name.category_id cell + _name.object_id special_details + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _units.code angstroms + _type.contents Text save_ -save_diffrn_radiation_wavelength.wt +save_cell.vector_a - _definition.id '_diffrn_radiation_wavelength.wt' - _alias.definition_id '_diffrn_radiation_wavelength_wt' - _definition.update 2012-11-26 + _definition.id '_cell.vector_a' + _definition.update 2021-07-07 _description.text ; - Relative intensity of a radiation used in the diffraction measurements. + The cell vector along the x axis. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id wt - _type.purpose Number - _type.source Assigned - _type.container Single + _name.category_id cell + _name.object_id vector_a + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none + _units.code angstroms + _method.purpose Evaluation + _method.expression +; + _cell.vector_a = _cell.orthogonal_matrix * Matrix([1,0,0]) +; save_ -save_diffrn_radiation_wavelength.xray_symbol +save_cell.vector_a_su - _definition.id '_diffrn_radiation_wavelength.xray_symbol' - _definition.update 2022-10-04 + _definition.id '_cell.vector_a_su' + _definition.update 2021-09-23 _description.text ; - IUPAC symbol for the X-ray wavelength for probe radiation. + Standard uncertainty of _cell.vector_a. ; - _name.category_id diffrn_radiation_wavelength - _name.object_id xray_symbol - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text - - 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.' + _name.category_id cell + _name.object_id vector_a_su + _name.linked_item_id '_cell.vector_a' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code angstroms save_ -save_DIFFRN_REFLN +save_cell.vector_b - _definition.id DIFFRN_REFLN - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_cell.vector_b' + _definition.update 2021-07-07 _description.text ; - The CATEGORY of data items which specify the reflection measurements, - prior to data reduction and merging. + The cell vector along the y axis. +; + _name.category_id cell + _name.object_id vector_b + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code angstroms + _method.purpose Evaluation + _method.expression +; + _cell.vector_b = _cell.orthogonal_matrix * Matrix([0,1,0]) ; - _name.category_id DIFFRN - _name.object_id DIFFRN_REFLN - _category_key.name '_diffrn_refln.hkl' save_ -save_diffrn_refln.angle_chi - - _definition.id '_diffrn_refln.angle_chi' - _alias.definition_id '_diffrn_refln_angle_chi' - _name.category_id diffrn_refln - _name.object_id angle_chi +save_cell.vector_b_su - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + _definition.id '_cell.vector_b_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _cell.vector_b. +; + _name.category_id cell + _name.object_id vector_b_su + _name.linked_item_id '_cell.vector_b' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code angstroms save_ -save_diffrn_refln.angle_kappa - - _definition.id '_diffrn_refln.angle_kappa' - _alias.definition_id '_diffrn_refln_angle_kappa' - _name.category_id diffrn_refln - _name.object_id angle_kappa +save_cell.vector_c - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + _definition.id '_cell.vector_c' + _definition.update 2021-07-07 + _description.text +; + The cell vector along the z axis. +; + _name.category_id cell + _name.object_id vector_c + _type.purpose Measurand + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code angstroms + _method.purpose Evaluation + _method.expression +; + _cell.vector_c = _cell.orthogonal_matrix * Matrix([0,0,1]) +; save_ -save_diffrn_refln.angle_omega - - _definition.id '_diffrn_refln.angle_omega' - _alias.definition_id '_diffrn_refln_angle_omega' - _name.category_id diffrn_refln - _name.object_id angle_omega +save_cell.vector_c_su - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + _definition.id '_cell.vector_c_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _cell.vector_c. +; + _name.category_id cell + _name.object_id vector_c_su + _name.linked_item_id '_cell.vector_c' + _type.purpose SU + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Real + _units.code angstroms save_ -save_diffrn_refln.angle_phi +save_cell.volume - _definition.id '_diffrn_refln.angle_phi' - _alias.definition_id '_diffrn_refln_angle_phi' - _name.category_id diffrn_refln - _name.object_id angle_phi + _definition.id '_cell.volume' + _alias.definition_id '_cell_volume' + _definition.update 2013-03-07 + _description.text +; + Volume of the crystal unit cell. +; + _name.category_id cell + _name.object_id volume + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstrom_cubed + _method.purpose Evaluation + _method.expression +; + With c as cell - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + _cell.volume = c.vector_a * ( c.vector_b ^ c.vector_c ) +; save_ -save_diffrn_refln.angle_psi +save_cell.volume_su - _definition.id '_diffrn_refln.angle_psi' - _alias.definition_id '_diffrn_refln_angle_psi' - _name.category_id diffrn_refln - _name.object_id angle_psi + _definition.id '_cell.volume_su' - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + loop_ + _alias.definition_id + '_cell_volume_su' + '_cell.volume_esd' -save_ + _definition.update 2014-06-08 + _description.text +; + Standard uncertainty of the volume of the crystal unit cell. +; + _name.category_id cell + _name.object_id volume_su + _name.linked_item_id '_cell.volume' + _type.purpose SU + _type.source Related + _type.container Single + _type.contents Real + _units.code angstrom_cubed -save_diffrn_refln.angle_theta +save_ - _definition.id '_diffrn_refln.angle_theta' - _alias.definition_id '_diffrn_refln_angle_theta' - _name.category_id diffrn_refln - _name.object_id angle_theta +save_CELL_MEASUREMENT - _import.get [{'file':templ_attr.cif 'save':diffr_angle}] + _definition.id CELL_MEASUREMENT + _definition.scope Category + _definition.class Set + _definition.update 2022-05-25 + _description.text +; + The CATEGORY of data items used to describe the measurement of + the cell parameters. +; + _name.category_id CELL + _name.object_id CELL_MEASUREMENT + _category_key.name '_cell_measurement.diffrn_id' save_ -save_diffrn_refln.attenuator_code +save_cell_measurement.condition_id - _definition.id '_diffrn_refln.attenuator_code' - _alias.definition_id '_diffrn_refln_attenuator_code' - _definition.update 2021-10-27 + _definition.id '_cell_measurement.condition_id' + _definition.update 2023-02-01 _description.text ; - Code identifying any attenuator setting for this reflection. + A pointer to the diffraction conditions used for cell measurement, + where different to the diffraction conditions used for data + collection. ; - _name.category_id diffrn_refln - _name.object_id attenuator_code - _name.linked_item_id '_diffrn_attenuator.code' + _name.category_id cell_measurement + _name.object_id condition_id + _name.linked_item_id '_diffrn.id' _type.purpose Link _type.source Related _type.container Single _type.contents Word + _method.purpose Definition + _method.expression +; + _enumeration.default = _cell_measurement.diffrn_id +; save_ -save_diffrn_refln.class_code +save_cell_measurement.diffrn_id - _definition.id '_diffrn_refln.class_code' - _alias.definition_id '_diffrn_refln_class_code' - _definition.update 2021-10-27 + _definition.id '_cell_measurement.diffrn_id' + _definition.update 2023-02-01 _description.text ; - Code for reflection class, if assigned. e.g. modulated structures + A pointer to the diffraction experiment to which the measured cell + has been applied. ; - _name.category_id diffrn_refln - _name.object_id class_code - _name.linked_item_id '_diffrn_reflns_class.code' + _name.category_id cell_measurement + _name.object_id diffrn_id + _name.linked_item_id '_diffrn.id' _type.purpose Link _type.source Related _type.container Single @@ -2009,178 +1781,187 @@ save_diffrn_refln.class_code save_ -save_diffrn_refln.counts_bg_1 +save_cell_measurement.pressure - _definition.id '_diffrn_refln.counts_bg_1' - _alias.definition_id '_diffrn_refln_counts_bg_1' - _definition.update 2022-11-22 + _definition.id '_cell_measurement.pressure' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn.ambient_pressure' + _alias.definition_id '_cell_measurement_pressure' + _definition.update 2022-05-25 _description.text ; - The measured background scattering on one side of a diffraction - peak when measuring using a point detector. - - Note that counts-per-second values should be converted to - total counts. + **DEPRECATED** - Standard uncertainties should not be quoted for these values. - If the standard uncertainties differ from the square root of - the number of counts, _diffrn_refln.intensity_* should be used. + The pressure at which the unit-cell parameters were measured + (not the pressure used to synthesize the sample). + Replaced by '_diffrn.ambient_pressure' ; - _name.category_id diffrn_refln - _name.object_id counts_bg_1 - _type.purpose Number + _name.category_id cell_measurement + _name.object_id pressure + _type.purpose Measurand _type.source Recorded _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code counts + _type.contents Real + _enumeration.range 0.0: + _units.code kilopascals save_ -save_diffrn_refln.counts_bg_2 +save_cell_measurement.pressure_su - _definition.id '_diffrn_refln.counts_bg_2' - _alias.definition_id '_diffrn_refln_counts_bg_2' - _definition.update 2022-11-22 + _definition.id '_cell_measurement.pressure_su' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn.ambient_pressure_su' + + loop_ + _alias.definition_id + '_cell_measurement_pressure_su' + '_cell_measurement.pressure_esd' + + _definition.update 2022-05-22 _description.text ; - The measured background counts on the other side of the - peak to the measurement of _diffrn_refln.counts_bg_1 - when measuring using a point detector. - - Note that counts-per-second values should be converted to - total counts. + ** DEPRECATED ** - Standard uncertainties should not be quoted for these values. - If the standard uncertainties differ from the square root of - the number of counts, _diffrn_refln.intensity_* should be used. + Standard uncertainty of the pressure at which + the unit-cell parameters were measured. ; - _name.category_id diffrn_refln - _name.object_id counts_bg_2 - _type.purpose Number - _type.source Recorded + _name.category_id cell_measurement + _name.object_id pressure_su + _name.linked_item_id '_cell_measurement.pressure' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code counts + _type.contents Real + _units.code kilopascals save_ -save_diffrn_refln.counts_net +save_cell_measurement.radiation - _definition.id '_diffrn_refln.counts_net' - _alias.definition_id '_diffrn_refln_counts_net' - _definition.update 2022-12-12 + _definition.id '_cell_measurement.radiation' + _definition_replaced.id 1 + _definition_replaced.by . + _alias.definition_id '_cell_measurement_radiation' + _definition.update 2022-05-22 _description.text ; - Counts measured in the reflection peak after background - subtraction. If background and peak counts were collected - for different times, the background counts must be scaled to - the peak counts prior to subtraction. + ** DEPRECATED ** - Note that counts-per-second values should be converted to - total counts. - - The value for this data item must be derived from count values. - If not, _diffrn_refln.intensity_* should be used. + Description of the radiation used to measure the unit-cell data. + Items from the DIFFRN_RADIATION category should be used instead + of this item. ; - _name.category_id diffrn_refln - _name.object_id counts_net - _type.purpose Measurand - _type.source Derived + _name.category_id cell_measurement + _name.object_id radiation + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _units.code counts + _type.contents Text + + loop_ + _description_example.case + 'neutron' + 'X-ray tube' + 'synchrotron' save_ -save_diffrn_refln.counts_net_su +save_cell_measurement.reflns_used - _definition.id '_diffrn_refln.counts_net_su' - _definition.update 2012-12-13 + _definition.id '_cell_measurement.reflns_used' + _alias.definition_id '_cell_measurement_reflns_used' + _definition.update 2021-03-01 _description.text ; - Standard uncertainty of _diffrn_refln.counts_net. + Total number of reflections used to determine the unit cell. + The reflections may be specified as cell_measurement_refln items. ; - _name.category_id diffrn_refln - _name.object_id counts_net_su - _name.linked_item_id '_diffrn_refln.counts_net' - _units.code counts - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id cell_measurement + _name.object_id reflns_used + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range 3: + _units.code none save_ -save_diffrn_refln.counts_peak +save_cell_measurement.temperature - _definition.id '_diffrn_refln.counts_peak' - _alias.definition_id '_diffrn_refln_counts_peak' - _definition.update 2022-11-22 + _definition.id '_cell_measurement.temperature' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn.ambient_temperature' + + loop_ + _alias.definition_id + '_cell_measurement_temperature' + '_cell_measurement_temp' + '_cell_measurement.temp' + + _definition.update 2022-05-25 _description.text ; - Counts measured in the reflection peak before background - subtraction. That is, the region of interest consists of - only the diffraction peak. + ** DEPRECATED ** - Note that counts-per-second values should be converted to - total counts. - - Standard uncertainties should not be quoted for these values. - If the standard uncertainties differ from the square root of - the number of counts, _diffrn_refln.intensity_* should be used. + The temperature at which the unit-cell parameters were measured + (not the temperature of synthesis). + _diffrn.ambient_temperature should be used instead of this item. ; - _name.category_id diffrn_refln - _name.object_id counts_peak - _type.purpose Number + _name.category_id cell_measurement + _name.object_id temperature + _type.purpose Measurand _type.source Recorded _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code counts + _type.contents Real + _enumeration.range 0.0: + _units.code kelvins save_ -save_diffrn_refln.counts_total +save_cell_measurement.temperature_su - _definition.id '_diffrn_refln.counts_total' - _alias.definition_id '_diffrn_refln_counts_total' - _definition.update 2022-11-22 + _definition.id '_cell_measurement.temperature_su' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn.ambient_temperature_su' + + loop_ + _alias.definition_id + '_cell_measurement_temp_su' + '_cell_measurement.temp_esd' + + _definition.update 2022-05-22 _description.text ; - Counts measured in the total reflection including background - and peak regions. That is, the region of interest consists of the - diffraction peak and an area of background immediately surrounding - the peak of interest. - - Note that counts-per-second values should be converted to - total counts. + ** DEPRECATED ** - Standard uncertainties should not be quoted for these values. - If the standard uncertainties differ from the square root of - the number of counts, _diffrn_refln.intensity_* should be used. + Standard uncertainty of the temperature of at which + the unit-cell parameters were measured. ; - _name.category_id diffrn_refln - _name.object_id counts_total - _type.purpose Number - _type.source Recorded + _name.category_id cell_measurement + _name.object_id temperature_su + _name.linked_item_id '_cell_measurement.temperature' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code counts + _type.contents Real + _units.code kelvins save_ -save_diffrn_refln.detect_slit_horiz +save_cell_measurement.theta_max - _definition.id '_diffrn_refln.detect_slit_horiz' - _alias.definition_id '_diffrn_refln_detect_slit_horiz' - _definition.update 2012-11-26 + _definition.id '_cell_measurement.theta_max' + _alias.definition_id '_cell_measurement_theta_max' + _definition.update 2012-11-22 _description.text ; - Total slit aperture angle in the diffraction plane. + Maximum theta scattering angle of reflections used to measure + the crystal unit cell. ; - _name.category_id diffrn_refln - _name.object_id detect_slit_horiz + _name.category_id cell_measurement + _name.object_id theta_max _type.purpose Number _type.source Recorded _type.container Single @@ -2190,17 +1971,18 @@ save_diffrn_refln.detect_slit_horiz save_ -save_diffrn_refln.detect_slit_vert +save_cell_measurement.theta_min - _definition.id '_diffrn_refln.detect_slit_vert' - _alias.definition_id '_diffrn_refln_detect_slit_vert' - _definition.update 2012-11-26 + _definition.id '_cell_measurement.theta_min' + _alias.definition_id '_cell_measurement_theta_min' + _definition.update 2012-11-22 _description.text ; - Total slit aperture angle perpendicular to the diffraction plane. + Minimum theta scattering angle of reflections used to measure + the crystal unit cell. ; - _name.category_id diffrn_refln - _name.object_id detect_slit_vert + _name.category_id cell_measurement + _name.object_id theta_min _type.purpose Number _type.source Recorded _type.container Single @@ -2210,37 +1992,63 @@ save_diffrn_refln.detect_slit_vert save_ -save_diffrn_refln.elapsed_time +save_cell_measurement.wavelength - _definition.id '_diffrn_refln.elapsed_time' - _alias.definition_id '_diffrn_refln_elapsed_time' - _definition.update 2012-11-26 + _definition.id '_cell_measurement.wavelength' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn_radiation_wavelength.value' + _alias.definition_id '_cell_measurement_wavelength' + _definition.update 2022-05-25 _description.text ; - Elapsed time from the start to the end of the intensity measurement. + ** DEPRECATED ** + + Wavelength of the radiation used to measure the unit cell. + Items from the _diffrn_radiation_wavelength category should + be used instead of this item. ; - _name.category_id diffrn_refln - _name.object_id elapsed_time + _name.category_id cell_measurement + _name.object_id wavelength _type.purpose Number - _type.source Recorded + _type.source Assigned _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code minutes + _units.code angstroms save_ -save_diffrn_refln.hkl +save_CELL_MEASUREMENT_REFLN - _definition.id '_diffrn_refln.hkl' + _definition.id CELL_MEASUREMENT_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 + _description.text +; + The CATEGORY of data items used to describe the reflection data + used in the measurement of the crystal unit cell. +; + _name.category_id CELL_MEASUREMENT + _name.object_id CELL_MEASUREMENT_REFLN + + loop_ + _category_key.name + '_cell_measurement_refln.index_h' + '_cell_measurement_refln.index_k' + '_cell_measurement_refln.index_l' + +save_ + +save_cell_measurement_refln.hkl + + _definition.id '_cell_measurement_refln.hkl' _definition.update 2021-03-01 _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. + Miller indices of a reflection used to measure the unit cell. ; - _name.category_id diffrn_refln + _name.category_id cell_measurement_refln _name.object_id hkl _type.purpose Number _type.source Derived @@ -2251,1490 +2059,1459 @@ save_diffrn_refln.hkl _method.purpose Evaluation _method.expression ; - With a as diffrn_refln + With c as cell_measurement_refln - _diffrn_refln.hkl = [a.index_h, a.index_h, a.index_l] + _cell_measurement_refln.hkl = [c.index_h, c.index_k, c.index_l] ; save_ -save_diffrn_refln.index_h +save_cell_measurement_refln.index_h - _definition.id '_diffrn_refln.index_h' - _alias.definition_id '_diffrn_refln_index_h' - _name.category_id diffrn_refln + _definition.id '_cell_measurement_refln.index_h' + _alias.definition_id '_cell_measurement_refln_index_h' + _name.category_id cell_measurement_refln _name.object_id index_h _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_refln.index_k +save_cell_measurement_refln.index_k - _definition.id '_diffrn_refln.index_k' - _alias.definition_id '_diffrn_refln_index_k' - _name.category_id diffrn_refln + _definition.id '_cell_measurement_refln.index_k' + _alias.definition_id '_cell_measurement_refln_index_k' + _name.category_id cell_measurement_refln _name.object_id index_k _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_refln.index_l +save_cell_measurement_refln.index_l - _definition.id '_diffrn_refln.index_l' - _alias.definition_id '_diffrn_refln_index_l' - _name.category_id diffrn_refln + _definition.id '_cell_measurement_refln.index_l' + _alias.definition_id '_cell_measurement_refln_index_l' + _name.category_id cell_measurement_refln _name.object_id index_l _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_refln.intensity_bg_1 +save_cell_measurement_refln.theta - _definition.id '_diffrn_refln.intensity_bg_1' - _definition.update 2022-11-22 + _definition.id '_cell_measurement_refln.theta' + _alias.definition_id '_cell_measurement_refln_theta' + _definition.update 2012-11-22 _description.text ; - The measured background intensity on one side of a diffraction - peak when measuring using a point detector. - - Use these entries for measurements where intensity values are not - counts (use _diffrn_refln.counts_* for event-counting measurements - where the standard uncertainty is estimated as the square root of - the number of counts). + Theta angle of reflection used to measure the crystal unit cell. ; - _name.category_id diffrn_refln - _name.object_id intensity_bg_1 + _name.category_id cell_measurement_refln + _name.object_id theta _type.purpose Measurand _type.source Recorded _type.container Single _type.contents Real - _units.code none + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_diffrn_refln.intensity_bg_1_su +save_cell_measurement_refln.theta_su - _definition.id '_diffrn_refln.intensity_bg_1_su' - _definition.update 2022-11-22 + _definition.id '_cell_measurement_refln.theta_su' + _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _diffrn_refln.intensity_bg_1. + Standard uncertainty of _cell_measurement_refln.theta. ; - _name.category_id diffrn_refln - _name.object_id intensity_bg_1_su - _name.linked_item_id '_diffrn_refln.intensity_bg_1' - _units.code none + _name.category_id cell_measurement_refln + _name.object_id theta_su + _name.linked_item_id '_cell_measurement_refln.theta' + _units.code degrees _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_diffrn_refln.intensity_bg_2 +save_DIFFRN_ATTENUATOR - _definition.id '_diffrn_refln.intensity_bg_2' - _definition.update 2022-11-22 + _definition.id DIFFRN_ATTENUATOR + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - The measured background counts on the other side of the - peak to the measurement of _diffrn_refln.intensity_bg_1 - when measuring using a point detector. + The CATEGORY of data items which specify the attenuators used in the + diffraction source. +; + _name.category_id DIFFRN + _name.object_id DIFFRN_ATTENUATOR + _category_key.name '_diffrn_attenuator.code' - Use these entries for measurements where intensity values are not - counts (use _diffrn_refln.counts_* for event-counting measurements - where the standard uncertainty is estimated as the square root of - the number of counts). +save_ + +save_diffrn_attenuator.code + + _definition.id '_diffrn_attenuator.code' + _alias.definition_id '_diffrn_attenuator_code' + _definition.update 2012-11-26 + _description.text ; - _name.category_id diffrn_refln - _name.object_id intensity_bg_2 - _type.purpose Measurand - _type.source Recorded + Code identifying a particular attenuator setting; referenced by the + _diffrn_refln.attenuator_code which is stored with the intensities. +; + _name.category_id diffrn_attenuator + _name.object_id code + _type.purpose Encode + _type.source Assigned _type.container Single - _type.contents Real - _units.code none + _type.contents Word save_ -save_diffrn_refln.intensity_bg_2_su +save_diffrn_attenuator.material - _definition.id '_diffrn_refln.intensity_bg_2_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_attenuator.material' + _alias.definition_id '_diffrn_attenuator_material' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _diffrn_refln.intensity_bg_2. + Description of the material from which the attenuator is made. ; - _name.category_id diffrn_refln - _name.object_id intensity_bg_2_su - _name.linked_item_id '_diffrn_refln.intensity_bg_2' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id diffrn_attenuator + _name.object_id material + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text save_ -save_diffrn_refln.intensity_net +save_diffrn_attenuator.scale - _definition.id '_diffrn_refln.intensity_net' - _alias.definition_id '_diffrn_refln_intensity_net' - _definition.update 2022-11-22 + _definition.id '_diffrn_attenuator.scale' + _alias.definition_id '_diffrn_attenuator_scale' + _definition.update 2012-11-26 _description.text ; - Net intensity in the reflection peak calculated from the - diffraction counts after the attenuator and standard scales - have been applied. + The scale factor applied to a measured intensity if it is reduced by + an attenuator identified by _diffrn_attenuator.code. ; - _name.category_id diffrn_refln - _name.object_id intensity_net - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_attenuator + _name.object_id scale + _type.purpose Number + _type.source Assigned _type.container Single _type.contents Real + _enumeration.range 1.0: _units.code none save_ -save_diffrn_refln.intensity_net_su - - _definition.id '_diffrn_refln.intensity_net_su' - - loop_ - _alias.definition_id - '_diffrn_refln_intensity_u' - '_diffrn_refln_intensity_sigma' - '_diffrn_refln.intensity_sigma' - '_diffrn_refln.intensity_u' +save_DIFFRN_DETECTOR - _definition.update 2012-12-13 + _definition.id DIFFRN_DETECTOR + _definition.scope Category + _definition.class Set + _definition.update 2023-01-13 _description.text ; - Standard uncertainty of _diffrn_refln.intensity_net. + The CATEGORY of data items which specify the detectors used + in the measurement of diffraction intensities. ; - _name.category_id diffrn_refln - _name.object_id intensity_net_su - _name.linked_item_id '_diffrn_refln.intensity_net' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id DIFFRN + _name.object_id DIFFRN_DETECTOR save_ -save_diffrn_refln.intensity_peak +save_diffrn_detector.area_resol_mean - _definition.id '_diffrn_refln.intensity_peak' - _definition.update 2022-11-22 + _definition.id '_diffrn_detector.area_resol_mean' + _alias.definition_id '_diffrn_detector_area_resol_mean' + _definition.update 2012-11-26 _description.text ; - Intensity measured in the reflection peak before background - subtraction. That is, the region of interest consists of - only the diffraction peak. - - Use these entries for measurements where intensity values are not - counts (use _diffrn_refln.counts_* for event-counting measurements - where the standard uncertainty is estimated as the square root of - the number of counts). -; - _name.category_id diffrn_refln - _name.object_id intensity_peak - _type.purpose Measurand - _type.source Recorded + The resolution limit of an area diffraction radiation detector. +; + _name.category_id diffrn_detector + _name.object_id area_resol_mean + _type.purpose Number + _type.source Assigned _type.container Single _type.contents Real - _units.code none + _enumeration.range 0.0: + _units.code pixels_per_millimetre save_ -save_diffrn_refln.intensity_peak_su +save_diffrn_detector.description - _definition.id '_diffrn_refln.intensity_peak_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_detector.description' + + loop_ + _alias.definition_id + '_diffrn_radiation_detector' + '_diffrn_detector' + '_diffrn_detector.detector' + + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _diffrn_refln.intensity_peak. + Description of the type of diffraction radiation detector. ; - _name.category_id diffrn_refln - _name.object_id intensity_peak_su - _name.linked_item_id '_diffrn_refln.intensity_peak' - _units.code none + _name.category_id diffrn_detector + _name.object_id description + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text - _import.get [{'file':templ_attr.cif 'save':general_su}] + loop_ + _description_example.case + 'photographic film' + 'scintillation counter' + 'CCD plate' + 'BF~3~ counter' save_ -save_diffrn_refln.intensity_total +save_diffrn_detector.details - _definition.id '_diffrn_refln.intensity_total' - _definition.update 2022-11-22 + _definition.id '_diffrn_detector.details' + _alias.definition_id '_diffrn_detector_details' + _definition.update 2012-11-26 _description.text ; - Intensity measured in the total reflection including background - and peak regions. That is, the region of interest consists of the - diffraction peak and an area of background immediately surrounding - the peak of interest. - - Use these entries for measurements where intensity values are not - counts (use _diffrn_refln.counts_* for event-counting measurements - where the standard uncertainty is estimated as the square root of - the number of counts). + Description of special aspects of the radiation detector. ; - _name.category_id diffrn_refln - _name.object_id intensity_total - _type.purpose Measurand + _name.category_id diffrn_detector + _name.object_id details + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _units.code none + _type.contents Text save_ -save_diffrn_refln.intensity_total_su +save_diffrn_detector.dtime - _definition.id '_diffrn_refln.intensity_total_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_detector.dtime' + + loop_ + _alias.definition_id + '_diffrn_detector_dtime' + '_diffrn_radiation.detector_dtime' + '_diffrn_radiation_detector_dtime' + + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _diffrn_refln.intensity_total. + The maximum time between two detector signals that cannot be resolved. ; - _name.category_id diffrn_refln - _name.object_id intensity_total_su - _name.linked_item_id '_diffrn_refln.intensity_total' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id diffrn_detector + _name.object_id dtime + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code microseconds save_ -save_diffrn_refln.scale_group_code +save_diffrn_detector.make - _definition.id '_diffrn_refln.scale_group_code' - _alias.definition_id '_diffrn_refln_scale_group_code' - _definition.update 2021-10-27 + _definition.id '_diffrn_detector.make' + + loop_ + _alias.definition_id + '_diffrn_detector_type' + '_diffrn_detector.type' + + _definition.update 2012-11-26 _description.text ; - Code identifying the scale applying to this reflection. + The make, model or name of the diffraction radiation detector. ; - _name.category_id diffrn_refln - _name.object_id scale_group_code - _name.linked_item_id '_diffrn_scale_group.code' - _type.purpose Link - _type.source Related + _name.category_id diffrn_detector + _name.object_id make + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Word + _type.contents Text save_ -save_diffrn_refln.scan_mode +save_DIFFRN_MEASUREMENT - _definition.id '_diffrn_refln.scan_mode' - _alias.definition_id '_diffrn_refln_scan_mode' - _definition.update 2023-01-13 + _definition.id DIFFRN_MEASUREMENT + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 _description.text ; - Code identifying the mode of scanning with a diffractometer. - See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. + The CATEGORY of data items which specify the details of the + diffraction measurement. ; - _name.category_id diffrn_refln - _name.object_id scan_mode - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text - - loop_ - _enumeration_set.state - _enumeration_set.detail - om 'Omega scan.' - ot 'Omega/2theta scan.' - q 'Q-scans (arbitrary reciprocal directions).' + _name.category_id DIFFRN + _name.object_id DIFFRN_MEASUREMENT save_ -save_diffrn_refln.scan_mode_backgd +save_diffrn_measurement.details + + _definition.id '_diffrn_measurement.details' + + loop_ + _alias.definition_id + '_diffrn_measurement_details' + '_diffrn.measurement_details' - _definition.id '_diffrn_refln.scan_mode_backgd' - _alias.definition_id '_diffrn_refln_scan_mode_backgd' _definition.update 2012-11-26 _description.text ; - Code identifying mode of scanning to measure the background intensity. + Description of special aspects of the diffraction measurement. ; - _name.category_id diffrn_refln - _name.object_id scan_mode_backgd - _type.purpose State - _type.source Assigned + _name.category_id diffrn_measurement + _name.object_id details + _type.purpose Describe + _type.source Recorded _type.container Single _type.contents Text - - loop_ - _enumeration_set.state - _enumeration_set.detail - st 'Stationary counter background.' - mo 'Moving counter background.' + _description_example.case '440 frames of 0.25\%' save_ -save_diffrn_refln.scan_rate +save_diffrn_measurement.device_class - _definition.id '_diffrn_refln.scan_rate' - _alias.definition_id '_diffrn_refln_scan_rate' - _definition.update 2013-03-07 + _definition.id '_diffrn_measurement.device_class' + + loop_ + _alias.definition_id + '_diffrn_measurement_device' + '_diffrn.measurement_device_class' + '_diffrn_measurement.device' + + _definition.update 2012-11-26 _description.text ; - Angular rate of scanning a reflection to measure the intensity. + Type of goniometer device used to mount and orient the specimen. ; - _name.category_id diffrn_refln - _name.object_id scan_rate - _type.purpose Number + _name.category_id diffrn_measurement + _name.object_id device_class + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code degree_per_minute + _type.contents Text + + loop_ + _description_example.case + 'three-circle diffractometer' + 'four-circle diffractometer' + '\k-geometry diffractometer' + 'oscillation camera' + 'precession camera' save_ -save_diffrn_refln.scan_time_backgd +save_diffrn_measurement.device_details + + _definition.id '_diffrn_measurement.device_details' + + loop_ + _alias.definition_id + '_diffrn_measurement_device_details' + '_diffrn.measurement_device_details' - _definition.id '_diffrn_refln.scan_time_backgd' - _alias.definition_id '_diffrn_refln_scan_time_backgd' _definition.update 2012-11-26 _description.text ; - Time spent measuring background counts. + Details of the goniometer device used in the diffraction experiment. ; - _name.category_id diffrn_refln - _name.object_id scan_time_backgd - _type.purpose Number + _name.category_id diffrn_measurement + _name.object_id device_details + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code seconds + _type.contents Text + _description_example.case + 'commercial goniometer modified locally to allow for 90\% \t arc' save_ -save_diffrn_refln.scan_width +save_diffrn_measurement.device_make - _definition.id '_diffrn_refln.scan_width' - _alias.definition_id '_diffrn_refln_scan_width' - _definition.update 2012-11-26 + _definition.id '_diffrn_measurement.device_make' + + loop_ + _alias.definition_id + '_diffrn_measurement_device_type' + '_diffrn.measurement_device_make' + '_diffrn_measurement.device_type' + + _definition.update 2013-03-07 _description.text ; - Angular scan width when measuring the peak intensity. + The make, model or name of the goniometer device used. ; - _name.category_id diffrn_refln - _name.object_id scan_width - _type.purpose Number + _name.category_id diffrn_measurement + _name.object_id device_make + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0:90.0 - _units.code degrees + _type.contents Text + + loop_ + _description_example.case + 'Supper model q' + 'Huber model r' + 'Enraf-Nonius model s' + 'home-made' save_ -save_diffrn_refln.sin_theta_over_lambda +save_diffrn_measurement.method - _definition.id '_diffrn_refln.sin_theta_over_lambda' + _definition.id '_diffrn_measurement.method' loop_ _alias.definition_id - '_diffrn_refln_sint/lambda' - '_diffrn_refln_sint_over_lambda' - '_diffrn_refln.sint_over_lambda' + '_diffrn_measurement_method' + '_diffrn.measurement_method' _definition.update 2012-11-26 _description.text ; - (sin theta)/lambda value for this reflection. + Description of scan method used to measure diffraction intensities. ; - _name.category_id diffrn_refln - _name.object_id sin_theta_over_lambda - _type.purpose Number + _name.category_id diffrn_measurement + _name.object_id method + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code reciprocal_angstroms + _type.contents Text + _description_example.case 'profile data from \q/2\q scans' save_ -save_diffrn_refln.standard_code +save_diffrn_measurement.specimen_attachment_type - _definition.id '_diffrn_refln.standard_code' - _alias.definition_id '_diffrn_refln_standard_code' - _definition.update 2021-10-27 + _definition.id '_diffrn_measurement.specimen_attachment_type' + _definition.update 2023-02-06 _description.text ; - Code identifying reflections measured repeated as standard intensity. - Must match a _diffrn_standard_refln.code values OR set to '.' if - it was not used as a intensity standard. + The way in which the sample is attached to the sample holder, + including the type of adhesive material used if relevant. The sample + holder is usually wholly outside the beam, whereas the attachment + method may cause non-sample material to be illuminated. If the + attachment method is not included in the list below, 'other' should be + chosen and details provided in _diffrn_measurement.specimen_support. ; - _name.category_id diffrn_refln - _name.object_id standard_code - _name.linked_item_id '_diffrn_standard_refln.code' - _type.purpose Link - _type.source Related + _name.category_id diffrn_measurement + _name.object_id specimen_attachment_type + _type.purpose State + _type.source Recorded _type.container Single _type.contents Word -save_ - -save_diffrn_refln.wavelength - - _definition.id '_diffrn_refln.wavelength' - _alias.definition_id '_diffrn_refln_wavelength' - _definition.update 2012-11-26 - _description.text + loop_ + _enumeration_set.state + _enumeration_set.detail + epoxy ; - Mean wavelength of radiation used to measure this intensity. + An epoxy glue. +; + oil +; + An oil. +; + grease +; + A type of grease, for example hydrocarbon or silicone grease. +; + frozen_liquid +; + A frozen liquid, not water or oil. +; + other +; + A method not listed here. +; + ice +; + The specimen is frozen in place using water ice. +; + mechanical +; + The specimen is held in place by mechanical forces, e.g. capillary or + pressure cell. ; - _name.category_id diffrn_refln - _name.object_id wavelength - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms save_ -save_diffrn_refln.wavelength_id +save_diffrn_measurement.specimen_support - _definition.id '_diffrn_refln.wavelength_id' - _alias.definition_id '_diffrn_refln_wavelength_id' - _definition.update 2021-10-27 + _definition.id '_diffrn_measurement.specimen_support' + + loop_ + _alias.definition_id + '_diffrn_measurement_specimen_support' + '_diffrn.measurement_specimen_support' + + _definition.update 2013-01-23 _description.text ; - Code identifying the wavelength in the diffrn_radiation_wavelength list. + Mounting method for the crystal specimen during data collection. ; - _name.category_id diffrn_refln - _name.object_id wavelength_id - _name.linked_item_id '_diffrn_radiation_wavelength.id' - _type.purpose Link - _type.source Related + _name.category_id diffrn_measurement + _name.object_id specimen_support + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Word + _type.contents Text + + loop_ + _description_example.case + 'glass capillary' + 'quartz capillary' + 'fiber' + 'metal loop' save_ -save_DIFFRN_REFLNS +save_DIFFRN_ORIENT - _definition.id DIFFRN_REFLNS + _definition.id DIFFRN_ORIENT _definition.scope Category _definition.class Set _definition.update 2012-11-26 _description.text ; - The CATEGORY of data items which specify the overall reflection - measurement information. + The CATEGORY of data items which specify the orientation of the crystal + axes to the diffractometer goniometer. ; _name.category_id DIFFRN - _name.object_id DIFFRN_REFLNS + _name.object_id DIFFRN_ORIENT save_ -save_diffrn_reflns.av_r_equivalents +save_DIFFRN_ORIENT_MATRIX - _definition.id '_diffrn_reflns.av_R_equivalents' - _alias.definition_id '_diffrn_reflns_av_R_equivalents' + _definition.id DIFFRN_ORIENT_MATRIX + _definition.scope Category + _definition.class Set _definition.update 2012-11-26 _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. + The CATEGORY of data items which specify the matrix specifying the + orientation of the crystal axes to the diffractometer goniometer. ; - _name.category_id diffrn_reflns - _name.object_id av_R_equivalents - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _name.category_id DIFFRN_ORIENT + _name.object_id DIFFRN_ORIENT_MATRIX save_ -save_diffrn_reflns.av_suneti_over_neti - - _definition.id '_diffrn_reflns.av_sunetI_over_netI' - - loop_ - _alias.definition_id - '_diffrn_reflns_av_sigmaI_over_netI' - '_diffrn_reflns_av_sigmaI/netI' - '_diffrn_reflns.av_unetI/netI' - '_diffrn_reflns_av_unetI/netI' - '_diffrn_reflns.av_sigmaI_over_netI' +save_diffrn_orient_matrix.type + _definition.id '_diffrn_orient_matrix.type' + _alias.definition_id '_diffrn_orient_matrix_type' _definition.update 2012-11-26 _description.text ; - Recorded [sum |su(netI)| / sum |netI|] for all measured reflections. + Description of orientation matrix and how it should be applied to define + the orientation of the crystal with respect to the diffractometer axes. ; - _name.category_id diffrn_reflns - _name.object_id av_sunetI_over_netI - _type.purpose Number - _type.source Derived + _name.category_id diffrn_orient_matrix + _name.object_id type + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _type.contents Text save_ -save_diffrn_reflns.laue_measured_fraction_full - - _definition.id '_diffrn_reflns.Laue_measured_fraction_full' - _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_full' - _definition.update 2019-01-09 - _description.text -; - Fraction of Laue group unique reflections (symmetry-independent in - the Laue group) measured out to the resolution given in - _diffrn_reflns.resolution_full or _diffrn_reflns.theta_full. - The Laue group always contains a centre of symmetry so that - the reflection h,k,l is always equivalent to the reflection - -h,-k,-l even in space groups without a centre of symmetry. - This number should not be less than 0.95, since it represents - the fraction of reflections measured in the part of the - diffraction pattern that is essentially complete. -; - _name.category_id diffrn_reflns - _name.object_id Laue_measured_fraction_full - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.95:1.0 - _units.code none +save_diffrn_orient_matrix.ub_11 -save_ + _definition.id '_diffrn_orient_matrix.UB_11' -save_diffrn_reflns.laue_measured_fraction_max + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_11' + '_diffrn_orient_matrix.UB[1][1]' - _definition.id '_diffrn_reflns.Laue_measured_fraction_max' - _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_max' - _definition.update 2021-03-03 - _description.text -; - Fraction of Laue group unique reflections (symmetry-independent in - the Laue group) measured out to the resolution given in - _diffrn_reflns.resolution_max or _diffrn_reflns.theta_max. - The Laue group always contains a centre of symmetry so that the - reflection h,k,l is always equivalent to the reflection -h,-k,-l - even in space groups without a centre of symmetry. -; - _name.category_id diffrn_reflns - _name.object_id Laue_measured_fraction_max - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none + _name.category_id diffrn_orient_matrix + _name.object_id UB_11 + + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.limit_h_max +save_diffrn_orient_matrix.ub_12 - _definition.id '_diffrn_reflns.limit_h_max' - _alias.definition_id '_diffrn_reflns_limit_h_max' - _name.category_id diffrn_reflns - _name.object_id limit_h_max + _definition.id '_diffrn_orient_matrix.UB_12' - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_12' + '_diffrn_orient_matrix.UB[1][2]' -save_ + _name.category_id diffrn_orient_matrix + _name.object_id UB_12 -save_diffrn_reflns.limit_h_min + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] - _definition.id '_diffrn_reflns.limit_h_min' - _alias.definition_id '_diffrn_reflns_limit_h_min' - _name.category_id diffrn_reflns - _name.object_id limit_h_min +save_ - _import.get [{'file':templ_attr.cif 'save':Miller_index}] +save_diffrn_orient_matrix.ub_13 -save_ + _definition.id '_diffrn_orient_matrix.UB_13' -save_diffrn_reflns.limit_k_max + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_13' + '_diffrn_orient_matrix.UB[1][3]' - _definition.id '_diffrn_reflns.limit_k_max' - _alias.definition_id '_diffrn_reflns_limit_k_max' - _name.category_id diffrn_reflns - _name.object_id limit_k_max + _name.category_id diffrn_orient_matrix + _name.object_id UB_13 - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.limit_k_min +save_diffrn_orient_matrix.ub_21 - _definition.id '_diffrn_reflns.limit_k_min' - _alias.definition_id '_diffrn_reflns_limit_k_min' - _name.category_id diffrn_reflns - _name.object_id limit_k_min + _definition.id '_diffrn_orient_matrix.UB_21' - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_21' + '_diffrn_orient_matrix.UB[2][1]' -save_ + _name.category_id diffrn_orient_matrix + _name.object_id UB_21 -save_diffrn_reflns.limit_l_max + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] - _definition.id '_diffrn_reflns.limit_l_max' - _alias.definition_id '_diffrn_reflns_limit_l_max' - _name.category_id diffrn_reflns - _name.object_id limit_l_max +save_ - _import.get [{'file':templ_attr.cif 'save':Miller_index}] +save_diffrn_orient_matrix.ub_22 -save_ + _definition.id '_diffrn_orient_matrix.UB_22' -save_diffrn_reflns.limit_l_min + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_22' + '_diffrn_orient_matrix.UB[2][2]' - _definition.id '_diffrn_reflns.limit_l_min' - _alias.definition_id '_diffrn_reflns_limit_l_min' - _name.category_id diffrn_reflns - _name.object_id limit_l_min + _name.category_id diffrn_orient_matrix + _name.object_id UB_22 - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.limit_max +save_diffrn_orient_matrix.ub_23 - _definition.id '_diffrn_reflns.limit_max' - _definition.update 2023-01-06 - _description.text -; - Maximum Miller indices of measured diffraction reflections. -; - _name.category_id diffrn_reflns - _name.object_id limit_max - _type.purpose Number - _type.source Assigned - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer - _units.code none - _method.purpose Evaluation - _method.expression -; - With t as diffrn_reflns + _definition.id '_diffrn_orient_matrix.UB_23' - _diffrn_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] -; + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_23' + '_diffrn_orient_matrix.UB[2][3]' + + _name.category_id diffrn_orient_matrix + _name.object_id UB_23 + + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.limit_min +save_diffrn_orient_matrix.ub_31 - _definition.id '_diffrn_reflns.limit_min' - _definition.update 2023-01-06 - _description.text -; - Minimum Miller indices of measured diffraction reflections. -; - _name.category_id diffrn_reflns - _name.object_id limit_min - _type.purpose Number - _type.source Assigned - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer - _units.code none - _method.purpose Evaluation - _method.expression -; - With t as diffrn_reflns + _definition.id '_diffrn_orient_matrix.UB_31' - _diffrn_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] -; + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_31' + '_diffrn_orient_matrix.UB[3][1]' + + _name.category_id diffrn_orient_matrix + _name.object_id UB_31 + + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.number +save_diffrn_orient_matrix.ub_32 - _definition.id '_diffrn_reflns.number' - _alias.definition_id '_diffrn_reflns_number' - _definition.update 2021-03-01 - _description.text -; - Total number of measured intensities, excluding reflections that are - classed as systematically absent arising from translational symmetry - in the crystal unit cell. -; - _name.category_id diffrn_reflns - _name.object_id number - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _definition.id '_diffrn_orient_matrix.UB_32' -save_ + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_32' + '_diffrn_orient_matrix.UB[3][2]' -save_diffrn_reflns.point_measured_fraction_full + _name.category_id diffrn_orient_matrix + _name.object_id UB_32 - _definition.id '_diffrn_reflns.point_measured_fraction_full' - _alias.definition_id - '_diffrn_reflns_point_group_measured_fraction_full' - _definition.update 2013-01-20 - _description.text -; - Fraction of crystal point-group unique reflections (i.e. - symmetry-independent in the crystal point group) measured - out to the resolution given in _diffrn_reflns.resolution_full - or _diffrn_reflns.theta_full. For space groups that do not - contain a centre of symmetry the reflections h,k,l and - -h,-k,-l are independent. This number should not be less - than 0.95, since it represents the fraction of reflections - measured in the part of the diffraction pattern that is - essentially complete. -; - _name.category_id diffrn_reflns - _name.object_id point_measured_fraction_full - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.95:1.0 - _units.code none + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.point_measured_fraction_max +save_diffrn_orient_matrix.ub_33 - _definition.id '_diffrn_reflns.point_measured_fraction_max' - _alias.definition_id - '_diffrn_reflns_point_group_measured_fraction_max' - _definition.update 2013-01-20 - _description.text -; - Fraction of crystal point-group unique reflections (i.e. - symmetry-independent in the crystal point group) measured - out to the resolution given in _diffrn_reflns.resolution_max - or _diffrn_reflns.theta_max. For space groups that do not - contain a centre of symmetry the reflections h,k,l and - -h,-k,-l are independent. -; - _name.category_id diffrn_reflns - _name.object_id point_measured_fraction_max - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0:1.0 - _units.code none + _definition.id '_diffrn_orient_matrix.UB_33' -save_ + loop_ + _alias.definition_id + '_diffrn_orient_matrix_UB_33' + '_diffrn_orient_matrix.UB[3][3]' -save_diffrn_reflns.reduction_process + _name.category_id diffrn_orient_matrix + _name.object_id UB_33 - _definition.id '_diffrn_reflns.reduction_process' - _alias.definition_id '_diffrn_reflns_reduction_process' - _definition.update 2012-11-26 - _description.text -; - How intensities were reduced to structure-factor magnitudes. -; - _name.category_id diffrn_reflns - _name.object_id reduction_process - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'data averaged using Fisher test' + _import.get + [{'file':templ_attr.cif 'save':orient_matrix}] save_ -save_diffrn_reflns.resolution_full +save_diffrn_orient_matrix.ubij - _definition.id '_diffrn_reflns.resolution_full' - _alias.definition_id '_diffrn_reflns_resolution_full' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_matrix.UBij' + _definition.update 2021-03-01 _description.text ; - The resolution at which the measured reflection count is close - to complete. The fraction of unique reflections measured out - to this angle is given by _diffrn.measured_fraction_theta_full. + The 3x3 matrix specifying the orientation of the crystal with + respect to the diffractometer axes. ; - _name.category_id diffrn_reflns - _name.object_id resolution_full + _name.category_id diffrn_orient_matrix + _name.object_id UBij _type.purpose Number - _type.source Recorded - _type.container Single + _type.source Derived + _type.container Matrix + _type.dimension '[3,3]' _type.contents Real - _enumeration.range 0.0: - _units.code reciprocal_angstroms + _units.code none + _method.purpose Evaluation + _method.expression +; + With o as diffrn_orient_matrix + + _diffrn_orient_matrix.UBIJ = [[ o.ub_11, o.ub_12, o.ub_13 ], + [ o.ub_21, o.ub_22, o.ub_23 ], + [ o.ub_31, o.ub_32, o.ub_33 ]] +; save_ -save_diffrn_reflns.resolution_max +save_DIFFRN_ORIENT_REFLN - _definition.id '_diffrn_reflns.resolution_max' - _alias.definition_id '_diffrn_reflns_resolution_max' - _definition.update 2013-02-22 + _definition.id DIFFRN_ORIENT_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Maximum resolution of the measured diffraction pattern. - The fraction of unique reflections measured out to this angle - is given by _diffrn.measured_fraction_theta_max. + 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. ; - _name.category_id diffrn_reflns - _name.object_id resolution_max - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code reciprocal_angstroms + _name.category_id DIFFRN_ORIENT + _name.object_id DIFFRN_ORIENT_REFLN + + loop_ + _category_key.name + '_diffrn_orient_refln.index_h' + '_diffrn_orient_refln.index_k' + '_diffrn_orient_refln.index_l' save_ -save_diffrn_reflns.theta_full +save_diffrn_orient_refln.angle_chi - _definition.id '_diffrn_reflns.theta_full' - _alias.definition_id '_diffrn_reflns_theta_full' - _definition.update 2023-01-13 - _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.measured_fraction_theta_full. -; - _name.category_id diffrn_reflns - _name.object_id theta_full - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0:90.0 - _units.code degrees + _definition.id '_diffrn_orient_refln.angle_chi' + _alias.definition_id '_diffrn_orient_refln_angle_chi' + _name.category_id diffrn_orient_refln + _name.object_id angle_chi + + _import.get [{'file':templ_attr.cif 'save':orient_angle}] save_ -save_diffrn_reflns.theta_max +save_diffrn_orient_refln.angle_chi_su - _definition.id '_diffrn_reflns.theta_max' - _alias.definition_id '_diffrn_reflns_theta_max' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_refln.angle_chi_su' + _definition.update 2021-09-23 _description.text ; - Maximum theta angle of the measured reflections. + Standard uncertainty of _diffrn_orient_refln.angle_chi. ; - _name.category_id diffrn_reflns - _name.object_id theta_max - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0:90.0 + _name.category_id diffrn_orient_refln + _name.object_id angle_chi_su + _name.linked_item_id '_diffrn_orient_refln.angle_chi' _units.code degrees + _import.get [{'file':templ_attr.cif 'save':general_su}] + save_ -save_diffrn_reflns.theta_min +save_diffrn_orient_refln.angle_kappa - _definition.id '_diffrn_reflns.theta_min' - _alias.definition_id '_diffrn_reflns_theta_min' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_refln.angle_kappa' + _alias.definition_id '_diffrn_orient_refln_angle_kappa' + _name.category_id diffrn_orient_refln + _name.object_id angle_kappa + + _import.get [{'file':templ_attr.cif 'save':orient_angle}] + +save_ + +save_diffrn_orient_refln.angle_kappa_su + + _definition.id '_diffrn_orient_refln.angle_kappa_su' + _definition.update 2021-09-23 _description.text ; - Minimum theta angle of the measured reflections. + Standard uncertainty of _diffrn_orient_refln.angle_kappa. ; - _name.category_id diffrn_reflns - _name.object_id theta_min - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0:90.0 + _name.category_id diffrn_orient_refln + _name.object_id angle_kappa_su + _name.linked_item_id '_diffrn_orient_refln.angle_kappa' _units.code degrees + _import.get [{'file':templ_attr.cif 'save':general_su}] + save_ -save_DIFFRN_REFLNS_CLASS +save_diffrn_orient_refln.angle_omega - _definition.id DIFFRN_REFLNS_CLASS - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 - _description.text -; - The CATEGORY of data items which specify different classes of - reflections in the raw measured diffraction data. -; - _name.category_id DIFFRN_REFLNS - _name.object_id DIFFRN_REFLNS_CLASS - _category_key.name '_diffrn_reflns_class.code' + _definition.id '_diffrn_orient_refln.angle_omega' + _alias.definition_id '_diffrn_orient_refln_angle_omega' + _name.category_id diffrn_orient_refln + _name.object_id angle_omega + + _import.get [{'file':templ_attr.cif 'save':orient_angle}] save_ -save_diffrn_reflns_class.av_r_eq +save_diffrn_orient_refln.angle_omega_su - _definition.id '_diffrn_reflns_class.av_R_eq' - _alias.definition_id '_diffrn_reflns_class_av_R_eq' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_refln.angle_omega_su' + _definition.update 2021-09-23 _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. + Standard uncertainty of _diffrn_orient_refln.angle_omega. ; - _name.category_id diffrn_reflns_class - _name.object_id av_R_eq - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _name.category_id diffrn_orient_refln + _name.object_id angle_omega_su + _name.linked_item_id '_diffrn_orient_refln.angle_omega' + _units.code degrees -save_ + _import.get [{'file':templ_attr.cif 'save':general_su}] -save_diffrn_reflns_class.av_sui_over_i +save_ - _definition.id '_diffrn_reflns_class.av_suI_over_I' +save_diffrn_orient_refln.angle_phi - loop_ - _alias.definition_id - '_diffrn_reflns_class_av_uI_over_I' - '_diffrn_reflns_class.av_uI/I' - '_diffrn_reflns_class_av_uI/I' - '_diffrn_reflns_class.av_sgI/I' - '_diffrn_reflns_class_av_sgI/I' + _definition.id '_diffrn_orient_refln.angle_phi' + _alias.definition_id '_diffrn_orient_refln_angle_phi' + _name.category_id diffrn_orient_refln + _name.object_id angle_phi - _definition.update 2014-07-22 - _description.text -; - Recorded [sum|su(net I)|/sum|net I|] in a reflection class. -; - _name.category_id diffrn_reflns_class - _name.object_id av_suI_over_I - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _import.get [{'file':templ_attr.cif 'save':orient_angle}] save_ -save_diffrn_reflns_class.code +save_diffrn_orient_refln.angle_phi_su - _definition.id '_diffrn_reflns_class.code' - _alias.definition_id '_diffrn_reflns_class_code' - _definition.update 2021-10-27 + _definition.id '_diffrn_orient_refln.angle_phi_su' + _definition.update 2021-09-23 _description.text ; - Code identifying a reflection class. + Standard uncertainty of _diffrn_orient_refln.angle_phi. ; - _name.category_id diffrn_reflns_class - _name.object_id code - _type.purpose Encode - _type.source Assigned - _type.container Single - _type.contents Word - _description_example.case m2 + _name.category_id diffrn_orient_refln + _name.object_id angle_phi_su + _name.linked_item_id '_diffrn_orient_refln.angle_phi' + _units.code degrees + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_diffrn_reflns_class.d_res_high +save_diffrn_orient_refln.angle_psi - _definition.id '_diffrn_reflns_class.d_res_high' - _alias.definition_id '_diffrn_reflns_class_d_res_high' - _definition.update 2012-11-26 - _description.text -; - Highest resolution in reflection class i.e. smallest d value in class. -; - _name.category_id diffrn_reflns_class - _name.object_id d_res_high - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _definition.id '_diffrn_orient_refln.angle_psi' + _alias.definition_id '_diffrn_orient_refln_angle_psi' + _name.category_id diffrn_orient_refln + _name.object_id angle_psi + + _import.get [{'file':templ_attr.cif 'save':orient_angle}] save_ -save_diffrn_reflns_class.d_res_low +save_diffrn_orient_refln.angle_psi_su - _definition.id '_diffrn_reflns_class.d_res_low' - _alias.definition_id '_diffrn_reflns_class_d_res_low' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_refln.angle_psi_su' + _definition.update 2021-09-23 _description.text ; - Lowest resolution in reflection class i.e. largest d value in class. + Standard uncertainty of _diffrn_orient_refln.angle_psi. ; - _name.category_id diffrn_reflns_class - _name.object_id d_res_low - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _name.category_id diffrn_orient_refln + _name.object_id angle_psi_su + _name.linked_item_id '_diffrn_orient_refln.angle_psi' + _units.code degrees + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_diffrn_reflns_class.description +save_diffrn_orient_refln.angle_theta - _definition.id '_diffrn_reflns_class.description' - _alias.definition_id '_diffrn_reflns_class_description' - _definition.update 2012-11-26 + _definition.id '_diffrn_orient_refln.angle_theta' + _alias.definition_id '_diffrn_orient_refln_angle_theta' + _name.category_id diffrn_orient_refln + _name.object_id angle_theta + + _import.get [{'file':templ_attr.cif 'save':orient_angle}] + +save_ + +save_diffrn_orient_refln.angle_theta_su + + _definition.id '_diffrn_orient_refln.angle_theta_su' + _definition.update 2021-09-23 _description.text ; - Description of a reflection class. + Standard uncertainty of _diffrn_orient_refln.angle_theta. ; - _name.category_id diffrn_reflns_class - _name.object_id description - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'm=1 first order satellites' + _name.category_id diffrn_orient_refln + _name.object_id angle_theta_su + _name.linked_item_id '_diffrn_orient_refln.angle_theta' + _units.code degrees + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_diffrn_reflns_class.number +save_diffrn_orient_refln.hkl - _definition.id '_diffrn_reflns_class.number' - _alias.definition_id '_diffrn_reflns_class_number' + _definition.id '_diffrn_orient_refln.hkl' _definition.update 2021-03-01 _description.text ; - Number of measured intensities for a reflection class, excluding - the systematic absences arising from centring translations. + Miller indices of a reflection used to define the orientation matrix. ; - _name.category_id diffrn_reflns_class - _name.object_id number + _name.category_id diffrn_orient_refln + _name.object_id hkl _type.purpose Number _type.source Derived - _type.container Single + _type.container Matrix + _type.dimension '[3]' _type.contents Integer - _enumeration.range 0: _units.code none - -save_ - -save_DIFFRN_REFLNS_TRANSF_MATRIX - - _definition.id DIFFRN_REFLNS_TRANSF_MATRIX - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 - _description.text + _method.purpose Evaluation + _method.expression ; - 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| + With a as diffrn_orient_refln + + _diffrn_orient_refln.hkl = [a.index_h, a.index_k, a.index_l] ; - _name.category_id DIFFRN_REFLNS - _name.object_id DIFFRN_REFLNS_TRANSF_MATRIX save_ -save_diffrn_reflns_transf_matrix.11 - - _definition.id '_diffrn_reflns_transf_matrix.11' - - loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_11' - '_diffrn_reflns.transf_matrix[1][1]' +save_diffrn_orient_refln.index_h - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 11 + _definition.id '_diffrn_orient_refln.index_h' + _alias.definition_id '_diffrn_orient_refln_index_h' + _name.category_id diffrn_orient_refln + _name.object_id index_h - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_reflns_transf_matrix.12 - - _definition.id '_diffrn_reflns_transf_matrix.12' - - loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_12' - '_diffrn_reflns.transf_matrix[1][2]' +save_diffrn_orient_refln.index_k - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 12 + _definition.id '_diffrn_orient_refln.index_k' + _alias.definition_id '_diffrn_orient_refln_index_k' + _name.category_id diffrn_orient_refln + _name.object_id index_k - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_reflns_transf_matrix.13 +save_diffrn_orient_refln.index_l - _definition.id '_diffrn_reflns_transf_matrix.13' + _definition.id '_diffrn_orient_refln.index_l' + _alias.definition_id '_diffrn_orient_refln_index_l' + _name.category_id diffrn_orient_refln + _name.object_id index_l - loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_13' - '_diffrn_reflns.transf_matrix[1][3]' + _import.get [{'file':templ_attr.cif 'save':Miller_index}] - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 13 +save_ - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] +save_DIFFRN_RADIATION + + _definition.id DIFFRN_RADIATION + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _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. +; + _name.category_id DIFFRN + _name.object_id DIFFRN_RADIATION save_ -save_diffrn_reflns_transf_matrix.21 +save_diffrn_radiation.collimation - _definition.id '_diffrn_reflns_transf_matrix.21' + _definition.id '_diffrn_radiation.collimation' + _alias.definition_id '_diffrn_radiation_collimation' + _definition.update 2012-11-26 + _description.text +; + Description of the collimation or focusing applied to the radiation. +; + _name.category_id diffrn_radiation + _name.object_id collimation + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_21' - '_diffrn_reflns.transf_matrix[2][1]' - - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 21 - - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _description_example.case + '0.3 mm double-pinhole' + '0.5 mm' + 'focusing mirrors' save_ -save_diffrn_reflns_transf_matrix.22 +save_diffrn_radiation.filter_edge - _definition.id '_diffrn_reflns_transf_matrix.22' + _definition.id '_diffrn_radiation.filter_edge' + _alias.definition_id '_diffrn_radiation_filter_edge' + _definition.update 2012-11-26 + _description.text +; + Absorption edge of the radiation filter used. +; + _name.category_id diffrn_radiation + _name.object_id filter_edge + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms - loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_22' - '_diffrn_reflns.transf_matrix[2][2]' +save_ - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 22 +save_diffrn_radiation.inhomogeneity - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _definition.id '_diffrn_radiation.inhomogeneity' + _alias.definition_id '_diffrn_radiation_inhomogeneity' + _definition.update 2012-11-26 + _description.text +; + Half-width of the incident beam perpendicular to the diffraction plane. +; + _name.category_id diffrn_radiation + _name.object_id inhomogeneity + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code millimetres save_ -save_diffrn_reflns_transf_matrix.23 +save_diffrn_radiation.monochromator - _definition.id '_diffrn_reflns_transf_matrix.23' + _definition.id '_diffrn_radiation.monochromator' + _alias.definition_id '_diffrn_radiation_monochromator' + _definition.update 2012-11-26 + _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. +; + _name.category_id diffrn_radiation + _name.object_id monochromator + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_23' - '_diffrn_reflns.transf_matrix[2][3]' - - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 23 - - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _description_example.case + 'Zr filter' + 'Ge 220' + 'none' + 'equatorial mounted graphite' save_ -save_diffrn_reflns_transf_matrix.31 +save_diffrn_radiation.polarisn_norm - _definition.id '_diffrn_reflns_transf_matrix.31' + _definition.id '_diffrn_radiation.polarisn_norm' + _alias.definition_id '_diffrn_radiation_polarisn_norm' + _definition.update 2012-11-26 + _description.text +; + The angle, as viewed from the specimen, between the perpendicular + component of the polarisation and the diffraction plane. +; + _name.category_id diffrn_radiation + _name.object_id polarisn_norm + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range -180.0:180.0 + _units.code degrees - loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_31' - '_diffrn_reflns.transf_matrix[3][1]' +save_ - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 31 +save_diffrn_radiation.polarisn_ratio - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _definition.id '_diffrn_radiation.polarisn_ratio' + _alias.definition_id '_diffrn_radiation_polarisn_ratio' + _definition.update 2012-11-26 + _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). +; + _name.category_id diffrn_radiation + _name.object_id polarisn_ratio + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code none save_ -save_diffrn_reflns_transf_matrix.32 +save_diffrn_radiation.probe - _definition.id '_diffrn_reflns_transf_matrix.32' + _definition.id '_diffrn_radiation.probe' + _alias.definition_id '_diffrn_radiation_probe' + _definition.update 2012-11-26 + _description.text +; + Enumerated code for the nature of radiation used (i.e. name of + subatomic particle or region of the electromagnetic spectrum). +; + _name.category_id diffrn_radiation + _name.object_id probe + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_32' - '_diffrn_reflns.transf_matrix[3][2]' - - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 32 - - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _enumeration_set.state + x-ray + neutron + electron + gamma save_ -save_diffrn_reflns_transf_matrix.33 +save_diffrn_radiation.type - _definition.id '_diffrn_reflns_transf_matrix.33' + _definition.id '_diffrn_radiation.type' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn_radiation_wavelength.type' + _alias.definition_id '_diffrn_radiation_type' + _definition.update 2022-10-04 + _description.text +; + DEPRECATED. Use _diffrn_radiation_wavelength.type. Details of the + radiation source or energy spectrum. +; + _name.category_id diffrn_radiation + _name.object_id type + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text loop_ - _alias.definition_id - '_diffrn_reflns_transf_matrix_33' - '_diffrn_reflns.transf_matrix[3][3]' - - _name.category_id diffrn_reflns_transf_matrix - _name.object_id 33 - - _import.get - [{'file':templ_attr.cif 'save':transf_matrix}] + _description_example.case + 'Mo K\a' + 'Cu K\a' + 'Cu K\a~1~' + 'Cu K-L~2,3~' + 'white-beam' save_ -save_diffrn_reflns_transf_matrix.tij +save_diffrn_radiation.xray_symbol - _definition.id '_diffrn_reflns_transf_matrix.TIJ' - _definition.update 2021-03-01 + _definition.id '_diffrn_radiation.xray_symbol' + _definition_replaced.id 1 + _definition_replaced.by '_diffrn_radiation_wavelength.xray_symbol' + _alias.definition_id '_diffrn_radiation_xray_symbol' + _definition.update 2022-10-04 _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| -; - _name.category_id diffrn_reflns_transf_matrix - _name.object_id TIJ - _type.purpose Number - _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' - _type.contents Real - _units.code none - _method.purpose Evaluation - _method.expression + DEPRECATED. Use _diffrn_radiation_wavelength.xray_symbol. IUPAC + symbol for the X-ray wavelength for probe radiation. ; - With t as diffrn_reflns_transf_matrix + _name.category_id diffrn_radiation + _name.object_id xray_symbol + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text - _diffrn_reflns_transf_matrix.TIJ = [[t.11, t.12, t.13], - [t.21, t.22, t.23], - [t.31, t.32, t.33]] -; + 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.' save_ -save_DIFFRN_SCALE_GROUP +save_DIFFRN_RADIATION_WAVELENGTH - _definition.id DIFFRN_SCALE_GROUP + _definition.id DIFFRN_RADIATION_WAVELENGTH _definition.scope Category _definition.class Loop _definition.update 2021-06-29 _description.text ; - The CATEGORY of data items which specify the groups of reflections in - the raw measured diffraction data with different relative scales. + 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. ; - _name.category_id DIFFRN - _name.object_id DIFFRN_SCALE_GROUP - _category_key.name '_diffrn_scale_group.code' + _name.category_id DIFFRN_RADIATION + _name.object_id DIFFRN_RADIATION_WAVELENGTH + _category_key.name '_diffrn_radiation_wavelength.id' save_ -save_diffrn_scale_group.code +save_diffrn_radiation_wavelength.details - _definition.id '_diffrn_scale_group.code' - _alias.definition_id '_diffrn_scale_group_code' - _definition.update 2021-10-27 - _description.text -; - Code identifying a specific scale group of reflections (e.g. for - multi-film or multi-crystal data). The code must match a - _diffrn_refln.scale_group_code in the DIFFRN_REFLN list. -; - _name.category_id diffrn_scale_group - _name.object_id code - _type.purpose Encode - _type.source Assigned - _type.container Single - _type.contents Word + _definition.id '_diffrn_radiation_wavelength.details' loop_ - _description_example.case - 1 - 2 - 3 - s1 - A - B - c1 - c2 - c3 - -save_ - -save_diffrn_scale_group.i_net + _alias.definition_id + '_diffrn_radiation_wavelength_details' + '_diffrn_radiation.wavelength_details' - _definition.id '_diffrn_scale_group.I_net' - _alias.definition_id '_diffrn_scale_group_I_net' - _definition.update 2021-03-03 + _definition.update 2012-11-26 _description.text ; - Scale for a specific measurement group of reflections. Is multiplied - with the net intensity to place all intensities on a common scale. + Information about the determination of the radiation + diffrn_radiation_wavelength that is not conveyed completely by an + enumerated value of _diffrn_radiation_wavelength.determination. ; - _name.category_id diffrn_scale_group - _name.object_id I_net - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_radiation_wavelength + _name.object_id details + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _type.contents Text save_ -save_diffrn_scale_group.i_net_su +save_diffrn_radiation_wavelength.determination - _definition.id '_diffrn_scale_group.I_net_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_radiation_wavelength.determination' + + loop_ + _alias.definition_id + '_diffrn_radiation_wavelength_determination' + '_diffrn_radiation.wavelength_determination' + + _definition.update 2023-01-13 _description.text ; - Standard uncertainty of _diffrn_scale_group.I_net. + Method by which the radiation wavelength was determined. ; - _name.category_id diffrn_scale_group - _name.object_id I_net_su - _name.linked_item_id '_diffrn_scale_group.I_net' - _units.code none + _name.category_id diffrn_radiation_wavelength + _name.object_id determination + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text - _import.get [{'file':templ_attr.cif 'save':general_su}] + loop_ + _enumeration_set.state + _enumeration_set.detail + fundamental + 'Fundamental property of matter, e.g. MoK\a.' + estimated + 'Estimated, e.g. from monochromator angle or time of flight.' + refined + 'Refined using a standard crystal with known cell parameters.' save_ -save_DIFFRN_SOURCE +save_diffrn_radiation_wavelength.id - _definition.id DIFFRN_SOURCE - _definition.scope Category - _definition.class Set - _definition.update 2012-11-26 + _definition.id '_diffrn_radiation_wavelength.id' + + loop_ + _alias.definition_id + '_diffrn_radiation_wavelength_id' + '_diffrn_radiation.wavelength_id' + + _definition.update 2021-10-27 _description.text ; - The CATEGORY of data items which specify information about the - radiation source. + Code identifying a radiation used in the diffraction measurements. + This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id ; - _name.category_id DIFFRN - _name.object_id DIFFRN_SOURCE + _name.category_id diffrn_radiation_wavelength + _name.object_id id + _type.purpose Encode + _type.source Assigned + _type.container Single + _type.contents Word + _description_example.case x2 save_ -save_diffrn_source.beamline +save_diffrn_radiation_wavelength.type - _definition.id '_diffrn_source.beamline' - _definition.update 2021-03-01 + _definition.id '_diffrn_radiation_wavelength.type' + _definition.update 2022-10-04 _description.text ; - The name of the beamline at the synchrotron or other - large-scale experimental facility at which the experiment - was conducted. + Details of the radiation source or energy spectrum. ; - _name.category_id diffrn_source - _name.object_id beamline + _name.category_id diffrn_radiation_wavelength + _name.object_id type _type.purpose Describe _type.source Recorded _type.container Single _type.contents Text - _description_example.case I19 + + loop_ + _description_example.case + 'Mo K\a' + 'Cu K\a' + 'Cu K\a~1~' + 'Cu K-L~2,3~' + 'white-beam' save_ -save_diffrn_source.current +save_diffrn_radiation_wavelength.value + + _definition.id '_diffrn_radiation_wavelength.value' + + loop_ + _alias.definition_id + '_diffrn_radiation_wavelength' + '_diffrn_radiation_wavelength.wavelength' - _definition.id '_diffrn_source.current' - _alias.definition_id '_diffrn_source_current' _definition.update 2012-11-26 _description.text ; - Generator current at which the radiation source device was operated. + Wavelength of radiation used in diffraction measurements. ; - _name.category_id diffrn_source - _name.object_id current - _type.purpose Number + _name.category_id diffrn_radiation_wavelength + _name.object_id value + _type.purpose Measurand _type.source Assigned _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code milliamperes + _units.code angstroms save_ -save_diffrn_source.description - - _definition.id '_diffrn_source.description' +save_diffrn_radiation_wavelength.value_su - loop_ - _definition_replaced.id - _definition_replaced.by - 1 '_diffrn_source.device' - 2 '_diffrn_source.details' + _definition.id '_diffrn_radiation_wavelength.value_su' loop_ _alias.definition_id - '_diffrn_source' - '_diffrn_radiation_source' - '_diffrn_source.source' + '_diffrn_radiation_wavelength_su' + '_diffrn_radiation_wavelength.wavelength_su' - _definition.update 2023-01-16 + _definition.update 2021-08-03 _description.text ; - The general class of the source of radiation. This is deprecated. - Use _diffrn_source.device and _diffrn_source.details. + Standard uncertainty of the wavelength of radiation used in diffraction + measurements. ; - _name.category_id diffrn_source - _name.object_id description - _type.purpose Describe - _type.source Recorded + _name.category_id diffrn_radiation_wavelength + _name.object_id value_su + _name.linked_item_id '_diffrn_radiation_wavelength.value' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Text + _type.contents Real + _units.code angstroms save_ -save_diffrn_source.details +save_diffrn_radiation_wavelength.wt - _definition.id '_diffrn_source.details' - _alias.definition_id '_diffrn_source_details' - _definition.update 2021-08-18 + _definition.id '_diffrn_radiation_wavelength.wt' + _alias.definition_id '_diffrn_radiation_wavelength_wt' + _definition.update 2012-11-26 _description.text ; - A description of special aspects of the source not covered by - other data items. + Relative intensity of a radiation used in the diffraction measurements. ; - _name.category_id diffrn_source - _name.object_id details - _type.purpose Describe - _type.source Recorded + _name.category_id diffrn_radiation_wavelength + _name.object_id wt + _type.purpose Number + _type.source Assigned _type.container Single - _type.contents Text + _type.contents Real + _enumeration.range 0.0:1.0 + _units.code none save_ -save_diffrn_source.device +save_diffrn_radiation_wavelength.xray_symbol - _definition.id '_diffrn_source.device' - _definition.update 2018-02-26 + _definition.id '_diffrn_radiation_wavelength.xray_symbol' + _definition.update 2022-10-04 _description.text ; - Enumerated code for the device providing the source of radiation. + IUPAC symbol for the X-ray wavelength for probe radiation. ; - _name.category_id diffrn_source - _name.object_id device + _name.category_id diffrn_radiation_wavelength + _name.object_id xray_symbol _type.purpose State _type.source Assigned _type.container Single @@ -3743,415 +3520,366 @@ save_diffrn_source.device loop_ _enumeration_set.state _enumeration_set.detail - tube 'Sealed X-ray tube.' - nuclear 'Nuclear reactor.' - spallation 'Spallation source.' - elect-micro 'Electron microscope.' - rot_anode 'Rotating-anode X-ray tube.' - synch 'Synchrotron.' + 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.' save_ -save_diffrn_source.facility +save_DIFFRN_REFLN - _definition.id '_diffrn_source.facility' - _definition.update 2020-09-18 + _definition.id DIFFRN_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - The name of the synchrotron or other large-scale - experimental facility at which the experiment was - conducted. Names should conform to the spelling and - format used in the 'Light Sources of the World' listing - of lightsources.org - (https://lightsources.org/lightsources-of-the-world/) + The CATEGORY of data items which specify the reflection measurements, + prior to data reduction and merging. ; - _name.category_id diffrn_source - _name.object_id facility - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'Diamond Light Source' + _name.category_id DIFFRN + _name.object_id DIFFRN_REFLN + _category_key.name '_diffrn_refln.hkl' save_ -save_diffrn_source.make +save_diffrn_refln.angle_chi - _definition.id '_diffrn_source.make' + _definition.id '_diffrn_refln.angle_chi' + _alias.definition_id '_diffrn_refln_angle_chi' + _name.category_id diffrn_refln + _name.object_id angle_chi - loop_ - _alias.definition_id - '_diffrn_source_make' - '_diffrn_source.type' - '_diffrn_source_type' + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] - _definition.update 2021-07-26 - _description.text -; - Description of the make, model or name of the source device. - Large scale facilities should use _diffrn_source.facility and - _diffrn_source.beamline to identify the source of radiation. -; - _name.category_id diffrn_source - _name.object_id make - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'Rigaku RU2012-05-07' +save_ + +save_diffrn_refln.angle_kappa + + _definition.id '_diffrn_refln.angle_kappa' + _alias.definition_id '_diffrn_refln_angle_kappa' + _name.category_id diffrn_refln + _name.object_id angle_kappa + + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] save_ -save_diffrn_source.power +save_diffrn_refln.angle_omega - _definition.id '_diffrn_source.power' - _alias.definition_id '_diffrn_source_power' - _definition.update 2012-11-26 - _description.text -; - Generator power at which the radiation source device was operated. -; - _name.category_id diffrn_source - _name.object_id power - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code kilowatts + _definition.id '_diffrn_refln.angle_omega' + _alias.definition_id '_diffrn_refln_angle_omega' + _name.category_id diffrn_refln + _name.object_id angle_omega + + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] save_ -save_diffrn_source.size +save_diffrn_refln.angle_phi - _definition.id '_diffrn_source.size' - _alias.definition_id '_diffrn_source_size' - _definition.update 2012-11-26 - _description.text -; - Description of the collimated source beam as viewed from the sample. -; - _name.category_id diffrn_source - _name.object_id size - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _definition.id '_diffrn_refln.angle_phi' + _alias.definition_id '_diffrn_refln_angle_phi' + _name.category_id diffrn_refln + _name.object_id angle_phi - loop_ - _description_example.case - '8mm x 0.4 mm fine-focus' - 'broad focus' + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] save_ -save_diffrn_source.take_off_angle +save_diffrn_refln.angle_psi - _definition.id '_diffrn_source.take_off_angle' + _definition.id '_diffrn_refln.angle_psi' + _alias.definition_id '_diffrn_refln_angle_psi' + _name.category_id diffrn_refln + _name.object_id angle_psi - loop_ - _alias.definition_id - '_diffrn_source_take-off_angle' - '_diffrn_source.take-off_angle' + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] - _definition.update 2013-02-22 - _description.text -; - The complement of the angle in degrees between the normal - to the surface of the X-ray tube target and the primary - X-ray beam for beams generated by traditional X-ray tubes. -; - _name.category_id diffrn_source - _name.object_id take_off_angle - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0:90 - _units.code degrees +save_ + +save_diffrn_refln.angle_theta + + _definition.id '_diffrn_refln.angle_theta' + _alias.definition_id '_diffrn_refln_angle_theta' + _name.category_id diffrn_refln + _name.object_id angle_theta + + _import.get [{'file':templ_attr.cif 'save':diffr_angle}] save_ -save_diffrn_source.target +save_diffrn_refln.attenuator_code - _definition.id '_diffrn_source.target' - _alias.definition_id '_diffrn_source_target' + _definition.id '_diffrn_refln.attenuator_code' + _alias.definition_id '_diffrn_refln_attenuator_code' _definition.update 2021-10-27 _description.text ; - Chemical element symbol for the radiation source target (usually - the anode). This can be used also for spallation sources. + Code identifying any attenuator setting for this reflection. ; - _name.category_id diffrn_source - _name.object_id target - _type.purpose State - _type.source Assigned + _name.category_id diffrn_refln + _name.object_id attenuator_code + _name.linked_item_id '_diffrn_attenuator.code' + _type.purpose Link + _type.source Related _type.container Single _type.contents Word - _import.get - [{'file':templ_enum.cif 'save':element_symbol}] - save_ -save_diffrn_source.voltage +save_diffrn_refln.class_code - _definition.id '_diffrn_source.voltage' - _alias.definition_id '_diffrn_source_voltage' - _definition.update 2012-11-26 + _definition.id '_diffrn_refln.class_code' + _alias.definition_id '_diffrn_refln_class_code' + _definition.update 2021-10-27 _description.text ; - Generator voltage at which the radiation source device was operated. + Code for reflection class, if assigned. e.g. modulated structures ; - _name.category_id diffrn_source - _name.object_id voltage - _type.purpose Number - _type.source Assigned + _name.category_id diffrn_refln + _name.object_id class_code + _name.linked_item_id '_diffrn_reflns_class.code' + _type.purpose Link + _type.source Related _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code kilovolts + _type.contents Word save_ -save_DIFFRN_STANDARDS +save_diffrn_refln.counts_bg_1 - _definition.id DIFFRN_STANDARDS - _definition.scope Category - _definition.class Set - _definition.update 2023-01-10 + _definition.id '_diffrn_refln.counts_bg_1' + _alias.definition_id '_diffrn_refln_counts_bg_1' + _definition.update 2022-11-22 _description.text ; - The CATEGORY of data items which specify information about the - standard reflections used in the diffraction measurement process. -; - _name.category_id DIFFRN - _name.object_id DIFFRN_STANDARDS - -save_ - -save_diffrn_standards.decay_percent - - _definition.id '_diffrn_standards.decay_percent' + The measured background scattering on one side of a diffraction + peak when measuring using a point detector. - loop_ - _alias.definition_id - '_diffrn_standards_decay_%' - '_diffrn_standards.decay_%' - '_diffrn_standards_decay_percent' + Note that counts-per-second values should be converted to + total counts. - _definition.update 2023-01-13 - _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. If no measurable decay has occurred, the - standard uncertainty should be quoted to indicate the maximum - possible value the decay might have. A range of 3 standard - uncertainties is considered possible. Thus 0.0(1) would indicate - a decay of less than 0.3% or an enhancement of less than 0.3%. + Standard uncertainties should not be quoted for these values. + If the standard uncertainties differ from the square root of + the number of counts, _diffrn_refln.intensity_* should be used. ; - _name.category_id diffrn_standards - _name.object_id decay_percent - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_refln + _name.object_id counts_bg_1 + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range :100 - _units.code none - - loop_ - _description_example.case - _description_example.detail - 0.5(1) 'Represents a decay between 0.2% and 0.8%.' - -1(1) 'Change in standards between 2% decay and 4% rise.' - 0.0(2) 'Change in standards between 0.6% decay and 0.6% rise.' + _type.contents Integer + _enumeration.range 0: + _units.code counts save_ -save_diffrn_standards.decay_percent_su +save_diffrn_refln.counts_bg_2 - _definition.id '_diffrn_standards.decay_percent_su' - _definition.update 2023-01-10 + _definition.id '_diffrn_refln.counts_bg_2' + _alias.definition_id '_diffrn_refln_counts_bg_2' + _definition.update 2022-11-22 _description.text ; - Standard uncertainty of _diffrn_standards.decay_percent. -; - _name.category_id diffrn_standards - _name.object_id decay_percent_su - _name.linked_item_id '_diffrn_standards.decay_percent' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] - -save_ + The measured background counts on the other side of the + peak to the measurement of _diffrn_refln.counts_bg_1 + when measuring using a point detector. -save_diffrn_standards.interval_count + Note that counts-per-second values should be converted to + total counts. - _definition.id '_diffrn_standards.interval_count' - _alias.definition_id '_diffrn_standards_interval_count' - _definition.update 2023-01-10 - _description.text -; - Reflection count between the standard reflection measurements. + Standard uncertainties should not be quoted for these values. + If the standard uncertainties differ from the square root of + the number of counts, _diffrn_refln.intensity_* should be used. ; - _name.category_id diffrn_standards - _name.object_id interval_count + _name.category_id diffrn_refln + _name.object_id counts_bg_2 _type.purpose Number - _type.source Assigned + _type.source Recorded _type.container Single _type.contents Integer _enumeration.range 0: - _units.code none + _units.code counts save_ -save_diffrn_standards.interval_time +save_diffrn_refln.counts_net - _definition.id '_diffrn_standards.interval_time' - _alias.definition_id '_diffrn_standards_interval_time' - _definition.update 2023-01-10 + _definition.id '_diffrn_refln.counts_net' + _alias.definition_id '_diffrn_refln_counts_net' + _definition.update 2022-12-12 _description.text ; - Time between the standard reflection measurements. + Counts measured in the reflection peak after background + subtraction. If background and peak counts were collected + for different times, the background counts must be scaled to + the peak counts prior to subtraction. + + Note that counts-per-second values should be converted to + total counts. + + The value for this data item must be derived from count values. + If not, _diffrn_refln.intensity_* should be used. ; - _name.category_id diffrn_standards - _name.object_id interval_time - _type.purpose Number - _type.source Assigned + _name.category_id diffrn_refln + _name.object_id counts_net + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.: - _units.code minutes + _units.code counts + +save_ + +save_diffrn_refln.counts_net_su + + _definition.id '_diffrn_refln.counts_net_su' + _definition.update 2012-12-13 + _description.text +; + Standard uncertainty of _diffrn_refln.counts_net. +; + _name.category_id diffrn_refln + _name.object_id counts_net_su + _name.linked_item_id '_diffrn_refln.counts_net' + _units.code counts + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_diffrn_standards.number +save_diffrn_refln.counts_peak - _definition.id '_diffrn_standards.number' - _alias.definition_id '_diffrn_standards_number' - _definition.update 2023-01-10 + _definition.id '_diffrn_refln.counts_peak' + _alias.definition_id '_diffrn_refln_counts_peak' + _definition.update 2022-11-22 _description.text ; - Number of unique standard reflections used in measurements. + Counts measured in the reflection peak before background + subtraction. That is, the region of interest consists of + only the diffraction peak. + + Note that counts-per-second values should be converted to + total counts. + + Standard uncertainties should not be quoted for these values. + If the standard uncertainties differ from the square root of + the number of counts, _diffrn_refln.intensity_* should be used. ; - _name.category_id diffrn_standards - _name.object_id number + _name.category_id diffrn_refln + _name.object_id counts_peak _type.purpose Number - _type.source Assigned + _type.source Recorded _type.container Single _type.contents Integer _enumeration.range 0: - _units.code none + _units.code counts save_ -save_diffrn_standards.scale_su_average - - _definition.id '_diffrn_standards.scale_su_average' - - loop_ - _alias.definition_id - '_diffrn_standards_scale_sigma' - '_diffrn_standards.scale_sigma' - '_diffrn_standards.scale_u' - '_diffrn_standards_scale_u' +save_diffrn_refln.counts_total - _definition.update 2023-01-10 + _definition.id '_diffrn_refln.counts_total' + _alias.definition_id '_diffrn_refln_counts_total' + _definition.update 2022-11-22 _description.text ; - The average standard uncertainty of the individual standard scales - applied to the intensity data. + Counts measured in the total reflection including background + and peak regions. That is, the region of interest consists of the + diffraction peak and an area of background immediately surrounding + the peak of interest. + + Note that counts-per-second values should be converted to + total counts. + + Standard uncertainties should not be quoted for these values. + If the standard uncertainties differ from the square root of + the number of counts, _diffrn_refln.intensity_* should be used. ; - _name.category_id diffrn_standards - _name.object_id scale_su_average - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_refln + _name.object_id counts_total + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _type.contents Integer + _enumeration.range 0: + _units.code counts save_ -save_diffrn_standards.scale_su_average_su +save_diffrn_refln.detect_slit_horiz - _definition.id '_diffrn_standards.scale_su_average_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_refln.detect_slit_horiz' + _alias.definition_id '_diffrn_refln_detect_slit_horiz' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _diffrn_standards.scale_su_average. + Total slit aperture angle in the diffraction plane. ; - _name.category_id diffrn_standards - _name.object_id scale_su_average_su - _name.linked_item_id '_diffrn_standards.scale_su_average' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id diffrn_refln + _name.object_id detect_slit_horiz + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_DIFFRN_STANDARD_REFLN +save_diffrn_refln.detect_slit_vert - _definition.id DIFFRN_STANDARD_REFLN - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_diffrn_refln.detect_slit_vert' + _alias.definition_id '_diffrn_refln_detect_slit_vert' + _definition.update 2012-11-26 _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. + Total slit aperture angle perpendicular to the diffraction plane. ; - _name.category_id DIFFRN_STANDARDS - _name.object_id DIFFRN_STANDARD_REFLN - - loop_ - _category_key.name - '_diffrn_standard_refln.index_h' - '_diffrn_standard_refln.index_k' - '_diffrn_standard_refln.index_l' + _name.category_id diffrn_refln + _name.object_id detect_slit_vert + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_diffrn_standard_refln.code - - _definition.id '_diffrn_standard_refln.code' - - loop_ - _alias.definition_id - '_diffrn_standard_refln_code' - '_diffrn_standard_refln.diffrn_id' +save_diffrn_refln.elapsed_time - _definition.update 2021-10-27 + _definition.id '_diffrn_refln.elapsed_time' + _alias.definition_id '_diffrn_refln_elapsed_time' + _definition.update 2012-11-26 _description.text ; - Code identifying a standard reflection used to monitor source - intensity variations or crystal degradation or movement during - data collection. + Elapsed time from the start to the end of the intensity measurement. ; - _name.category_id diffrn_standard_refln - _name.object_id code - _type.purpose Encode - _type.source Assigned + _name.category_id diffrn_refln + _name.object_id elapsed_time + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Word - _description_example.case s1 + _type.contents Real + _enumeration.range 0.0: + _units.code minutes save_ -save_diffrn_standard_refln.hkl +save_diffrn_refln.hkl - _definition.id '_diffrn_standard_refln.hkl' + _definition.id '_diffrn_refln.hkl' _definition.update 2021-03-01 _description.text ; - Miller indices of a standard reflection. + 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. ; - _name.category_id diffrn_standard_refln + _name.category_id diffrn_refln _name.object_id hkl _type.purpose Number _type.source Derived @@ -4162,4247 +3890,4616 @@ save_diffrn_standard_refln.hkl _method.purpose Evaluation _method.expression ; - With d as diffrn_standard_refln + With a as diffrn_refln - _diffrn_standard_refln.hkl = [d.index_h, d.index_h, d.index_l] + _diffrn_refln.hkl = [a.index_h, a.index_h, a.index_l] ; save_ -save_diffrn_standard_refln.index_h +save_diffrn_refln.index_h - _definition.id '_diffrn_standard_refln.index_h' - _alias.definition_id '_diffrn_standard_refln_index_h' - _name.category_id diffrn_standard_refln + _definition.id '_diffrn_refln.index_h' + _alias.definition_id '_diffrn_refln_index_h' + _name.category_id diffrn_refln _name.object_id index_h _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_standard_refln.index_k +save_diffrn_refln.index_k - _definition.id '_diffrn_standard_refln.index_k' - _alias.definition_id '_diffrn_standard_refln_index_k' - _name.category_id diffrn_standard_refln + _definition.id '_diffrn_refln.index_k' + _alias.definition_id '_diffrn_refln_index_k' + _name.category_id diffrn_refln _name.object_id index_k _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_diffrn_standard_refln.index_l +save_diffrn_refln.index_l - _definition.id '_diffrn_standard_refln.index_l' - _alias.definition_id '_diffrn_standard_refln_index_l' - _name.category_id diffrn_standard_refln + _definition.id '_diffrn_refln.index_l' + _alias.definition_id '_diffrn_refln_index_l' + _name.category_id diffrn_refln _name.object_id index_l _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_REFLN +save_diffrn_refln.intensity_bg_1 + + _definition.id '_diffrn_refln.intensity_bg_1' + _definition.update 2022-11-22 + _description.text +; + The measured background intensity on one side of a diffraction + peak when measuring using a point detector. + + Use these entries for measurements where intensity values are not + counts (use _diffrn_refln.counts_* for event-counting measurements + where the standard uncertainty is estimated as the square root of + the number of counts). +; + _name.category_id diffrn_refln + _name.object_id intensity_bg_1 + _type.purpose Measurand + _type.source Recorded + _type.container Single + _type.contents Real + _units.code none + +save_ + +save_diffrn_refln.intensity_bg_1_su + + _definition.id '_diffrn_refln.intensity_bg_1_su' + _definition.update 2022-11-22 + _description.text +; + Standard uncertainty of _diffrn_refln.intensity_bg_1. +; + _name.category_id diffrn_refln + _name.object_id intensity_bg_1_su + _name.linked_item_id '_diffrn_refln.intensity_bg_1' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] + +save_ + +save_diffrn_refln.intensity_bg_2 + + _definition.id '_diffrn_refln.intensity_bg_2' + _definition.update 2022-11-22 + _description.text +; + The measured background counts on the other side of the + peak to the measurement of _diffrn_refln.intensity_bg_1 + when measuring using a point detector. + + Use these entries for measurements where intensity values are not + counts (use _diffrn_refln.counts_* for event-counting measurements + where the standard uncertainty is estimated as the square root of + the number of counts). +; + _name.category_id diffrn_refln + _name.object_id intensity_bg_2 + _type.purpose Measurand + _type.source Recorded + _type.container Single + _type.contents Real + _units.code none + +save_ + +save_diffrn_refln.intensity_bg_2_su - _definition.id REFLN - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_diffrn_refln.intensity_bg_2_su' + _definition.update 2021-09-23 _description.text ; - The CATEGORY of data items used to describe the reflection data - used in the refinement of a crystallographic structure model. + Standard uncertainty of _diffrn_refln.intensity_bg_2. ; - _name.category_id DIFFRACTION - _name.object_id REFLN + _name.category_id diffrn_refln + _name.object_id intensity_bg_2_su + _name.linked_item_id '_diffrn_refln.intensity_bg_2' + _units.code none - loop_ - _category_key.name - '_refln.index_h' - '_refln.index_k' - '_refln.index_l' + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_refln.a_calc +save_diffrn_refln.intensity_net - _definition.id '_refln.A_calc' - _alias.definition_id '_refln_A_calc' - _definition.update 2012-11-26 + _definition.id '_diffrn_refln.intensity_net' + _alias.definition_id '_diffrn_refln_intensity_net' + _definition.update 2022-11-22 _description.text ; - The calculated real structure-factor component A =|Fcalc|cos(phase) + Net intensity in the reflection peak calculated from the + diffraction counts after the attenuator and standard scales + have been applied. ; - _name.category_id refln - _name.object_id A_calc + _name.category_id diffrn_refln + _name.object_id intensity_net _type.purpose Measurand _type.source Derived _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.A_calc = Real ( _refln.F_complex ) -; + _units.code none save_ -save_refln.a_calc_su +save_diffrn_refln.intensity_net_su - _definition.id '_refln.A_calc_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_refln.intensity_net_su' + + loop_ + _alias.definition_id + '_diffrn_refln_intensity_u' + '_diffrn_refln_intensity_sigma' + '_diffrn_refln.intensity_sigma' + '_diffrn_refln.intensity_u' + + _definition.update 2012-12-13 _description.text ; - Standard uncertainty of _refln.A_calc. + Standard uncertainty of _diffrn_refln.intensity_net. ; - _name.category_id refln - _name.object_id A_calc_su - _name.linked_item_id '_refln.A_calc' + _name.category_id diffrn_refln + _name.object_id intensity_net_su + _name.linked_item_id '_diffrn_refln.intensity_net' + _units.code none _import.get [{'file':templ_attr.cif 'save':general_su}] - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = - "femtometres" Else If (_diffrn_radiation.probe == "electron") - _units.code = "volts" Else - _units.code = "electrons" -; - save_ -save_refln.a_meas +save_diffrn_refln.intensity_peak - _definition.id '_refln.A_meas' - _alias.definition_id '_refln_A_meas' - _definition.update 2012-11-26 + _definition.id '_diffrn_refln.intensity_peak' + _definition.update 2022-11-22 _description.text ; - The measured real structure-factor component A =|Fmeas|cos(phase) + Intensity measured in the reflection peak before background + subtraction. That is, the region of interest consists of + only the diffraction peak. + + Use these entries for measurements where intensity values are not + counts (use _diffrn_refln.counts_* for event-counting measurements + where the standard uncertainty is estimated as the square root of + the number of counts). ; - _name.category_id refln - _name.object_id A_meas + _name.category_id diffrn_refln + _name.object_id intensity_peak _type.purpose Measurand - _type.source Derived + _type.source Recorded _type.container Single _type.contents Real - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" -; + _units.code none save_ -save_refln.a_meas_su +save_diffrn_refln.intensity_peak_su - _definition.id '_refln.A_meas_su' + _definition.id '_diffrn_refln.intensity_peak_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _refln.A_meas. + Standard uncertainty of _diffrn_refln.intensity_peak. ; - _name.category_id refln - _name.object_id A_meas_su - _name.linked_item_id '_refln.A_meas' + _name.category_id diffrn_refln + _name.object_id intensity_peak_su + _name.linked_item_id '_diffrn_refln.intensity_peak' + _units.code none _import.get [{'file':templ_attr.cif 'save':general_su}] - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" -; - save_ -save_refln.b_calc +save_diffrn_refln.intensity_total - _definition.id '_refln.B_calc' - _alias.definition_id '_refln_B_calc' - _definition.update 2012-11-26 + _definition.id '_diffrn_refln.intensity_total' + _definition.update 2022-11-22 _description.text ; - The calculated imaginary structure-factor component B =|Fcalc|sin(phase) + Intensity measured in the total reflection including background + and peak regions. That is, the region of interest consists of the + diffraction peak and an area of background immediately surrounding + the peak of interest. + + Use these entries for measurements where intensity values are not + counts (use _diffrn_refln.counts_* for event-counting measurements + where the standard uncertainty is estimated as the square root of + the number of counts). ; - _name.category_id refln - _name.object_id B_calc + _name.category_id diffrn_refln + _name.object_id intensity_total _type.purpose Measurand - _type.source Derived + _type.source Recorded _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.B_calc = Imag ( _refln.F_complex ) -; + _units.code none save_ -save_refln.b_calc_su +save_diffrn_refln.intensity_total_su - _definition.id '_refln.B_calc_su' + _definition.id '_diffrn_refln.intensity_total_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _refln.B_calc. + Standard uncertainty of _diffrn_refln.intensity_total. ; - _name.category_id refln - _name.object_id B_calc_su - _name.linked_item_id '_refln.B_calc' + _name.category_id diffrn_refln + _name.object_id intensity_total_su + _name.linked_item_id '_diffrn_refln.intensity_total' + _units.code none _import.get [{'file':templ_attr.cif 'save':general_su}] - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = - "femtometres" Else If (_diffrn_radiation.probe == "electron") - _units.code = "volts" Else - _units.code = "electrons" -; - save_ -save_refln.b_meas +save_diffrn_refln.scale_group_code - _definition.id '_refln.B_meas' - _alias.definition_id '_refln_B_meas' - _definition.update 2012-11-26 + _definition.id '_diffrn_refln.scale_group_code' + _alias.definition_id '_diffrn_refln_scale_group_code' + _definition.update 2021-10-27 _description.text ; - The measured imaginary structure-factor component B =|Fmeas|sin(phase) + Code identifying the scale applying to this reflection. ; - _name.category_id refln - _name.object_id B_meas - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_refln + _name.object_id scale_group_code + _name.linked_item_id '_diffrn_scale_group.code' + _type.purpose Link + _type.source Related _type.container Single - _type.contents Real - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" -; + _type.contents Word save_ -save_refln.b_meas_su +save_diffrn_refln.scan_mode - _definition.id '_refln.B_meas_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_refln.scan_mode' + _alias.definition_id '_diffrn_refln_scan_mode' + _definition.update 2023-01-13 _description.text ; - Standard uncertainty of _refln.B_meas. + Code identifying the mode of scanning with a diffractometer. + See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. ; - _name.category_id refln - _name.object_id B_meas_su - _name.linked_item_id '_refln.B_meas' + _name.category_id diffrn_refln + _name.object_id scan_mode + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text + + loop_ + _enumeration_set.state + _enumeration_set.detail + om 'Omega scan.' + ot 'Omega/2theta scan.' + q 'Q-scans (arbitrary reciprocal directions).' - _import.get [{'file':templ_attr.cif 'save':general_su}] +save_ - _method.purpose Definition - _method.expression +save_diffrn_refln.scan_mode_backgd + + _definition.id '_diffrn_refln.scan_mode_backgd' + _alias.definition_id '_diffrn_refln_scan_mode_backgd' + _definition.update 2012-11-26 + _description.text ; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" + Code identifying mode of scanning to measure the background intensity. ; + _name.category_id diffrn_refln + _name.object_id scan_mode_backgd + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text + + loop_ + _enumeration_set.state + _enumeration_set.detail + st 'Stationary counter background.' + mo 'Moving counter background.' save_ -save_refln.class_code +save_diffrn_refln.scan_rate - _definition.id '_refln.class_code' - _alias.definition_id '_refln_class_code' - _definition.update 2021-10-27 + _definition.id '_diffrn_refln.scan_rate' + _alias.definition_id '_diffrn_refln_scan_rate' + _definition.update 2013-03-07 _description.text ; - Code identifying the class to which this reflection has been - assigned. This code must match a value of _reflns_class.code. - Reflections may be grouped into classes for a variety of - purposes. For example, for modulated structures each reflection - class may be defined by the number m=sum|m~i~|, where the m~i~ - are the integer coefficients that, in addition to h,k,l, index - the corresponding diffraction vector in the basis defined - for the reciprocal lattice. + Angular rate of scanning a reflection to measure the intensity. ; - _name.category_id refln - _name.object_id class_code - _name.linked_item_id '_reflns_class.code' - _type.purpose Link - _type.source Related + _name.category_id diffrn_refln + _name.object_id scan_rate + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Word + _type.contents Real + _enumeration.range 0.0: + _units.code degree_per_minute save_ -save_refln.d_spacing +save_diffrn_refln.scan_time_backgd - _definition.id '_refln.d_spacing' - _alias.definition_id '_refln_d_spacing' + _definition.id '_diffrn_refln.scan_time_backgd' + _alias.definition_id '_diffrn_refln_scan_time_backgd' _definition.update 2012-11-26 _description.text ; - The distance in angstroms between lattice planes in the crystal - with the indices _refln.hkl for this reflection. + Time spent measuring background counts. ; - _name.category_id refln - _name.object_id d_spacing + _name.category_id diffrn_refln + _name.object_id scan_time_backgd _type.purpose Number - _type.source Derived + _type.source Recorded _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code angstroms - _method.purpose Evaluation - _method.expression -; - _refln.d_spacing = 1 / (2 * _refln.sin_theta_over_lambda) -; + _units.code seconds save_ -save_refln.f_calc +save_diffrn_refln.scan_width - _definition.id '_refln.F_calc' - _alias.definition_id '_refln_F_calc' - _definition.update 2013-02-21 + _definition.id '_diffrn_refln.scan_width' + _alias.definition_id '_diffrn_refln_scan_width' + _definition.update 2012-11-26 _description.text ; - The structure factor amplitude for the reflection calculated from - the atom site data. + Angular scan width when measuring the peak intensity. ; - _name.category_id refln - _name.object_id F_calc - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_refln + _name.object_id scan_width + _type.purpose Number + _type.source Recorded _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 ) -; + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_refln.f_calc_su +save_diffrn_refln.sin_theta_over_lambda - _definition.id '_refln.F_calc_su' - _definition.update 2021-09-23 - _description.text -; - Standard uncertainty of _refln.F_calc. -; - _name.category_id refln - _name.object_id F_calc_su - _name.linked_item_id '_refln.F_calc' + _definition.id '_diffrn_refln.sin_theta_over_lambda' - _import.get [{'file':templ_attr.cif 'save':general_su}] + loop_ + _alias.definition_id + '_diffrn_refln_sint/lambda' + '_diffrn_refln_sint_over_lambda' + '_diffrn_refln.sint_over_lambda' - _method.purpose Definition - _method.expression + _definition.update 2012-11-26 + _description.text ; - If (_diffrn_radiation.probe == "neutron") _units.code = - "femtometres" Else If (_diffrn_radiation.probe == "electron") - _units.code = "volts" Else - _units.code = "electrons" + (sin theta)/lambda value for this reflection. ; + _name.category_id diffrn_refln + _name.object_id sin_theta_over_lambda + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms save_ -save_refln.f_complex +save_diffrn_refln.standard_code - _definition.id '_refln.F_complex' - _alias.definition_id '_refln_F_complex' - _definition.update 2016-05-13 + _definition.id '_diffrn_refln.standard_code' + _alias.definition_id '_diffrn_refln_standard_code' + _definition.update 2021-10-27 _description.text ; - The structure factor vector for the reflection calculated from - the atom site data. + Code identifying reflections measured repeated as standard intensity. + Must match a _diffrn_standard_refln.code values OR set to '.' if + it was not used as a intensity standard. ; - _name.category_id refln - _name.object_id F_complex - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_refln + _name.object_id standard_code + _name.linked_item_id '_diffrn_standard_refln.code' + _type.purpose Link + _type.source Related _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 - - Loop a as atom_site { - - f = a.site_symmetry_multiplicity * a.occupancy * ( - r.form_factor_table [a.type_symbol] + - _atom_type_scat[a.type_symbol].dispersion ) + _type.contents Word - Loop s as space_group_symop { +save_ - t = Exp(-h * s.R * a.tensor_beta * s.RT * h) +save_diffrn_refln.wavelength - fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T))) - } } - _refln.F_complex = fc / _space_group.multiplicity + _definition.id '_diffrn_refln.wavelength' + _alias.definition_id '_diffrn_refln_wavelength' + _definition.update 2012-11-26 + _description.text ; + Mean wavelength of radiation used to measure this intensity. +; + _name.category_id diffrn_refln + _name.object_id wavelength + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code angstroms save_ -save_refln.f_complex_su +save_diffrn_refln.wavelength_id - _definition.id '_refln.F_complex_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_refln.wavelength_id' + _alias.definition_id '_diffrn_refln_wavelength_id' + _definition.update 2021-10-27 _description.text ; - Standard uncertainty of _refln.F_complex. + Code identifying the wavelength in the diffrn_radiation_wavelength list. ; - _name.category_id refln - _name.object_id F_complex_su - _name.linked_item_id '_refln.F_complex' + _name.category_id diffrn_refln + _name.object_id wavelength_id + _name.linked_item_id '_diffrn_radiation_wavelength.id' + _type.purpose Link + _type.source Related + _type.container Single + _type.contents Word - _import.get [{'file':templ_attr.cif 'save':general_su}] +save_ - _method.purpose Definition - _method.expression +save_DIFFRN_REFLNS + + _definition.id DIFFRN_REFLNS + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _description.text ; - If (_diffrn_radiation.probe == "neutron") _units.code = - "femtometres" Else If (_diffrn_radiation.probe == "electron") - _units.code = "volts" Else - _units.code = "electrons" + The CATEGORY of data items which specify the overall reflection + measurement information. ; + _name.category_id DIFFRN + _name.object_id DIFFRN_REFLNS save_ -save_refln.f_meas +save_diffrn_reflns.av_r_equivalents - _definition.id '_refln.F_meas' - _alias.definition_id '_refln_F_meas' - _definition.update 2013-02-21 + _definition.id '_diffrn_reflns.av_R_equivalents' + _alias.definition_id '_diffrn_reflns_av_R_equivalents' + _definition.update 2012-11-26 _description.text ; - The structure factor amplitude for the reflection derived from the - measured intensities. + 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. ; - _name.category_id refln - _name.object_id F_meas - _type.purpose Measurand + _name.category_id diffrn_reflns + _name.object_id av_R_equivalents + _type.purpose Number _type.source Derived _type.container Single _type.contents Real - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" -; + _enumeration.range 0.0: + _units.code none save_ -save_refln.f_meas_su +save_diffrn_reflns.av_suneti_over_neti - _definition.id '_refln.F_meas_su' + _definition.id '_diffrn_reflns.av_sunetI_over_netI' loop_ _alias.definition_id - '_refln_F_sigma' - '_refln.F_meas_sigma' - '_refln_F_meas_su' + '_diffrn_reflns_av_sigmaI_over_netI' + '_diffrn_reflns_av_sigmaI/netI' + '_diffrn_reflns.av_unetI/netI' + '_diffrn_reflns_av_unetI/netI' + '_diffrn_reflns.av_sigmaI_over_netI' - _definition.update 2021-03-03 + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of the measured structure factor amplitude. + Recorded [sum |su(netI)| / sum |netI|] for all measured reflections. ; - _name.category_id refln - _name.object_id F_meas_su - _name.linked_item_id '_refln.F_meas' - _type.purpose SU - _type.source Related + _name.category_id diffrn_reflns + _name.object_id av_sunetI_over_netI + _type.purpose Number + _type.source Derived _type.container Single _type.contents Real - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" - Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" - Else _units.code = "electrons" -; + _enumeration.range 0.0: + _units.code none save_ -save_refln.f_squared_calc +save_diffrn_reflns.laue_measured_fraction_full - _definition.id '_refln.F_squared_calc' - _alias.definition_id '_refln_F_squared_calc' - _definition.update 2012-11-26 + _definition.id '_diffrn_reflns.Laue_measured_fraction_full' + _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_full' + _definition.update 2019-01-09 _description.text ; - The structure factor amplitude squared for the reflection calculated from - the atom site data. + Fraction of Laue group unique reflections (symmetry-independent in + the Laue group) measured out to the resolution given in + _diffrn_reflns.resolution_full or _diffrn_reflns.theta_full. + The Laue group always contains a centre of symmetry so that + the reflection h,k,l is always equivalent to the reflection + -h,-k,-l even in space groups without a centre of symmetry. + This number should not be less than 0.95, since it represents + the fraction of reflections measured in the part of the + diffraction pattern that is essentially complete. ; - _name.category_id refln - _name.object_id F_squared_calc - _type.purpose Measurand + _name.category_id diffrn_reflns + _name.object_id Laue_measured_fraction_full + _type.purpose Number _type.source Derived _type.container Single _type.contents Real - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") - _units.code = "femtometre_squared" - Else If (_diffrn_radiation.probe == "electron") - _units.code = "volt_squared" - Else _units.code = "electron_squared" -; + _enumeration.range 0.95:1.0 + _units.code none save_ -save_refln.f_squared_calc_su +save_diffrn_reflns.laue_measured_fraction_max - _definition.id '_refln.F_squared_calc_su' - _definition.update 2021-09-23 + _definition.id '_diffrn_reflns.Laue_measured_fraction_max' + _alias.definition_id '_diffrn_reflns_Laue_measured_fraction_max' + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _refln.F_squared_calc. + Fraction of Laue group unique reflections (symmetry-independent in + the Laue group) measured out to the resolution given in + _diffrn_reflns.resolution_max or _diffrn_reflns.theta_max. + The Laue group always contains a centre of symmetry so that the + reflection h,k,l is always equivalent to the reflection -h,-k,-l + even in space groups without a centre of symmetry. ; - _name.category_id refln - _name.object_id F_squared_calc_su - _name.linked_item_id '_refln.F_squared_calc' + _name.category_id diffrn_reflns + _name.object_id Laue_measured_fraction_max + _type.purpose Number + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + _units.code none - _import.get [{'file':templ_attr.cif 'save':general_su}] +save_ - _method.purpose Definition - _method.expression -; - If (_diffrn_radiation.probe == "neutron") - _units.code = "femtometre_squared" - Else If (_diffrn_radiation.probe == "electron") - _units.code = "volt_squared" - Else _units.code = "electron_squared" -; +save_diffrn_reflns.limit_h_max + + _definition.id '_diffrn_reflns.limit_h_max' + _alias.definition_id '_diffrn_reflns_limit_h_max' + _name.category_id diffrn_reflns + _name.object_id limit_h_max + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_refln.f_squared_meas +save_diffrn_reflns.limit_h_min - _definition.id '_refln.F_squared_meas' - _alias.definition_id '_refln_F_squared_meas' - _definition.update 2013-02-21 + _definition.id '_diffrn_reflns.limit_h_min' + _alias.definition_id '_diffrn_reflns_limit_h_min' + _name.category_id diffrn_reflns + _name.object_id limit_h_min + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_diffrn_reflns.limit_k_max + + _definition.id '_diffrn_reflns.limit_k_max' + _alias.definition_id '_diffrn_reflns_limit_k_max' + _name.category_id diffrn_reflns + _name.object_id limit_k_max + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_diffrn_reflns.limit_k_min + + _definition.id '_diffrn_reflns.limit_k_min' + _alias.definition_id '_diffrn_reflns_limit_k_min' + _name.category_id diffrn_reflns + _name.object_id limit_k_min + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_diffrn_reflns.limit_l_max + + _definition.id '_diffrn_reflns.limit_l_max' + _alias.definition_id '_diffrn_reflns_limit_l_max' + _name.category_id diffrn_reflns + _name.object_id limit_l_max + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_diffrn_reflns.limit_l_min + + _definition.id '_diffrn_reflns.limit_l_min' + _alias.definition_id '_diffrn_reflns_limit_l_min' + _name.category_id diffrn_reflns + _name.object_id limit_l_min + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_diffrn_reflns.limit_max + + _definition.id '_diffrn_reflns.limit_max' + _definition.update 2023-01-06 _description.text ; - The structure factor amplitude for the reflection derived from the - measured intensities. + Maximum Miller indices of measured diffraction reflections. ; - _name.category_id refln - _name.object_id F_squared_meas - _type.purpose Measurand - _type.source Derived - _type.container Single - _type.contents Real - _method.purpose Definition + _name.category_id diffrn_reflns + _name.object_id limit_max + _type.purpose Number + _type.source Assigned + _type.container Matrix + _type.dimension '[3]' + _type.contents Integer + _units.code none + _method.purpose Evaluation _method.expression ; - If (_diffrn_radiation.probe == "neutron") - _units.code = "femtometre_squared" - Else If (_diffrn_radiation.probe == "electron") - _units.code = "volt_squared" - Else _units.code = "electron_squared" + With t as diffrn_reflns + + _diffrn_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] ; save_ -save_refln.f_squared_meas_su - - _definition.id '_refln.F_squared_meas_su' - - loop_ - _alias.definition_id - '_refln_F_squared_sigma' - '_refln.F_squared_sigma' - '_refln_F_squared_meas_su' +save_diffrn_reflns.limit_min - _definition.update 2021-03-03 + _definition.id '_diffrn_reflns.limit_min' + _definition.update 2023-01-06 _description.text -; - Standard uncertainty of the measured structure factor squared. -; - _name.category_id refln - _name.object_id F_squared_meas_su - _name.linked_item_id '_refln.F_squared_meas' - _type.purpose SU - _type.source Related - _type.container Single - _type.contents Real - _method.purpose Definition +; + Minimum Miller indices of measured diffraction reflections. +; + _name.category_id diffrn_reflns + _name.object_id limit_min + _type.purpose Number + _type.source Assigned + _type.container Matrix + _type.dimension '[3]' + _type.contents Integer + _units.code none + _method.purpose Evaluation _method.expression ; - If (_diffrn_radiation.probe == "neutron") - _units.code = "femtometre_squared" - Else If (_diffrn_radiation.probe == "electron") - _units.code = "volt_squared" - Else _units.code = "electron_squared" + With t as diffrn_reflns + + _diffrn_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] ; save_ -save_refln.fom +save_diffrn_reflns.number - _definition.id '_refln.fom' + _definition.id '_diffrn_reflns.number' + _alias.definition_id '_diffrn_reflns_number' _definition.update 2021-03-01 _description.text ; - The figure of merit m for this reflection. - - int P~alpha~ exp(i*alpha) dalpha - m = -------------------------------- - int P~alpha~ dalpha - - P~a~ = the probability that the phase angle a is correct - - int is taken over the range alpha = 0 to 2 pi. + Total number of measured intensities, excluding reflections that are + classed as systematically absent arising from translational symmetry + in the crystal unit cell. ; - _name.category_id refln - _name.object_id fom + _name.category_id diffrn_reflns + _name.object_id number _type.purpose Number _type.source Derived _type.container Single - _type.contents Real + _type.contents Integer + _enumeration.range 0: _units.code none save_ -save_refln.form_factor_table +save_diffrn_reflns.point_measured_fraction_full - _definition.id '_refln.form_factor_table' - _definition.update 2021-07-20 + _definition.id '_diffrn_reflns.point_measured_fraction_full' + _alias.definition_id + '_diffrn_reflns_point_group_measured_fraction_full' + _definition.update 2013-01-20 _description.text ; - Atomic scattering factor table for the scattering angle - of this diffraction vector and atom types in structure. + Fraction of crystal point-group unique reflections (i.e. + symmetry-independent in the crystal point group) measured + out to the resolution given in _diffrn_reflns.resolution_full + or _diffrn_reflns.theta_full. For space groups that do not + contain a centre of symmetry the reflections h,k,l and + -h,-k,-l are independent. This number should not be less + than 0.95, since it represents the fraction of reflections + measured in the part of the diffraction pattern that is + essentially complete. ; - _name.category_id refln - _name.object_id form_factor_table + _name.category_id diffrn_reflns + _name.object_id point_measured_fraction_full _type.purpose Number _type.source Derived - _type.container Table + _type.container Single _type.contents Real + _enumeration.range 0.95:1.0 _units.code none - _method.purpose Evaluation - _method.expression -; - 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.hkl +save_diffrn_reflns.point_measured_fraction_max - _definition.id '_refln.hkl' - _definition.update 2021-03-01 + _definition.id '_diffrn_reflns.point_measured_fraction_max' + _alias.definition_id + '_diffrn_reflns_point_group_measured_fraction_max' + _definition.update 2013-01-20 _description.text ; - The Miller indices as a reciprocal space vector. + Fraction of crystal point-group unique reflections (i.e. + symmetry-independent in the crystal point group) measured + out to the resolution given in _diffrn_reflns.resolution_max + or _diffrn_reflns.theta_max. For space groups that do not + contain a centre of symmetry the reflections h,k,l and + -h,-k,-l are independent. ; - _name.category_id refln - _name.object_id hkl + _name.category_id diffrn_reflns + _name.object_id point_measured_fraction_max _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer + _type.container Single + _type.contents Real + _enumeration.range 0:1.0 _units.code none - _method.purpose Evaluation - _method.expression -; - With r as refln - - _refln.hkl = [r.index_h, r.index_k, r.index_l] -; save_ -save_refln.include_status - - _definition.id '_refln.include_status' - - loop_ - _alias.definition_id - '_refln_include_status' - '_refln_observed_status' - '_refln.observed_status' - '_refln.status' +save_diffrn_reflns.reduction_process - _definition.update 2023-01-13 + _definition.id '_diffrn_reflns.reduction_process' + _alias.definition_id '_diffrn_reflns_reduction_process' + _definition.update 2012-11-26 _description.text ; - Code indicating how the reflection was included in the refinement - and R-factor calculations. + How intensities were reduced to structure-factor magnitudes. ; - _name.category_id refln - _name.object_id include_status - _type.purpose State - _type.source Assigned + _name.category_id diffrn_reflns + _name.object_id reduction_process + _type.purpose Describe + _type.source Recorded _type.container Single _type.contents Text - - loop_ - _enumeration_set.state - _enumeration_set.detail - o 'ob : within _reflns.threshold_expression; within d-res limits.' - < 'lt : without _reflns.threshold_expression; within d-res limits.' - - 'sa : systematically absent reflection due to symmetry.' - x 'du : deemed unreliable measurement -- not used.' - h 'hd : above _refine_ls.d_res_high.' - l 'ld : below _refine_ls.d_res_low.' + _description_example.case 'data averaged using Fisher test' save_ -save_refln.index_h - - _definition.id '_refln.index_h' - _alias.definition_id '_refln_index_h' - _name.category_id refln - _name.object_id index_h +save_diffrn_reflns.resolution_full - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _definition.id '_diffrn_reflns.resolution_full' + _alias.definition_id '_diffrn_reflns_resolution_full' + _definition.update 2012-11-26 + _description.text +; + The resolution at which the measured reflection count is close + to complete. The fraction of unique reflections measured out + to this angle is given by _diffrn.measured_fraction_theta_full. +; + _name.category_id diffrn_reflns + _name.object_id resolution_full + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms save_ -save_refln.index_k - - _definition.id '_refln.index_k' - _alias.definition_id '_refln_index_k' - _name.category_id refln - _name.object_id index_k +save_diffrn_reflns.resolution_max - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _definition.id '_diffrn_reflns.resolution_max' + _alias.definition_id '_diffrn_reflns_resolution_max' + _definition.update 2013-02-22 + _description.text +; + Maximum resolution of the measured diffraction pattern. + The fraction of unique reflections measured out to this angle + is given by _diffrn.measured_fraction_theta_max. +; + _name.category_id diffrn_reflns + _name.object_id resolution_max + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms save_ -save_refln.index_l +save_diffrn_reflns.theta_full - _definition.id '_refln.index_l' - _alias.definition_id '_refln_index_l' - _name.category_id refln - _name.object_id index_l + _definition.id '_diffrn_reflns.theta_full' + _alias.definition_id '_diffrn_reflns_theta_full' + _definition.update 2023-01-13 + _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.measured_fraction_theta_full. +; + _name.category_id diffrn_reflns + _name.object_id theta_full + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees - _import.get [{'file':templ_attr.cif 'save':Miller_index}] +save_ + +save_diffrn_reflns.theta_max + + _definition.id '_diffrn_reflns.theta_max' + _alias.definition_id '_diffrn_reflns_theta_max' + _definition.update 2012-11-26 + _description.text +; + Maximum theta angle of the measured reflections. +; + _name.category_id diffrn_reflns + _name.object_id theta_max + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_refln.intensity_calc +save_diffrn_reflns.theta_min - _definition.id '_refln.intensity_calc' - _alias.definition_id '_refln_intensity_calc' + _definition.id '_diffrn_reflns.theta_min' + _alias.definition_id '_diffrn_reflns_theta_min' _definition.update 2012-11-26 _description.text ; - The intensity of the reflection calculated from the atom site data. + Minimum theta angle of the measured reflections. ; - _name.category_id refln - _name.object_id intensity_calc - _type.purpose Measurand - _type.source Derived + _name.category_id diffrn_reflns + _name.object_id theta_min + _type.purpose Number + _type.source Recorded _type.container Single _type.contents Real - _enumeration.range 0.: - _units.code none - _method.purpose Evaluation - _method.expression -; - _refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor -; + _enumeration.range 0.0:90.0 + _units.code degrees save_ -save_refln.intensity_calc_su +save_DIFFRN_REFLNS_CLASS - _definition.id '_refln.intensity_calc_su' - _definition.update 2021-09-23 + _definition.id DIFFRN_REFLNS_CLASS + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Standard uncertainty of _refln.intensity_calc. + The CATEGORY of data items which specify different classes of + reflections in the raw measured diffraction data. ; - _name.category_id refln - _name.object_id intensity_calc_su - _name.linked_item_id '_refln.intensity_calc' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id DIFFRN_REFLNS + _name.object_id DIFFRN_REFLNS_CLASS + _category_key.name '_diffrn_reflns_class.code' save_ -save_refln.intensity_meas +save_diffrn_reflns_class.av_r_eq - _definition.id '_refln.intensity_meas' - _alias.definition_id '_refln_intensity_meas' - _definition.update 2013-04-11 + _definition.id '_diffrn_reflns_class.av_R_eq' + _alias.definition_id '_diffrn_reflns_class_av_R_eq' + _definition.update 2012-11-26 _description.text ; - The intensity of the reflection derived from the diffraction measurements. + 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. ; - _name.category_id refln - _name.object_id intensity_meas - _type.purpose Measurand - _type.source Recorded + _name.category_id diffrn_reflns_class + _name.object_id av_R_eq + _type.purpose Number + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.: + _enumeration.range 0.0: _units.code none save_ -save_refln.intensity_meas_su +save_diffrn_reflns_class.av_sui_over_i - _definition.id '_refln.intensity_meas_su' + _definition.id '_diffrn_reflns_class.av_suI_over_I' loop_ _alias.definition_id - '_refln_intensity_meas_su' - '_refln.intensity_sigma' - '_refln_intensity_sigma' + '_diffrn_reflns_class_av_uI_over_I' + '_diffrn_reflns_class.av_uI/I' + '_diffrn_reflns_class_av_uI/I' + '_diffrn_reflns_class.av_sgI/I' + '_diffrn_reflns_class_av_sgI/I' - _definition.update 2021-03-03 + _definition.update 2014-07-22 _description.text ; - Standard uncertainty of the measured intensity. + Recorded [sum|su(net I)|/sum|net I|] in a reflection class. ; - _name.category_id refln - _name.object_id intensity_meas_su - _name.linked_item_id '_refln.intensity_meas' - _type.purpose SU - _type.source Related + _name.category_id diffrn_reflns_class + _name.object_id av_suI_over_I + _type.purpose Number + _type.source Derived _type.container Single _type.contents Real + _enumeration.range 0.0: _units.code none save_ -save_refln.lp_factor +save_diffrn_reflns_class.code - _definition.id '_refln.Lp_factor' - _alias.definition_id '_refln_Lp_factor' + _definition.id '_diffrn_reflns_class.code' + _alias.definition_id '_diffrn_reflns_class_code' + _definition.update 2021-10-27 + _description.text +; + Code identifying a reflection class. +; + _name.category_id diffrn_reflns_class + _name.object_id code + _type.purpose Encode + _type.source Assigned + _type.container Single + _type.contents Word + _description_example.case m2 + +save_ + +save_diffrn_reflns_class.d_res_high + + _definition.id '_diffrn_reflns_class.d_res_high' + _alias.definition_id '_diffrn_reflns_class_d_res_high' _definition.update 2012-11-26 _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. + Highest resolution in reflection class i.e. smallest d value in class. ; - _name.category_id refln - _name.object_id Lp_factor + _name.category_id diffrn_reflns_class + _name.object_id d_res_high _type.purpose Number - _type.source Recorded + _type.source Assigned _type.container Single _type.contents Real - _enumeration.range 0.: - _units.code none + _enumeration.range 0.0: + _units.code angstroms save_ -save_refln.mean_path_length_tbar +save_diffrn_reflns_class.d_res_low - _definition.id '_refln.mean_path_length_tbar' - _alias.definition_id '_refln_mean_path_length_tbar' + _definition.id '_diffrn_reflns_class.d_res_low' + _alias.definition_id '_diffrn_reflns_class_d_res_low' _definition.update 2012-11-26 _description.text ; - Mean path length through the crystal for this diffraction vector. + Lowest resolution in reflection class i.e. largest d value in class. ; - _name.category_id refln - _name.object_id mean_path_length_tbar + _name.category_id diffrn_reflns_class + _name.object_id d_res_low _type.purpose Number - _type.source Recorded + _type.source Assigned _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code millimetres + _units.code angstroms + +save_ + +save_diffrn_reflns_class.description + + _definition.id '_diffrn_reflns_class.description' + _alias.definition_id '_diffrn_reflns_class_description' + _definition.update 2012-11-26 + _description.text +; + Description of a reflection class. +; + _name.category_id diffrn_reflns_class + _name.object_id description + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text + _description_example.case 'm=1 first order satellites' + +save_ + +save_diffrn_reflns_class.number + + _definition.id '_diffrn_reflns_class.number' + _alias.definition_id '_diffrn_reflns_class_number' + _definition.update 2021-03-01 + _description.text +; + Number of measured intensities for a reflection class, excluding + the systematic absences arising from centring translations. +; + _name.category_id diffrn_reflns_class + _name.object_id number + _type.purpose Number + _type.source Derived + _type.container Single + _type.contents Integer + _enumeration.range 0: + _units.code none + +save_ + +save_DIFFRN_REFLNS_TRANSF_MATRIX + + _definition.id DIFFRN_REFLNS_TRANSF_MATRIX + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _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| +; + _name.category_id DIFFRN_REFLNS + _name.object_id DIFFRN_REFLNS_TRANSF_MATRIX + +save_ + +save_diffrn_reflns_transf_matrix.11 + + _definition.id '_diffrn_reflns_transf_matrix.11' + + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_11' + '_diffrn_reflns.transf_matrix[1][1]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 11 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] + +save_ + +save_diffrn_reflns_transf_matrix.12 + + _definition.id '_diffrn_reflns_transf_matrix.12' + + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_12' + '_diffrn_reflns.transf_matrix[1][2]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 12 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] + +save_ + +save_diffrn_reflns_transf_matrix.13 + + _definition.id '_diffrn_reflns_transf_matrix.13' -save_ + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_13' + '_diffrn_reflns.transf_matrix[1][3]' -save_refln.phase_calc + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 13 - _definition.id '_refln.phase_calc' - _alias.definition_id '_refln_phase_calc' - _definition.update 2013-04-27 - _description.text -; - The phase of the calculated structure-factor. -; - _name.category_id refln - _name.object_id phase_calc - _type.purpose Measurand - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.:360. - _units.code degrees - _method.purpose Evaluation - _method.expression -; - phase = Atan2d ( _refln.B_calc, _refln.A_calc ) - If(phase < 0.) _refln.phase_calc = phase + 360. - Else _refln.phase_calc = phase -; + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.phase_calc_su +save_diffrn_reflns_transf_matrix.21 - _definition.id '_refln.phase_calc_su' - _definition.update 2021-09-23 - _description.text -; - Standard uncertainty of _refln.phase_calc. -; - _name.category_id refln - _name.object_id phase_calc_su - _name.linked_item_id '_refln.phase_calc' - _units.code degrees + _definition.id '_diffrn_reflns_transf_matrix.21' - _import.get [{'file':templ_attr.cif 'save':general_su}] + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_21' + '_diffrn_reflns.transf_matrix[2][1]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 21 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.phase_meas +save_diffrn_reflns_transf_matrix.22 - _definition.id '_refln.phase_meas' - _alias.definition_id '_refln_phase_meas' - _definition.update 2012-11-26 - _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. -; - _name.category_id refln - _name.object_id phase_meas - _type.purpose Measurand - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.:360. - _units.code degrees + _definition.id '_diffrn_reflns_transf_matrix.22' + + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_22' + '_diffrn_reflns.transf_matrix[2][2]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 22 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.phase_meas_su +save_diffrn_reflns_transf_matrix.23 - _definition.id '_refln.phase_meas_su' - _definition.update 2021-09-23 - _description.text -; - Standard uncertainty of _refln.phase_meas. -; - _name.category_id refln - _name.object_id phase_meas_su - _name.linked_item_id '_refln.phase_meas' - _units.code degrees + _definition.id '_diffrn_reflns_transf_matrix.23' - _import.get [{'file':templ_attr.cif 'save':general_su}] + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_23' + '_diffrn_reflns.transf_matrix[2][3]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 23 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.refinement_status +save_diffrn_reflns_transf_matrix.31 - _definition.id '_refln.refinement_status' - _alias.definition_id '_refln_refinement_status' - _definition.update 2012-11-26 - _description.text -; - Status code of reflection in the structure refinement process. -; - _name.category_id refln - _name.object_id refinement_status - _type.purpose State - _type.source Assigned - _type.container Single - _type.contents Text + _definition.id '_diffrn_reflns_transf_matrix.31' loop_ - _enumeration_set.state - _enumeration_set.detail - incl 'Included in ls process.' - excl 'Excluded from ls process.' - extn 'Excluded due to extinction.' + _alias.definition_id + '_diffrn_reflns_transf_matrix_31' + '_diffrn_reflns.transf_matrix[3][1]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 31 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.scale_group_code +save_diffrn_reflns_transf_matrix.32 - _definition.id '_refln.scale_group_code' - _alias.definition_id '_refln_scale_group_code' - _definition.update 2021-11-04 - _description.text -; - Code identifying the scale (if there is more than one scale) used - convert the measured structure factor to a common absolute value. -; - _name.category_id refln - _name.object_id scale_group_code - _name.linked_item_id '_reflns_scale.group_code' - _type.purpose Link - _type.source Related - _type.container Single - _type.contents Word + _definition.id '_diffrn_reflns_transf_matrix.32' + + loop_ + _alias.definition_id + '_diffrn_reflns_transf_matrix_32' + '_diffrn_reflns.transf_matrix[3][2]' + + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 32 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] save_ -save_refln.sin_theta_over_lambda +save_diffrn_reflns_transf_matrix.33 - _definition.id '_refln.sin_theta_over_lambda' + _definition.id '_diffrn_reflns_transf_matrix.33' loop_ _alias.definition_id - '_refln_sint/lambda' - '_refln_sin_theta_over_lambda' - '_refln.sint_over_lambda' + '_diffrn_reflns_transf_matrix_33' + '_diffrn_reflns.transf_matrix[3][3]' - _definition.update 2013-03-07 + _name.category_id diffrn_reflns_transf_matrix + _name.object_id 33 + + _import.get + [{'file':templ_attr.cif 'save':transf_matrix}] + +save_ + +save_diffrn_reflns_transf_matrix.tij + + _definition.id '_diffrn_reflns_transf_matrix.TIJ' + _definition.update 2021-03-01 _description.text ; - The (sin theta)/lambda value for this reflection. + 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| ; - _name.category_id refln - _name.object_id sin_theta_over_lambda + _name.category_id diffrn_reflns_transf_matrix + _name.object_id TIJ _type.purpose Number _type.source Derived - _type.container Single + _type.container Matrix + _type.dimension '[3,3]' _type.contents Real - _enumeration.range 0.0: - _units.code reciprocal_angstroms + _units.code none _method.purpose Evaluation _method.expression ; - With r as refln - h = r.hkl - G = _cell.reciprocal_metric_tensor + With t as diffrn_reflns_transf_matrix - r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2. + _diffrn_reflns_transf_matrix.TIJ = [[t.11, t.12, t.13], + [t.21, t.22, t.23], + [t.31, t.32, t.33]] ; save_ -save_refln.symmetry_epsilon +save_DIFFRN_SCALE_GROUP - _definition.id '_refln.symmetry_epsilon' - _alias.definition_id '_refln_symmetry_epsilon' - _definition.update 2021-03-01 + _definition.id DIFFRN_SCALE_GROUP + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - The symmetry reinforcement factor corresponding to the number of - times the reflection indices are generated identically from the - space-group symmetry operations. + The CATEGORY of data items which specify the groups of reflections in + the raw measured diffraction data with different relative scales. ; - _name.category_id refln - _name.object_id symmetry_epsilon - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Integer - _enumeration.range 1:48 - _units.code none + _name.category_id DIFFRN + _name.object_id DIFFRN_SCALE_GROUP + _category_key.name '_diffrn_scale_group.code' save_ -save_refln.symmetry_multiplicity +save_diffrn_scale_group.code - _definition.id '_refln.symmetry_multiplicity' - _alias.definition_id '_refln_symmetry_multiplicity' - _definition.update 2021-03-01 + _definition.id '_diffrn_scale_group.code' + _alias.definition_id '_diffrn_scale_group_code' + _definition.update 2021-10-27 _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. + Code identifying a specific scale group of reflections (e.g. for + multi-film or multi-crystal data). The code must match a + _diffrn_refln.scale_group_code in the DIFFRN_REFLN list. ; - _name.category_id refln - _name.object_id symmetry_multiplicity - _type.purpose Number + _name.category_id diffrn_scale_group + _name.object_id code + _type.purpose Encode _type.source Assigned _type.container Single - _type.contents Integer - _enumeration.range 1:48 - _units.code none + _type.contents Word + + loop_ + _description_example.case + 1 + 2 + 3 + s1 + A + B + c1 + c2 + c3 save_ -save_refln.wavelength +save_diffrn_scale_group.i_net - _definition.id '_refln.wavelength' - _alias.definition_id '_refln_wavelength' - _definition.update 2012-11-26 + _definition.id '_diffrn_scale_group.I_net' + _alias.definition_id '_diffrn_scale_group_I_net' + _definition.update 2021-03-03 _description.text ; - The mean wavelength in angstroms of radiation used to measure - this reflection. This is an important parameter for data - collected using energy-dispersive detectors or the Laue method. + Scale for a specific measurement group of reflections. Is multiplied + with the net intensity to place all intensities on a common scale. ; - _name.category_id refln - _name.object_id wavelength - _type.purpose Number - _type.source Assigned + _name.category_id diffrn_scale_group + _name.object_id I_net + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code angstroms + _units.code none save_ -save_refln.wavelength_id +save_diffrn_scale_group.i_net_su - _definition.id '_refln.wavelength_id' - _alias.definition_id '_refln_wavelength_id' - _definition.update 2021-10-27 + _definition.id '_diffrn_scale_group.I_net_su' + _definition.update 2021-09-23 _description.text ; - Code identifying the wavelength in DIFFRN_RADIATION_WAVELENGTH list. + Standard uncertainty of _diffrn_scale_group.I_net. ; - _name.category_id refln - _name.object_id wavelength_id - _name.linked_item_id '_diffrn_radiation_wavelength.id' - _type.purpose Link - _type.source Related - _type.container Single - _type.contents Word + _name.category_id diffrn_scale_group + _name.object_id I_net_su + _name.linked_item_id '_diffrn_scale_group.I_net' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_REFLNS +save_DIFFRN_SOURCE - _definition.id REFLNS + _definition.id DIFFRN_SOURCE _definition.scope Category _definition.class Set _definition.update 2012-11-26 _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 similar measures to those defined in the - DIFFRN categories, but differ in that the parameters refer to the - reduced/transformed reflections which have been used to refine the - atom site data in the ATOM_SITE category. The DIFFRN definitions refer - to the diffraction measurements and the raw reflection data. + The CATEGORY of data items which specify information about the + radiation source. ; - _name.category_id DIFFRACTION - _name.object_id REFLNS + _name.category_id DIFFRN + _name.object_id DIFFRN_SOURCE save_ -save_reflns.apply_dispersion_to_fcalc +save_diffrn_source.beamline - _definition.id '_reflns.apply_dispersion_to_Fcalc' - _definition.update 2019-01-09 + _definition.id '_diffrn_source.beamline' + _definition.update 2021-03-01 _description.text ; - Yes or No flag on whether the anomalous dispersion scattering - components will be applied in the F complex calculation. - See _refln.F_complex + The name of the beamline at the synchrotron or other + large-scale experimental facility at which the experiment + was conducted. ; - _name.category_id reflns - _name.object_id apply_dispersion_to_Fcalc - _type.purpose State - _type.source Assigned + _name.category_id diffrn_source + _name.object_id beamline + _type.purpose Describe + _type.source Recorded _type.container Single _type.contents Text - - loop_ - _enumeration_set.state - _enumeration_set.detail - yes 'Apply dispersion.' - y 'Abbreviation for "yes".' - no 'Do not apply dispersion.' - n 'Abbreviation for "no".' + _description_example.case I19 save_ -save_reflns.d_resolution_high +save_diffrn_source.current - _definition.id '_reflns.d_resolution_high' - _alias.definition_id '_reflns_d_resolution_high' - _definition.update 2021-03-03 + _definition.id '_diffrn_source.current' + _alias.definition_id '_diffrn_source_current' + _definition.update 2012-11-26 _description.text ; - Highest resolution for the final REFLN data set. - This corresponds to the smallest interplanar d value. + Generator current at which the radiation source device was operated. ; - _name.category_id reflns - _name.object_id d_resolution_high + _name.category_id diffrn_source + _name.object_id current _type.purpose Number - _type.source Derived + _type.source Assigned _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code angstroms + _units.code milliamperes save_ -save_reflns.d_resolution_low +save_diffrn_source.description - _definition.id '_reflns.d_resolution_low' - _alias.definition_id '_reflns_d_resolution_low' - _definition.update 2021-03-03 + _definition.id '_diffrn_source.description' + + loop_ + _definition_replaced.id + _definition_replaced.by + 1 '_diffrn_source.device' + 2 '_diffrn_source.details' + + loop_ + _alias.definition_id + '_diffrn_source' + '_diffrn_radiation_source' + '_diffrn_source.source' + + _definition.update 2023-01-16 _description.text ; - Lowest resolution for the final REFLN data set. - This corresponds to the largest interplanar d value. + The general class of the source of radiation. This is deprecated. + Use _diffrn_source.device and _diffrn_source.details. ; - _name.category_id reflns - _name.object_id d_resolution_low - _type.purpose Number - _type.source Derived + _name.category_id diffrn_source + _name.object_id description + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _type.contents Text save_ -save_reflns.friedel_coverage +save_diffrn_source.details - _definition.id '_reflns.Friedel_coverage' - _alias.definition_id '_reflns_Friedel_coverage' - _definition.update 2019-01-09 + _definition.id '_diffrn_source.details' + _alias.definition_id '_diffrn_source_details' + _definition.update 2021-08-18 _description.text ; - The proportion of Friedel related reflections present in the number of - the 'independent reflections' specified by the item _reflns.number_total. + A description of special aspects of the source not covered by + other data items. +; + _name.category_id diffrn_source + _name.object_id details + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text - This proportion is calculated as the ratio: +save_ - [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) +save_diffrn_source.device - where, working from the DIFFRN_REFLN list, + _definition.id '_diffrn_source.device' + _definition.update 2018-02-26 + _description.text +; + Enumerated code for the device providing the source of radiation. +; + _name.category_id diffrn_source + _name.object_id device + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text - 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. + loop_ + _enumeration_set.state + _enumeration_set.detail + tube 'Sealed X-ray tube.' + nuclear 'Nuclear reactor.' + spallation 'Spallation source.' + elect-micro 'Electron microscope.' + rot_anode 'Rotating-anode X-ray tube.' + synch 'Synchrotron.' - (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. +save_ + +save_diffrn_source.facility + + _definition.id '_diffrn_source.facility' + _definition.update 2020-09-18 + _description.text ; - _name.category_id reflns - _name.object_id Friedel_coverage - _type.purpose Number + The name of the synchrotron or other large-scale + experimental facility at which the experiment was + conducted. Names should conform to the spelling and + format used in the 'Light Sources of the World' listing + of lightsources.org + (https://lightsources.org/lightsources-of-the-world/) +; + _name.category_id diffrn_source + _name.object_id facility + _type.purpose Describe _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none + _type.contents Text + _description_example.case 'Diamond Light Source' save_ -save_reflns.friedel_fraction_full +save_diffrn_source.make - _definition.id '_reflns.Friedel_fraction_full' - _alias.definition_id '_reflns_Friedel_fraction_full' - _definition.update 2013-01-20 + _definition.id '_diffrn_source.make' + + loop_ + _alias.definition_id + '_diffrn_source_make' + '_diffrn_source.type' + '_diffrn_source_type' + + _definition.update 2021-07-26 _description.text ; - The ratio of Friedel pairs measured to _diffrn_reflns.theta_full - to the number theoretically possible (ignoring reflections in - centric projections and systematic absences throughout). - In contrast to _reflns.Friedel_coverage this can take values in - the full range 0 to 1 for any non-centrosymmetric space group, - and so one can see at a glance how completely the Friedel pairs - have been measured. For centrosymmetric space groups the value - would be given as not-applicable '.' + Description of the make, model or name of the source device. + Large scale facilities should use _diffrn_source.facility and + _diffrn_source.beamline to identify the source of radiation. ; - _name.category_id reflns - _name.object_id Friedel_fraction_full - _type.purpose Number - _type.source Derived + _name.category_id diffrn_source + _name.object_id make + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none + _type.contents Text + _description_example.case 'Rigaku RU2012-05-07' save_ -save_reflns.friedel_fraction_max +save_diffrn_source.power - _definition.id '_reflns.Friedel_fraction_max' - _alias.definition_id '_reflns_Friedel_fraction_max' - _definition.update 2013-01-20 + _definition.id '_diffrn_source.power' + _alias.definition_id '_diffrn_source_power' + _definition.update 2012-11-26 _description.text ; - The ratio of Friedel pairs measured to _diffrn_reflns.theta_max - to the number theoretically possible (ignoring reflections in - centric projections and systematic absences throughout). - In contrast to _reflns.Friedel_coverage this can take values in - the full range 0 to 1 for any non-centrosymmetric space group, - and so one can see at a glance how completely the Friedel pairs - have been measured. For centrosymmetric space groups the value - would be given as not-applicable '.' + Generator power at which the radiation source device was operated. ; - _name.category_id reflns - _name.object_id Friedel_fraction_max + _name.category_id diffrn_source + _name.object_id power _type.purpose Number - _type.source Derived + _type.source Assigned _type.container Single _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none - -save_ - -save_reflns.limit_h_max - - _definition.id '_reflns.limit_h_max' - _alias.definition_id '_reflns_limit_h_max' - _name.category_id reflns - _name.object_id limit_h_max - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] - -save_ - -save_reflns.limit_h_min - - _definition.id '_reflns.limit_h_min' - _alias.definition_id '_reflns_limit_h_min' - _name.category_id reflns - _name.object_id limit_h_min - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] - -save_ - -save_reflns.limit_k_max - - _definition.id '_reflns.limit_k_max' - _alias.definition_id '_reflns_limit_k_max' - _name.category_id reflns - _name.object_id limit_k_max - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _enumeration.range 0.0: + _units.code kilowatts save_ -save_reflns.limit_k_min +save_diffrn_source.size - _definition.id '_reflns.limit_k_min' - _alias.definition_id '_reflns_limit_k_min' - _name.category_id reflns - _name.object_id limit_k_min + _definition.id '_diffrn_source.size' + _alias.definition_id '_diffrn_source_size' + _definition.update 2012-11-26 + _description.text +; + Description of the collimated source beam as viewed from the sample. +; + _name.category_id diffrn_source + _name.object_id size + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + loop_ + _description_example.case + '8mm x 0.4 mm fine-focus' + 'broad focus' save_ -save_reflns.limit_l_max - - _definition.id '_reflns.limit_l_max' - _alias.definition_id '_reflns_limit_l_max' - _name.category_id reflns - _name.object_id limit_l_max - - _import.get [{'file':templ_attr.cif 'save':Miller_index}] - -save_ +save_diffrn_source.take_off_angle -save_reflns.limit_l_min + _definition.id '_diffrn_source.take_off_angle' - _definition.id '_reflns.limit_l_min' - _alias.definition_id '_reflns_limit_l_min' - _name.category_id reflns - _name.object_id limit_l_min + loop_ + _alias.definition_id + '_diffrn_source_take-off_angle' + '_diffrn_source.take-off_angle' - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _definition.update 2013-02-22 + _description.text +; + The complement of the angle in degrees between the normal + to the surface of the X-ray tube target and the primary + X-ray beam for beams generated by traditional X-ray tubes. +; + _name.category_id diffrn_source + _name.object_id take_off_angle + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0:90 + _units.code degrees save_ -save_reflns.limit_max +save_diffrn_source.target - _definition.id '_reflns.limit_max' - _definition.update 2013-01-15 + _definition.id '_diffrn_source.target' + _alias.definition_id '_diffrn_source_target' + _definition.update 2021-10-27 _description.text ; - Maximum Miller indices of refined diffraction reflections. + Chemical element symbol for the radiation source target (usually + the anode). This can be used also for spallation sources. ; - _name.category_id reflns - _name.object_id limit_max - _type.purpose Number + _name.category_id diffrn_source + _name.object_id target + _type.purpose State _type.source Assigned - _type.container Matrix - _type.dimension '[3]' - _type.contents Real - _units.code none - _method.purpose Evaluation - _method.expression -; - With t as reflns + _type.container Single + _type.contents Word - _reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] -; + _import.get + [{'file':templ_enum.cif 'save':element_symbol}] save_ -save_reflns.limit_min +save_diffrn_source.voltage - _definition.id '_reflns.limit_min' - _definition.update 2013-01-15 + _definition.id '_diffrn_source.voltage' + _alias.definition_id '_diffrn_source_voltage' + _definition.update 2012-11-26 _description.text ; - Minimum Miller indices of refined diffraction reflections. + Generator voltage at which the radiation source device was operated. ; - _name.category_id reflns - _name.object_id limit_min + _name.category_id diffrn_source + _name.object_id voltage _type.purpose Number _type.source Assigned - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer - _units.code none - _method.purpose Evaluation - _method.expression -; - With t as reflns - - _reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] -; + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code kilovolts save_ -save_reflns.number_gt - - _definition.id '_reflns.number_gt' - - loop_ - _alias.definition_id - '_reflns_number_gt' - '_reflns_number_observed' - '_reflns_number_obs' - '_reflns.number_obs' +save_DIFFRN_STANDARDS - _definition.update 2023-01-13 + _definition.id DIFFRN_STANDARDS + _definition.scope Category + _definition.class Set + _definition.update 2023-01-10 _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 on the nature of the structure and the procedures used. + The CATEGORY of data items which specify information about the + standard reflections used in the diffraction measurement process. ; - _name.category_id reflns - _name.object_id number_gt - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _name.category_id DIFFRN + _name.object_id DIFFRN_STANDARDS save_ -save_reflns.number_total +save_diffrn_standards.decay_percent - _definition.id '_reflns.number_total' + _definition.id '_diffrn_standards.decay_percent' loop_ _alias.definition_id - '_reflns_number_total' - '_reflns_number_all' - '_reflns.number_all' + '_diffrn_standards_decay_%' + '_diffrn_standards.decay_%' + '_diffrn_standards_decay_percent' _definition.update 2023-01-13 _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 on the nature of the structure and the procedures used. + The percentage decrease in the mean of the intensities for the + standard reflections at the start to the finish of the measurement + process. This value affords a measure of the overall decay in + crystal quality during measurement. Negative values only occur in + exceptional instances where the final intensities are greater than + the initial ones. If no measurable decay has occurred, the + standard uncertainty should be quoted to indicate the maximum + possible value the decay might have. A range of 3 standard + uncertainties is considered possible. Thus 0.0(1) would indicate + a decay of less than 0.3% or an enhancement of less than 0.3%. ; - _name.category_id reflns - _name.object_id number_total - _type.purpose Number - _type.source Recorded + _name.category_id diffrn_standards + _name.object_id decay_percent + _type.purpose Measurand + _type.source Derived _type.container Single - _type.contents Integer - _enumeration.range 0: + _type.contents Real + _enumeration.range :100 _units.code none -save_ - -save_reflns.special_details + loop_ + _description_example.case + _description_example.detail + 0.5(1) 'Represents a decay between 0.2% and 0.8%.' + -1(1) 'Change in standards between 2% decay and 4% rise.' + 0.0(2) 'Change in standards between 0.6% decay and 0.6% rise.' - _definition.id '_reflns.special_details' +save_ - loop_ - _alias.definition_id - '_reflns_special_details' - '_reflns.details' +save_diffrn_standards.decay_percent_su - _definition.update 2012-11-26 + _definition.id '_diffrn_standards.decay_percent_su' + _definition.update 2023-01-10 _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. + Standard uncertainty of _diffrn_standards.decay_percent. ; - _name.category_id reflns - _name.object_id special_details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - -save_ + _name.category_id diffrn_standards + _name.object_id decay_percent_su + _name.linked_item_id '_diffrn_standards.decay_percent' + _units.code none -save_reflns.threshold_expression + _import.get [{'file':templ_attr.cif 'save':general_su}] - _definition.id '_reflns.threshold_expression' +save_ - loop_ - _alias.definition_id - '_reflns_threshold_expression' - '_reflns_observed_criterion' - '_reflns.observed_criterion' +save_diffrn_standards.interval_count - _definition.update 2012-11-26 + _definition.id '_diffrn_standards.interval_count' + _alias.definition_id '_diffrn_standards_interval_count' + _definition.update 2023-01-10 _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. + Reflection count between the standard reflection measurements. ; - _name.category_id reflns - _name.object_id threshold_expression - _type.purpose Describe - _type.source Recorded + _name.category_id diffrn_standards + _name.object_id interval_count + _type.purpose Number + _type.source Assigned _type.container Single - _type.contents Text - _description_example.case I>2u(I) + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_REFLNS_CLASS +save_diffrn_standards.interval_time - _definition.id REFLNS_CLASS - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_diffrn_standards.interval_time' + _alias.definition_id '_diffrn_standards_interval_time' + _definition.update 2023-01-10 _description.text ; - The CATEGORY of data items which specify the properties of reflections - in specific classes of reflections. + Time between the standard reflection measurements. ; - _name.category_id REFLNS - _name.object_id REFLNS_CLASS - _category_key.name '_reflns_class.code' + _name.category_id diffrn_standards + _name.object_id interval_time + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Real + _enumeration.range 0.: + _units.code minutes save_ -save_reflns_class.code +save_diffrn_standards.number - _definition.id '_reflns_class.code' - _alias.definition_id '_reflns_class_code' - _definition.update 2021-10-27 + _definition.id '_diffrn_standards.number' + _alias.definition_id '_diffrn_standards_number' + _definition.update 2023-01-10 _description.text ; - Code identifying a reflection class. + Number of unique standard reflections used in measurements. ; - _name.category_id reflns_class - _name.object_id code - _type.purpose Encode + _name.category_id diffrn_standards + _name.object_id number + _type.purpose Number _type.source Assigned _type.container Single - _type.contents Word - _description_example.case c1 + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_reflns_class.d_res_high +save_diffrn_standards.scale_su_average - _definition.id '_reflns_class.d_res_high' - _alias.definition_id '_reflns_class_d_res_high' - _definition.update 2021-03-03 + _definition.id '_diffrn_standards.scale_su_average' + + loop_ + _alias.definition_id + '_diffrn_standards_scale_sigma' + '_diffrn_standards.scale_sigma' + '_diffrn_standards.scale_u' + '_diffrn_standards_scale_u' + + _definition.update 2023-01-10 _description.text ; - Highest resolution for the reflections in this class. - This corresponds to the smallest interplanar d value. + The average standard uncertainty of the individual standard scales + applied to the intensity data. ; - _name.category_id reflns_class - _name.object_id d_res_high - _type.purpose Number - _type.source Assigned + _name.category_id diffrn_standards + _name.object_id scale_su_average + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code angstroms + _units.code none save_ -save_reflns_class.d_res_low +save_diffrn_standards.scale_su_average_su - _definition.id '_reflns_class.d_res_low' - _alias.definition_id '_reflns_class_d_res_low' - _definition.update 2021-03-03 + _definition.id '_diffrn_standards.scale_su_average_su' + _definition.update 2021-09-23 _description.text ; - Lowest resolution for the reflections in this class. - This corresponds to the largest interplanar d value. + Standard uncertainty of _diffrn_standards.scale_su_average. ; - _name.category_id reflns_class - _name.object_id d_res_low - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _name.category_id diffrn_standards + _name.object_id scale_su_average_su + _name.linked_item_id '_diffrn_standards.scale_su_average' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_reflns_class.description +save_DIFFRN_STANDARD_REFLN - _definition.id '_reflns_class.description' - _alias.definition_id '_reflns_class_description' - _definition.update 2012-11-26 + _definition.id DIFFRN_STANDARD_REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Description of a reflection class. + 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. ; - _name.category_id reflns_class - _name.object_id description - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text - _description_example.case 'H0L0 common projection reflections' + _name.category_id DIFFRN_STANDARDS + _name.object_id DIFFRN_STANDARD_REFLN + + loop_ + _category_key.name + '_diffrn_standard_refln.index_h' + '_diffrn_standard_refln.index_k' + '_diffrn_standard_refln.index_l' save_ -save_reflns_class.number_gt +save_diffrn_standard_refln.code - _definition.id '_reflns_class.number_gt' + _definition.id '_diffrn_standard_refln.code' loop_ _alias.definition_id - '_reflns_class_number_observed' - '_reflns_class_number_gt' + '_diffrn_standard_refln_code' + '_diffrn_standard_refln.diffrn_id' - _definition.update 2023-01-13 + _definition.update 2021-10-27 _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 on the nature of the structure and the procedures used. + Code identifying a standard reflection used to monitor source + intensity variations or crystal degradation or movement during + data collection. ; - _name.category_id reflns_class - _name.object_id number_gt - _type.purpose Number - _type.source Recorded + _name.category_id diffrn_standard_refln + _name.object_id code + _type.purpose Encode + _type.source Assigned _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _type.contents Word + _description_example.case s1 save_ -save_reflns_class.number_total +save_diffrn_standard_refln.hkl - _definition.id '_reflns_class.number_total' - _alias.definition_id '_reflns_class_number_total' - _definition.update 2023-01-13 + _definition.id '_diffrn_standard_refln.hkl' + _definition.update 2021-03-01 _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 on the nature of the structure and the procedures used. + Miller indices of a standard reflection. ; - _name.category_id reflns_class - _name.object_id number_total + _name.category_id diffrn_standard_refln + _name.object_id hkl _type.purpose Number - _type.source Recorded - _type.container Single + _type.source Derived + _type.container Matrix + _type.dimension '[3]' _type.contents Integer - _enumeration.range 0: _units.code none - -save_ - -save_reflns_class.r_factor_all - - _definition.id '_reflns_class.R_factor_all' - _alias.definition_id '_reflns_class_R_factor_all' - _definition.update 2012-11-26 - _description.text + _method.purpose Evaluation + _method.expression ; - Residual factor for reflections in this class used in refinement. - - sum | F(meas) - F(calc) | - R(F all) = ------------------------ - sum | F(meas) | - - F(meas) = the measured structure-factor amplitudes - F(calc) = the calculated structure-factor amplitudes + With d as diffrn_standard_refln - and the sum is taken over the specified reflections + _diffrn_standard_refln.hkl = [d.index_h, d.index_h, d.index_l] ; - _name.category_id reflns_class - _name.object_id R_factor_all - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none save_ -save_reflns_class.r_factor_gt +save_diffrn_standard_refln.index_h - _definition.id '_reflns_class.R_factor_gt' + _definition.id '_diffrn_standard_refln.index_h' + _alias.definition_id '_diffrn_standard_refln_index_h' + _name.category_id diffrn_standard_refln + _name.object_id index_h - loop_ - _alias.definition_id - '_reflns_class_R_factor_gt' - '_reflns_class_R_factor_observed' + _import.get [{'file':templ_attr.cif 'save':Miller_index}] - _definition.update 2012-11-26 - _description.text -; - Residual factor for the reflections in this class judged - significantly intense (i.e. greater than required by the - _reflns.threshold_expression) and included in the refinement. +save_ - sum | F(meas_gt) - F(calc) | - R(F gt) = -------------------------------- - sum | F(meas_gt) | +save_diffrn_standard_refln.index_k - F(meas) = the measured structure-factor amplitudes - F(calc) = the calculated structure-factor amplitudes + _definition.id '_diffrn_standard_refln.index_k' + _alias.definition_id '_diffrn_standard_refln_index_k' + _name.category_id diffrn_standard_refln + _name.object_id index_k - and the sum is taken over the specified reflections -; - _name.category_id reflns_class - _name.object_id R_factor_gt - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_reflns_class.r_fsqd_factor - - _definition.id '_reflns_class.R_Fsqd_factor' - _alias.definition_id '_reflns_class_R_Fsqd_factor' - _definition.update 2012-11-26 - _description.text -; - Residual factor R(F^2^) for reflections in this class judged - significantly intense (i.e. greater than required by the - _reflns.threshold_expression) and included in the refinement. - - sum | F(meas_gt)^2^ - F(calc)^2^ | - R(Fsqd gt) = ------------------------------------ - sum F(meas_gt)^2^ +save_diffrn_standard_refln.index_l - F(meas_gt)^2^ = square of the 'observed' structure-factor - F(calc )^2^ = square of the calculated structure-factor + _definition.id '_diffrn_standard_refln.index_l' + _alias.definition_id '_diffrn_standard_refln_index_l' + _name.category_id diffrn_standard_refln + _name.object_id index_l - and the sum is taken over the specified reflections -; - _name.category_id reflns_class - _name.object_id R_Fsqd_factor - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_reflns_class.r_i_factor +save_REFLN - _definition.id '_reflns_class.R_I_factor' - _alias.definition_id '_reflns_class_R_I_factor' - _definition.update 2012-11-26 + _definition.id REFLN + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Residual factor R(I) for reflections in this class judged - significantly intense (i.e. greater than required by the - _reflns.threshold_expression) and included in the refinement. - - sum | I(meas_gt) - I(calc) | - R(I gt) = ---------------------------- - sum | I(meas_gt) | - - I(meas_gt) = the net 'observed' intensity - I(calc ) = the net calculated intensity - - and the sum is taken over the specified reflections + The CATEGORY of data items used to describe the reflection data + used in the refinement of a crystallographic structure model. ; - _name.category_id reflns_class - _name.object_id R_I_factor - _type.purpose Number - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _name.category_id DIFFRACTION + _name.object_id REFLN + + loop_ + _category_key.name + '_refln.index_h' + '_refln.index_k' + '_refln.index_l' save_ -save_reflns_class.wr_factor_all +save_refln.a_calc - _definition.id '_reflns_class.wR_factor_all' - _alias.definition_id '_reflns_class_wR_factor_all' + _definition.id '_refln.A_calc' + _alias.definition_id '_refln_A_calc' _definition.update 2012-11-26 _description.text ; - For each reflection class, the weighted residual factors for all - reflections included in the refinement. The reflections also - satisfy the resolution limits established by - _reflns_class.d_res_high and _reflns_class.d_res_low. - - ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ - wR = ( ------------------------------- ) - ( sum w Y(meas)^2^ ) - - Y(meas) = the measured amplitudes specified by - _refine_ls.structure_factor_coef - Y(calc) = the calculated amplitudes specified by - _refine_ls.structure_factor_coef - w = the least-squares weights - - and the sum is taken over the reflections of this class. + The calculated real structure-factor component A =|Fcalc|cos(phase) ; - _name.category_id reflns_class - _name.object_id wR_factor_all - _type.purpose Number + _name.category_id refln + _name.object_id A_calc + _type.purpose Measurand _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code none + + 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.A_calc = Real ( _refln.F_complex ) +; save_ -save_REFLNS_SCALE +save_refln.a_calc_su - _definition.id REFLNS_SCALE - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_refln.A_calc_su' + _definition.update 2021-09-23 _description.text ; - The CATEGORY of data items which specify the scales needed to place - measured structure factor coefficients on the same absolute scale. + Standard uncertainty of _refln.A_calc. ; - _name.category_id REFLNS - _name.object_id REFLNS_SCALE - _category_key.name '_reflns_scale.group_code' - -save_ + _name.category_id refln + _name.object_id A_calc_su + _name.linked_item_id '_refln.A_calc' -save_reflns_scale.group_code + _import.get [{'file':templ_attr.cif 'save':general_su}] - _definition.id '_reflns_scale.group_code' - _alias.definition_id '_reflns_scale_group_code' - _definition.update 2021-11-04 - _description.text + _method.purpose Definition + _method.expression ; - Code identifying a reflection scale group. These names need not - correspond to _diffrn_scale_group.code names. + If (_diffrn_radiation.probe == "neutron") _units.code = + "femtometres" Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts" Else + _units.code = "electrons" ; - _name.category_id reflns_scale - _name.object_id group_code - _type.purpose Encode - _type.source Assigned - _type.container Single - _type.contents Word save_ -save_reflns_scale.meas_f +save_refln.a_meas - _definition.id '_reflns_scale.meas_F' - _alias.definition_id '_reflns_scale_meas_F' + _definition.id '_refln.A_meas' + _alias.definition_id '_refln_A_meas' _definition.update 2012-11-26 _description.text ; - Structure factor scale for this scale group. + The measured real structure-factor component A =|Fmeas|cos(phase) ; - _name.category_id reflns_scale - _name.object_id meas_F + _name.category_id refln + _name.object_id A_meas _type.purpose Measurand _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code none + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; save_ -save_reflns_scale.meas_f_su +save_refln.a_meas_su - _definition.id '_reflns_scale.meas_F_su' + _definition.id '_refln.A_meas_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _reflns_scale.meas_F. + Standard uncertainty of _refln.A_meas. ; - _name.category_id reflns_scale - _name.object_id meas_F_su - _name.linked_item_id '_reflns_scale.meas_F' - _units.code none + _name.category_id refln + _name.object_id A_meas_su + _name.linked_item_id '_refln.A_meas' _import.get [{'file':templ_attr.cif 'save':general_su}] + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ -save_reflns_scale.meas_f_squared +save_refln.b_calc - _definition.id '_reflns_scale.meas_F_squared' - _alias.definition_id '_reflns_scale_meas_F_squared' + _definition.id '_refln.B_calc' + _alias.definition_id '_refln_B_calc' _definition.update 2012-11-26 _description.text ; - Structure factor squared scale for this scale group. + The calculated imaginary structure-factor component B =|Fcalc|sin(phase) ; - _name.category_id reflns_scale - _name.object_id meas_F_squared + _name.category_id refln + _name.object_id B_calc _type.purpose Measurand _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code none + + 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.B_calc = Imag ( _refln.F_complex ) +; save_ -save_reflns_scale.meas_f_squared_su +save_refln.b_calc_su - _definition.id '_reflns_scale.meas_F_squared_su' + _definition.id '_refln.B_calc_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _reflns_scale.meas_F_squared. + Standard uncertainty of _refln.B_calc. ; - _name.category_id reflns_scale - _name.object_id meas_F_squared_su - _name.linked_item_id '_reflns_scale.meas_F_squared' - _units.code none + _name.category_id refln + _name.object_id B_calc_su + _name.linked_item_id '_refln.B_calc' _import.get [{'file':templ_attr.cif 'save':general_su}] + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = + "femtometres" Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts" Else + _units.code = "electrons" +; + save_ -save_reflns_scale.meas_intensity +save_refln.b_meas - _definition.id '_reflns_scale.meas_intensity' - _alias.definition_id '_reflns_scale_meas_intensity' + _definition.id '_refln.B_meas' + _alias.definition_id '_refln_B_meas' _definition.update 2012-11-26 _description.text ; - Net intensity scale for this scale group. + The measured imaginary structure-factor component B =|Fmeas|sin(phase) ; - _name.category_id reflns_scale - _name.object_id meas_intensity + _name.category_id refln + _name.object_id B_meas _type.purpose Measurand _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: - _units.code none + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; save_ -save_reflns_scale.meas_intensity_su +save_refln.b_meas_su - _definition.id '_reflns_scale.meas_intensity_su' + _definition.id '_refln.B_meas_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _reflns_scale.meas_intensity. + Standard uncertainty of _refln.B_meas. ; - _name.category_id reflns_scale - _name.object_id meas_intensity_su - _name.linked_item_id '_reflns_scale.meas_intensity' - _units.code none + _name.category_id refln + _name.object_id B_meas_su + _name.linked_item_id '_refln.B_meas' _import.get [{'file':templ_attr.cif 'save':general_su}] + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; + save_ -save_REFLNS_SHELL +save_refln.class_code - _definition.id REFLNS_SHELL - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_refln.class_code' + _alias.definition_id '_refln_class_code' + _definition.update 2021-10-27 _description.text ; - The CATEGORY of data items which specify the information about - reflections divided into shells bounded by d resolution limits. + Code identifying the class to which this reflection has been + assigned. This code must match a value of _reflns_class.code. + Reflections may be grouped into classes for a variety of + purposes. For example, for modulated structures each reflection + class may be defined by the number m=sum|m~i~|, where the m~i~ + are the integer coefficients that, in addition to h,k,l, index + the corresponding diffraction vector in the basis defined + for the reciprocal lattice. ; - _name.category_id REFLNS - _name.object_id REFLNS_SHELL - - loop_ - _category_key.name - '_reflns_shell.d_res_low' - '_reflns_shell.d_res_high' + _name.category_id refln + _name.object_id class_code + _name.linked_item_id '_reflns_class.code' + _type.purpose Link + _type.source Related + _type.container Single + _type.contents Word save_ -save_reflns_shell.d_res_high +save_refln.d_spacing - _definition.id '_reflns_shell.d_res_high' - _alias.definition_id '_reflns_shell_d_res_high' - _definition.update 2021-03-03 + _definition.id '_refln.d_spacing' + _alias.definition_id '_refln_d_spacing' + _definition.update 2012-11-26 _description.text ; - Highest resolution for the reflections in this shell. - This corresponds to the smallest interplanar d value. + The distance in angstroms between lattice planes in the crystal + with the indices _refln.hkl for this reflection. ; - _name.category_id reflns_shell - _name.object_id d_res_high + _name.category_id refln + _name.object_id d_spacing _type.purpose Number - _type.source Assigned + _type.source Derived _type.container Single _type.contents Real _enumeration.range 0.0: _units.code angstroms + _method.purpose Evaluation + _method.expression +; + _refln.d_spacing = 1 / (2 * _refln.sin_theta_over_lambda) +; save_ -save_reflns_shell.d_res_limits +save_refln.f_calc - _definition.id '_reflns_shell.d_res_limits' - _definition.update 2012-11-26 + _definition.id '_refln.F_calc' + _alias.definition_id '_refln_F_calc' + _definition.update 2013-02-21 _description.text ; - Resolution for the reflections in this shell stored as - the list of lowest and highest values. This is the - category key. + The structure factor amplitude for the reflection calculated from + the atom site data. ; - _name.category_id reflns_shell - _name.object_id d_res_limits - _type.purpose Number + _name.category_id refln + _name.object_id F_calc + _type.purpose Measurand _type.source Derived - _type.container List - _type.dimension '[2]' + _type.container Single _type.contents Real - _units.code angstroms - _method.purpose Evaluation - _method.expression -; - With s as reflns_shell - _reflns_shell.d_res_limits = [ s.d_res_low, s.d_res_high ] + 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_reflns_shell.d_res_low +save_refln.f_calc_su - _definition.id '_reflns_shell.d_res_low' - _alias.definition_id '_reflns_shell_d_res_low' - _definition.update 2021-03-03 + _definition.id '_refln.F_calc_su' + _definition.update 2021-09-23 _description.text ; - Lowest resolution for the reflections in this shell. - This corresponds to the largest interplanar d value. + Standard uncertainty of _refln.F_calc. +; + _name.category_id refln + _name.object_id F_calc_su + _name.linked_item_id '_refln.F_calc' + + _import.get [{'file':templ_attr.cif 'save':general_su}] + + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = + "femtometres" Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts" Else + _units.code = "electrons" ; - _name.category_id reflns_shell - _name.object_id d_res_low - _type.purpose Number - _type.source Assigned - _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms save_ -save_reflns_shell.meani_over_sui_all - - _definition.id '_reflns_shell.meanI_over_suI_all' - - loop_ - _alias.definition_id - '_reflns_shell_meanI_over_uI_all' - '_reflns_shell_meanI_over_sigI_all' - '_reflns_shell.meanI_over_sigI_all' - '_reflns_shell.meanI_over_uI_all' +save_refln.f_complex - _definition.update 2012-11-26 + _definition.id '_refln.F_complex' + _alias.definition_id '_refln_F_complex' + _definition.update 2016-05-13 _description.text ; - Ratio of the mean intensity in a shell to the mean standard uncertainty - of the intensities in the shell. + The structure factor vector for the reflection calculated from + the atom site data. ; - _name.category_id reflns_shell - _name.object_id meanI_over_suI_all - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_complex + _type.purpose Measurand + _type.source Derived _type.container Single - _type.contents Real - _enumeration.range 0: - _units.code none + _type.contents Complex -save_ + 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 -save_reflns_shell.meani_over_sui_gt + fc = Complex (0., 0.) + h = r.hkl - _definition.id '_reflns_shell.meanI_over_suI_gt' + Loop a as atom_site { - loop_ - _alias.definition_id - '_reflns_shell_meanI_over_sigI_obs' - '_reflns_shell.meanI_over_sigI_obs' - '_reflns_shell.meanI_over_sigI_gt' - '_reflns_shell_meanI_over_sigI_gt' - '_reflns_shell.meanI_over_uI_gt' - '_reflns_shell_meanI_over_uI_gt' + f = a.site_symmetry_multiplicity * a.occupancy * ( + r.form_factor_table [a.type_symbol] + + _atom_type_scat[a.type_symbol].dispersion ) - _definition.update 2012-11-26 - _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. + Loop s as space_group_symop { + + t = Exp(-h * s.R * a.tensor_beta * s.RT * h) + + fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T))) + } } + _refln.F_complex = fc / _space_group.multiplicity ; - _name.category_id reflns_shell - _name.object_id meanI_over_suI_gt - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0: - _units.code none save_ -save_reflns_shell.number_measured_all +save_refln.f_complex_su - _definition.id '_reflns_shell.number_measured_all' - _alias.definition_id '_reflns_shell_number_measured_all' - _definition.update 2021-03-01 + _definition.id '_refln.F_complex_su' + _definition.update 2021-09-23 _description.text ; - Total count of reflections measured for this resolution shell. + Standard uncertainty of _refln.F_complex. ; - _name.category_id reflns_shell - _name.object_id number_measured_all - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _name.category_id refln + _name.object_id F_complex_su + _name.linked_item_id '_refln.F_complex' -save_ + _import.get [{'file':templ_attr.cif 'save':general_su}] -save_reflns_shell.number_measured_gt + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = + "femtometres" Else If (_diffrn_radiation.probe == "electron") + _units.code = "volts" Else + _units.code = "electrons" +; - _definition.id '_reflns_shell.number_measured_gt' +save_ - loop_ - _alias.definition_id - '_reflns_shell_number_measured_obs' - '_reflns_shell.number_measured_obs' - '_reflns_shell_number_measured_gt' +save_refln.f_meas - _definition.update 2021-03-01 + _definition.id '_refln.F_meas' + _alias.definition_id '_refln_F_meas' + _definition.update 2013-02-21 _description.text ; - Number of reflections measured for this resolution shell which are - significantly intense (see _reflns.threshold_expression). + The structure factor amplitude for the reflection derived from the + measured intensities. ; - _name.category_id reflns_shell - _name.object_id number_measured_gt - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_meas + _type.purpose Measurand + _type.source Derived _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _type.contents Real + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; save_ -save_reflns_shell.number_possible +save_refln.f_meas_su - _definition.id '_reflns_shell.number_possible' + _definition.id '_refln.F_meas_su' loop_ _alias.definition_id - '_reflns_shell_number_possible' - '_reflns_shell.number_possible_all' + '_refln_F_sigma' + '_refln.F_meas_sigma' + '_refln_F_meas_su' - _definition.update 2021-03-01 + _definition.update 2021-03-03 _description.text ; - Count of symmetry-unique reflections possible in this reflection shell. + Standard uncertainty of the measured structure factor amplitude. ; - _name.category_id reflns_shell - _name.object_id number_possible - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_meas_su + _name.linked_item_id '_refln.F_meas' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _type.contents Real + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres" + Else If (_diffrn_radiation.probe == "electron") _units.code = "volts" + Else _units.code = "electrons" +; save_ -save_reflns_shell.number_unique_all +save_refln.f_squared_calc - _definition.id '_reflns_shell.number_unique_all' - _alias.definition_id '_reflns_shell_number_unique_all' - _definition.update 2021-03-01 + _definition.id '_refln.F_squared_calc' + _alias.definition_id '_refln_F_squared_calc' + _definition.update 2012-11-26 _description.text ; - Count of symmetry-unique reflections present in this reflection shell. + The structure factor amplitude squared for the reflection calculated from + the atom site data. ; - _name.category_id reflns_shell - _name.object_id number_unique_all - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_squared_calc + _type.purpose Measurand + _type.source Derived _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none + _type.contents Real + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometre_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volt_squared" + Else _units.code = "electron_squared" +; save_ -save_reflns_shell.number_unique_gt +save_refln.f_squared_calc_su - _definition.id '_reflns_shell.number_unique_gt' + _definition.id '_refln.F_squared_calc_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _refln.F_squared_calc. +; + _name.category_id refln + _name.object_id F_squared_calc_su + _name.linked_item_id '_refln.F_squared_calc' - loop_ - _alias.definition_id - '_reflns_shell_number_unique_gt' - '_reflns_shell_number_unique_obs' - '_reflns_shell.number_unique_obs' + _import.get [{'file':templ_attr.cif 'save':general_su}] - _definition.update 2021-03-01 - _description.text + _method.purpose Definition + _method.expression ; - Number of symmetry-unique reflections present in this reflection shell - which are significantly intense (see _reflns.threshold_expression). + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometre_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volt_squared" + Else _units.code = "electron_squared" ; - _name.category_id reflns_shell - _name.object_id number_unique_gt - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Integer - _enumeration.range 0: - _units.code none save_ -save_reflns_shell.percent_possible_all - - _definition.id '_reflns_shell.percent_possible_all' - _alias.definition_id '_reflns_shell_percent_possible_all' - _definition.update 2012-11-26 +save_refln.f_squared_meas + + _definition.id '_refln.F_squared_meas' + _alias.definition_id '_refln_F_squared_meas' + _definition.update 2013-02-21 _description.text ; - Percentage of reflections present in this shell over that possible. + The structure factor amplitude for the reflection derived from the + measured intensities. ; - _name.category_id reflns_shell - _name.object_id percent_possible_all - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_squared_meas + _type.purpose Measurand + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0:100.0 - _units.code none + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometre_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volt_squared" + Else _units.code = "electron_squared" +; save_ -save_reflns_shell.percent_possible_gt +save_refln.f_squared_meas_su - _definition.id '_reflns_shell.percent_possible_gt' + _definition.id '_refln.F_squared_meas_su' loop_ _alias.definition_id - '_reflns_shell_percent_possible_gt' - '_reflns_shell_percent_possible_obs' - '_reflns_shell.percent_possible_obs' + '_refln_F_squared_sigma' + '_refln.F_squared_sigma' + '_refln_F_squared_meas_su' - _definition.update 2012-11-26 + _definition.update 2021-03-03 _description.text ; - Percentage of reflections present in this shell which are significantly - intense (see _reflns.threshold_expression), over that possible. + Standard uncertainty of the measured structure factor squared. ; - _name.category_id reflns_shell - _name.object_id percent_possible_gt - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id F_squared_meas_su + _name.linked_item_id '_refln.F_squared_meas' + _type.purpose SU + _type.source Related _type.container Single _type.contents Real - _enumeration.range 0.0:100.0 - _units.code none + _method.purpose Definition + _method.expression +; + If (_diffrn_radiation.probe == "neutron") + _units.code = "femtometre_squared" + Else If (_diffrn_radiation.probe == "electron") + _units.code = "volt_squared" + Else _units.code = "electron_squared" +; save_ -save_reflns_shell.rmerge_f_all +save_refln.fom - _definition.id '_reflns_shell.Rmerge_F_all' - _alias.definition_id '_reflns_shell_Rmerge_F_all' - _definition.update 2012-11-26 + _definition.id '_refln.fom' + _definition.update 2021-03-01 _description.text ; - Rmerge(F) for all reflections in a given shell. + The figure of merit m for this reflection. - sum~i~ ( sum~j~ | F~j~ - | ) - Rmerge(F) = -------------------------------- - sum~i~ ( sum~j~ ) + int P~alpha~ exp(i*alpha) dalpha + m = -------------------------------- + int P~alpha~ dalpha - F~j~ = the amplitude of the jth observation of reflection i - = the mean of the amplitudes of all observations of - reflection i + P~a~ = the probability that the phase angle a is correct - sum~i~ is taken over all reflections - sum~j~ is taken over all observations of each reflection. + int is taken over the range alpha = 0 to 2 pi. ; - _name.category_id reflns_shell - _name.object_id Rmerge_F_all + _name.category_id refln + _name.object_id fom _type.purpose Number - _type.source Recorded + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0: _units.code none save_ -save_reflns_shell.rmerge_f_gt - - _definition.id '_reflns_shell.Rmerge_F_gt' - - loop_ - _alias.definition_id - '_reflns_shell_Rmerge_F_obs' - '_reflns_shell.Rmerge_F_obs' - '_reflns_shell_Rmerge_F_gt' +save_refln.form_factor_table - _definition.update 2012-11-26 + _definition.id '_refln.form_factor_table' + _definition.update 2021-07-20 _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. + Atomic scattering factor table for the scattering angle + of this diffraction vector and atom types in structure. ; - _name.category_id reflns_shell - _name.object_id Rmerge_F_gt + _name.category_id refln + _name.object_id form_factor_table _type.purpose Number - _type.source Recorded - _type.container Single + _type.source Derived + _type.container Table _type.contents Real - _enumeration.range 0.0: _units.code none + _method.purpose Evaluation + _method.expression +; + With r as refln -save_ + table = Table () + s = r.sin_theta_over_lambda -save_reflns_shell.rmerge_i_all + Loop t as atom_type { - _definition.id '_reflns_shell.Rmerge_I_all' - _alias.definition_id '_reflns_shell_Rmerge_I_all' - _definition.update 2012-11-26 - _description.text + 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 ; - Rmerge(I) for all reflections in a given shell. - sum~i~ ( sum~j~ | I~j~ - | ) - Rmerge(I) = -------------------------------- - sum~i~ ( sum~j~ ) +save_ - I~j~ = the intensity of the jth observation of reflection i - = the mean of the intensities of all observations of - reflection i +save_refln.hkl - sum~i~ is taken over all reflections - sum~j~ is taken over all observations of each reflection. + _definition.id '_refln.hkl' + _definition.update 2021-03-01 + _description.text ; - _name.category_id reflns_shell - _name.object_id Rmerge_I_all + The Miller indices as a reciprocal space vector. +; + _name.category_id refln + _name.object_id hkl _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0: + _type.source Derived + _type.container Matrix + _type.dimension '[3]' + _type.contents Integer _units.code none + _method.purpose Evaluation + _method.expression +; + With r as refln + + _refln.hkl = [r.index_h, r.index_k, r.index_l] +; save_ -save_reflns_shell.rmerge_i_gt +save_refln.include_status - _definition.id '_reflns_shell.Rmerge_I_gt' + _definition.id '_refln.include_status' loop_ _alias.definition_id - '_reflns_shell_Rmerge_I_obs' - '_reflns_shell.Rmerge_I_obs' - '_reflns_shell_Rmerge_I_gt' + '_refln_include_status' + '_refln_observed_status' + '_refln.observed_status' + '_refln.status' - _definition.update 2012-11-26 + _definition.update 2023-01-13 _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. + Code indicating how the reflection was included in the refinement + and R-factor calculations. ; - _name.category_id reflns_shell - _name.object_id Rmerge_I_gt - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id include_status + _type.purpose State + _type.source Assigned _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code none + _type.contents Text + + loop_ + _enumeration_set.state + _enumeration_set.detail + o 'ob : within _reflns.threshold_expression; within d-res limits.' + < 'lt : without _reflns.threshold_expression; within d-res limits.' + - 'sa : systematically absent reflection due to symmetry.' + x 'du : deemed unreliable measurement -- not used.' + h 'hd : above _refine_ls.d_res_high.' + l 'ld : below _refine_ls.d_res_low.' save_ -save_EXPTL +save_refln.index_h - _definition.id EXPTL - _definition.scope Category - _definition.class Set - _definition.update 2023-01-13 - _description.text -; - The CATEGORY of data items used to specify the experimental work - prior to diffraction measurements. These include crystallization - crystal measurements and absorption-correction techniques used. -; - _name.category_id CIF_CORE - _name.object_id EXPTL + _definition.id '_refln.index_h' + _alias.definition_id '_refln_index_h' + _name.category_id refln + _name.object_id index_h + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_refln.index_k + + _definition.id '_refln.index_k' + _alias.definition_id '_refln_index_k' + _name.category_id refln + _name.object_id index_k + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_exptl.crystals_number +save_refln.index_l - _definition.id '_exptl.crystals_number' - _alias.definition_id '_exptl_crystals_number' - _definition.update 2021-03-01 + _definition.id '_refln.index_l' + _alias.definition_id '_refln_index_l' + _name.category_id refln + _name.object_id index_l + + _import.get [{'file':templ_attr.cif 'save':Miller_index}] + +save_ + +save_refln.intensity_calc + + _definition.id '_refln.intensity_calc' + _alias.definition_id '_refln_intensity_calc' + _definition.update 2012-11-26 _description.text ; - Total number of crystals used in the measurement of intensities. + The intensity of the reflection calculated from the atom site data. ; - _name.category_id exptl - _name.object_id crystals_number - _type.purpose Number - _type.source Recorded + _name.category_id refln + _name.object_id intensity_calc + _type.purpose Measurand + _type.source Derived _type.container Single - _type.contents Integer - _enumeration.range 1: + _type.contents Real + _enumeration.range 0.: _units.code none + _method.purpose Evaluation + _method.expression +; + _refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor +; save_ -save_exptl.method +save_refln.intensity_calc_su - _definition.id '_exptl.method' - _definition.update 2014-06-12 + _definition.id '_refln.intensity_calc_su' + _definition.update 2021-09-23 _description.text ; - The method used in the experiment. + Standard uncertainty of _refln.intensity_calc. ; - _name.category_id exptl - _name.object_id method - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _name.category_id refln + _name.object_id intensity_calc_su + _name.linked_item_id '_refln.intensity_calc' + _units.code none - loop_ - _description_example.case - 'single-crystal x-ray diffraction' - 'single-crystal neutron diffraction' - 'single-crystal electron diffraction' - 'fiber x-ray diffraction' - 'fiber neutron diffraction' - 'fiber electron diffraction' - 'single-crystal joint x-ray and neutron diffraction' - 'single-crystal joint x-ray and electron diffraction' - 'solution nmr' - 'solid-state nmr' - 'theoretical model' - 'other' + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_exptl.method_details +save_refln.intensity_meas - _definition.id '_exptl.method_details' - _definition.update 2014-06-12 + _definition.id '_refln.intensity_meas' + _alias.definition_id '_refln_intensity_meas' + _definition.update 2013-04-11 _description.text ; - A description of special aspects of the experimental method. + The intensity of the reflection derived from the diffraction measurements. ; - _name.category_id exptl - _name.object_id method_details - _type.purpose Describe + _name.category_id refln + _name.object_id intensity_meas + _type.purpose Measurand _type.source Recorded _type.container Single - _type.contents Text - - loop_ - _description_example.case - '29 structures' - 'minimized average structure' + _type.contents Real + _enumeration.range 0.: + _units.code none save_ -save_exptl.special_details +save_refln.intensity_meas_su - _definition.id '_exptl.special_details' + _definition.id '_refln.intensity_meas_su' loop_ _alias.definition_id - '_exptl_special_details' - '_exptl.details' + '_refln_intensity_meas_su' + '_refln.intensity_sigma' + '_refln_intensity_sigma' - _definition.update 2012-11-22 + _definition.update 2021-03-03 _description.text ; - Details of the experiment prior to intensity measurement. - See also _exptl_crystal.preparation + Standard uncertainty of the measured intensity. ; - _name.category_id exptl - _name.object_id special_details - _type.purpose Describe - _type.source Recorded + _name.category_id refln + _name.object_id intensity_meas_su + _name.linked_item_id '_refln.intensity_meas' + _type.purpose SU + _type.source Related _type.container Single - _type.contents Text + _type.contents Real + _units.code none save_ -save_exptl.transmission_factor_max +save_refln.lp_factor - _definition.id '_exptl.transmission_factor_max' - _alias.definition_id '_exptl_transmission_factor_max' - _definition.update 2013-04-11 + _definition.id '_refln.Lp_factor' + _alias.definition_id '_refln_Lp_factor' + _definition.update 2012-11-26 _description.text ; - The calculated maximum value of the transmission factor for - the specimen. Its value does not include the effects of - absorption in the specimen mount. The presence of this - item does not imply that the structure factors have been - corrected for absorption. For the applied correction see - _exptl_absorpt.correction_T_max. + 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. ; - _name.category_id exptl - _name.object_id transmission_factor_max - _type.purpose Measurand - _type.source Derived + _name.category_id refln + _name.object_id Lp_factor + _type.purpose Number + _type.source Recorded _type.container Single _type.contents Real - _enumeration.range 0.0:1.0 + _enumeration.range 0.: _units.code none save_ -save_exptl.transmission_factor_max_su +save_refln.mean_path_length_tbar - _definition.id '_exptl.transmission_factor_max_su' - _definition.update 2021-09-23 + _definition.id '_refln.mean_path_length_tbar' + _alias.definition_id '_refln_mean_path_length_tbar' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _exptl.transmission_factor_max. + Mean path length through the crystal for this diffraction vector. ; - _name.category_id exptl - _name.object_id transmission_factor_max_su - _name.linked_item_id '_exptl.transmission_factor_max' - _units.code none - - _import.get [{'file':templ_attr.cif 'save':general_su}] + _name.category_id refln + _name.object_id mean_path_length_tbar + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code millimetres save_ -save_exptl.transmission_factor_min +save_refln.phase_calc - _definition.id '_exptl.transmission_factor_min' - _alias.definition_id '_exptl_transmission_factor_min' - _definition.update 2013-04-11 + _definition.id '_refln.phase_calc' + _alias.definition_id '_refln_phase_calc' + _definition.update 2013-04-27 _description.text ; - The calculated minimum value of the transmission factor for - the specimen. Its value does not include the effects of - absorption in the specimen mount. The presence of this - item does not imply that the structure factors have been - corrected for absorption. For the applied correction see - _exptl_absorpt.correction_T_min. + The phase of the calculated structure-factor. ; - _name.category_id exptl - _name.object_id transmission_factor_min + _name.category_id refln + _name.object_id phase_calc _type.purpose Measurand _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0:1.0 - _units.code none + _enumeration.range 0.:360. + _units.code degrees + _method.purpose Evaluation + _method.expression +; + phase = Atan2d ( _refln.B_calc, _refln.A_calc ) + If(phase < 0.) _refln.phase_calc = phase + 360. + Else _refln.phase_calc = phase +; save_ -save_exptl.transmission_factor_min_su +save_refln.phase_calc_su - _definition.id '_exptl.transmission_factor_min_su' + _definition.id '_refln.phase_calc_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _exptl.transmission_factor_min. + Standard uncertainty of _refln.phase_calc. ; - _name.category_id exptl - _name.object_id transmission_factor_min_su - _name.linked_item_id '_exptl.transmission_factor_min' - _units.code none + _name.category_id refln + _name.object_id phase_calc_su + _name.linked_item_id '_refln.phase_calc' + _units.code degrees _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_CELL +save_refln.phase_meas - _definition.id CELL - _definition.scope Category - _definition.class Set - _definition.update 2012-11-22 + _definition.id '_refln.phase_meas' + _alias.definition_id '_refln_phase_meas' + _definition.update 2012-11-26 _description.text ; - The CATEGORY of data items used to describe the parameters of - the crystal unit cell and their measurement. + 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. ; - _name.category_id EXPTL - _name.object_id CELL + _name.category_id refln + _name.object_id phase_meas + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.:360. + _units.code degrees save_ -save_cell.angle_alpha +save_refln.phase_meas_su - _definition.id '_cell.angle_alpha' - _alias.definition_id '_cell_angle_alpha' - _name.category_id cell - _name.object_id angle_alpha + _definition.id '_refln.phase_meas_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _refln.phase_meas. +; + _name.category_id refln + _name.object_id phase_meas_su + _name.linked_item_id '_refln.phase_meas' + _units.code degrees - _import.get [{'file':templ_attr.cif 'save':cell_angle}] + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_cell.angle_alpha_su +save_refln.refinement_status - _definition.id '_cell.angle_alpha_su' + _definition.id '_refln.refinement_status' + _alias.definition_id '_refln_refinement_status' + _definition.update 2012-11-26 + _description.text +; + Status code of reflection in the structure refinement process. +; + _name.category_id refln + _name.object_id refinement_status + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text loop_ - _alias.definition_id - '_cell_angle_alpha_su' - '_cell.angle_alpha_esd' - - _name.category_id cell - _name.object_id angle_alpha_su - _name.linked_item_id '_cell.angle_alpha' - - _import.get - [{'file':templ_attr.cif 'save':cell_angle_su}] + _enumeration_set.state + _enumeration_set.detail + incl 'Included in ls process.' + excl 'Excluded from ls process.' + extn 'Excluded due to extinction.' save_ -save_cell.angle_beta - - _definition.id '_cell.angle_beta' - _alias.definition_id '_cell_angle_beta' - _name.category_id cell - _name.object_id angle_beta +save_refln.scale_group_code - _import.get [{'file':templ_attr.cif 'save':cell_angle}] + _definition.id '_refln.scale_group_code' + _alias.definition_id '_refln_scale_group_code' + _definition.update 2021-11-04 + _description.text +; + Code identifying the scale (if there is more than one scale) used + convert the measured structure factor to a common absolute value. +; + _name.category_id refln + _name.object_id scale_group_code + _name.linked_item_id '_reflns_scale.group_code' + _type.purpose Link + _type.source Related + _type.container Single + _type.contents Word save_ -save_cell.angle_beta_su +save_refln.sin_theta_over_lambda - _definition.id '_cell.angle_beta_su' + _definition.id '_refln.sin_theta_over_lambda' loop_ _alias.definition_id - '_cell_angle.beta_su' - '_cell_angle_beta_su' - '_cell.angle_beta_esd' + '_refln_sint/lambda' + '_refln_sin_theta_over_lambda' + '_refln.sint_over_lambda' - _name.category_id cell - _name.object_id angle_beta_su - _name.linked_item_id '_cell.angle_beta' + _definition.update 2013-03-07 + _description.text +; + The (sin theta)/lambda value for this reflection. +; + _name.category_id refln + _name.object_id sin_theta_over_lambda + _type.purpose Number + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0: + _units.code reciprocal_angstroms + _method.purpose Evaluation + _method.expression +; + With r as refln + h = r.hkl + G = _cell.reciprocal_metric_tensor - _import.get - [{'file':templ_attr.cif 'save':cell_angle_su}] + r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2. +; save_ -save_cell.angle_gamma - - _definition.id '_cell.angle_gamma' - _alias.definition_id '_cell_angle_gamma' - _name.category_id cell - _name.object_id angle_gamma +save_refln.symmetry_epsilon - _import.get [{'file':templ_attr.cif 'save':cell_angle}] + _definition.id '_refln.symmetry_epsilon' + _alias.definition_id '_refln_symmetry_epsilon' + _definition.update 2021-03-01 + _description.text +; + The symmetry reinforcement factor corresponding to the number of + times the reflection indices are generated identically from the + space-group symmetry operations. +; + _name.category_id refln + _name.object_id symmetry_epsilon + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range 1:48 + _units.code none save_ -save_cell.angle_gamma_su - - _definition.id '_cell.angle_gamma_su' - - loop_ - _alias.definition_id - '_cell_angle.gamma_su' - '_cell_angle_gamma_su' - '_cell.angle_gamma_esd' - - _name.category_id cell - _name.object_id angle_gamma_su - _name.linked_item_id '_cell.angle_gamma' +save_refln.symmetry_multiplicity - _import.get - [{'file':templ_attr.cif 'save':cell_angle_su}] + _definition.id '_refln.symmetry_multiplicity' + _alias.definition_id '_refln_symmetry_multiplicity' + _definition.update 2021-03-01 + _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. +; + _name.category_id refln + _name.object_id symmetry_multiplicity + _type.purpose Number + _type.source Assigned + _type.container Single + _type.contents Integer + _enumeration.range 1:48 + _units.code none save_ -save_cell.atomic_mass +save_refln.wavelength - _definition.id '_cell.atomic_mass' - _definition.update 2012-11-22 + _definition.id '_refln.wavelength' + _alias.definition_id '_refln_wavelength' + _definition.update 2012-11-26 _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. + The mean wavelength in angstroms of radiation used to measure + this reflection. This is an important parameter for data + collected using energy-dispersive detectors or the Laue method. ; - _name.category_id cell - _name.object_id atomic_mass + _name.category_id refln + _name.object_id wavelength _type.purpose Number - _type.source Derived + _type.source Assigned _type.container Single _type.contents Real - _enumeration.range 0.: - _units.code dalton - _method.purpose Evaluation - _method.expression + _enumeration.range 0.0: + _units.code angstroms + +save_ + +save_refln.wavelength_id + + _definition.id '_refln.wavelength_id' + _alias.definition_id '_refln_wavelength_id' + _definition.update 2021-10-27 + _description.text ; - mass = 0. + Code identifying the wavelength in DIFFRN_RADIATION_WAVELENGTH list. +; + _name.category_id refln + _name.object_id wavelength_id + _name.linked_item_id '_diffrn_radiation_wavelength.id' + _type.purpose Link + _type.source Related + _type.container Single + _type.contents Word - Loop t as atom_type { +save_ - mass += t.number_in_cell * t.atomic_mass - } - _cell.atomic_mass = mass +save_REFLNS + + _definition.id REFLNS + _definition.scope Category + _definition.class Set + _definition.update 2012-11-26 + _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 similar measures to those defined in the + DIFFRN categories, but differ in that the parameters refer to the + reduced/transformed reflections which have been used to refine the + atom site data in the ATOM_SITE category. The DIFFRN definitions refer + to the diffraction measurements and the raw reflection data. ; + _name.category_id DIFFRACTION + _name.object_id REFLNS save_ -save_cell.convert_uij_to_betaij +save_reflns.apply_dispersion_to_fcalc - _definition.id '_cell.convert_Uij_to_betaij' - _definition.update 2021-09-24 + _definition.id '_reflns.apply_dispersion_to_Fcalc' + _definition.update 2019-01-09 _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: + Yes or No flag on whether the anomalous dispersion scattering + components will be applied in the F complex calculation. + See _refln.F_complex +; + _name.category_id reflns + _name.object_id apply_dispersion_to_Fcalc + _type.purpose State + _type.source Assigned + _type.container Single + _type.contents Text - 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 ) + loop_ + _enumeration_set.state + _enumeration_set.detail + yes 'Apply dispersion.' + y 'Abbreviation for "yes".' + no 'Do not apply dispersion.' + n 'Abbreviation for "no".' - The conversion of the U or B matrices to the beta matrix +save_ - beta = C U C = C B C /8pi**2 +save_reflns.d_resolution_high - where C is conversion matrix defined here. + _definition.id '_reflns.d_resolution_high' + _alias.definition_id '_reflns_d_resolution_high' + _definition.update 2021-03-03 + _description.text +; + Highest resolution for the final REFLN data set. + This corresponds to the smallest interplanar d value. ; - _name.category_id cell - _name.object_id convert_Uij_to_betaij - _type.purpose Measurand + _name.category_id reflns + _name.object_id d_resolution_high + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.convert_Uij_to_betaij = 1.4142 * Pi * - Matrix([[ c.reciprocal_length_a, 0, 0 ], - [ 0, c.reciprocal_length_b, 0 ], - [ 0, 0, c.reciprocal_length_c ]]) -; + _enumeration.range 0.0: + _units.code angstroms save_ -save_cell.convert_uij_to_betaij_su +save_reflns.d_resolution_low - _definition.id '_cell.convert_Uij_to_betaij_su' - _definition.update 2021-09-23 + _definition.id '_reflns.d_resolution_low' + _alias.definition_id '_reflns_d_resolution_low' + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _cell.convert_Uij_to_betaij. + Lowest resolution for the final REFLN data set. + This corresponds to the largest interplanar d value. ; - _name.category_id cell - _name.object_id convert_Uij_to_betaij_su - _name.linked_item_id '_cell.convert_Uij_to_betaij' - _type.purpose SU + _name.category_id reflns + _name.object_id d_resolution_low + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms + _enumeration.range 0.0: + _units.code angstroms save_ -save_cell.convert_uiso_to_uij +save_reflns.friedel_coverage - _definition.id '_cell.convert_Uiso_to_Uij' - _definition.update 2021-07-07 + _definition.id '_reflns.Friedel_coverage' + _alias.definition_id '_reflns_Friedel_coverage' + _definition.update 2019-01-09 _description.text ; - The reciprocal space matrix for converting the isotropic Uiso - atomic displacement parameter to the anisotropic matrix Uij. + The proportion of Friedel related reflections present in the number of + the 'independent reflections' specified by the item _reflns.number_total. - | 1 cos(gamma*) cos(beta*) | - U[i,j] = Uiso * | cos(gamma*) 1 cos(alpha*) | - | cos(beta*) cos(alpha*) 1 | + 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. ; - _name.category_id cell - _name.object_id convert_Uiso_to_Uij - _type.purpose Measurand - _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _name.category_id reflns + _name.object_id Friedel_coverage + _type.purpose Number + _type.source Recorded + _type.container Single _type.contents Real + _enumeration.range 0.0:1.0 _units.code none - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.convert_Uiso_to_Uij = [[ 1., - Cosd(c.reciprocal_angle_gamma), Cosd(c.reciprocal_angle_beta) ], - [ Cosd(c.reciprocal_angle_gamma), 1., - Cosd(c.reciprocal_angle_alpha) ], [ - Cosd(c.reciprocal_angle_beta), Cosd(c.reciprocal_angle_alpha), 1. ]] -; save_ -save_cell.convert_uiso_to_uij_su +save_reflns.friedel_fraction_full - _definition.id '_cell.convert_Uiso_to_Uij_su' - _definition.update 2021-09-23 + _definition.id '_reflns.Friedel_fraction_full' + _alias.definition_id '_reflns_Friedel_fraction_full' + _definition.update 2013-01-20 _description.text ; - Standard uncertainty of _cell.convert_Uiso_to_Uij. + The ratio of Friedel pairs measured to _diffrn_reflns.theta_full + to the number theoretically possible (ignoring reflections in + centric projections and systematic absences throughout). + In contrast to _reflns.Friedel_coverage this can take values in + the full range 0 to 1 for any non-centrosymmetric space group, + and so one can see at a glance how completely the Friedel pairs + have been measured. For centrosymmetric space groups the value + would be given as not-applicable '.' ; - _name.category_id cell - _name.object_id convert_Uiso_to_Uij_su - _name.linked_item_id '_cell.convert_Uiso_to_Uij' - _type.purpose SU + _name.category_id reflns + _name.object_id Friedel_fraction_full + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real + _enumeration.range 0.0:1.0 _units.code none save_ -save_cell.formula_units_z +save_reflns.friedel_fraction_max - _definition.id '_cell.formula_units_Z' - _alias.definition_id '_cell_formula_units_Z' - _definition.update 2021-03-01 + _definition.id '_reflns.Friedel_fraction_max' + _alias.definition_id '_reflns_Friedel_fraction_max' + _definition.update 2013-01-20 _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. + The ratio of Friedel pairs measured to _diffrn_reflns.theta_max + to the number theoretically possible (ignoring reflections in + centric projections and systematic absences throughout). + In contrast to _reflns.Friedel_coverage this can take values in + the full range 0 to 1 for any non-centrosymmetric space group, + and so one can see at a glance how completely the Friedel pairs + have been measured. For centrosymmetric space groups the value + would be given as not-applicable '.' ; - _name.category_id cell - _name.object_id formula_units_Z + _name.category_id reflns + _name.object_id Friedel_fraction_max _type.purpose Number - _type.source Assigned + _type.source Derived _type.container Single - _type.contents Integer - _enumeration.range 1: + _type.contents Real + _enumeration.range 0.0:1.0 _units.code none save_ -save_cell.length_a +save_reflns.limit_h_max - _definition.id '_cell.length_a' - _alias.definition_id '_cell_length_a' - _name.category_id cell - _name.object_id length_a + _definition.id '_reflns.limit_h_max' + _alias.definition_id '_reflns_limit_h_max' + _name.category_id reflns + _name.object_id limit_h_max - _import.get [{'file':templ_attr.cif 'save':cell_length}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.length_a_su - - _definition.id '_cell.length_a_su' - - loop_ - _alias.definition_id - '_cell_length_a_su' - '_cell.length_a_esd' +save_reflns.limit_h_min - _name.category_id cell - _name.object_id length_a_su - _name.linked_item_id '_cell.length_a' + _definition.id '_reflns.limit_h_min' + _alias.definition_id '_reflns_limit_h_min' + _name.category_id reflns + _name.object_id limit_h_min - _import.get - [{'file':templ_attr.cif 'save':cell_length_su}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.length_b +save_reflns.limit_k_max - _definition.id '_cell.length_b' - _alias.definition_id '_cell_length_b' - _name.category_id cell - _name.object_id length_b + _definition.id '_reflns.limit_k_max' + _alias.definition_id '_reflns_limit_k_max' + _name.category_id reflns + _name.object_id limit_k_max - _import.get [{'file':templ_attr.cif 'save':cell_length}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.length_b_su - - _definition.id '_cell.length_b_su' - - loop_ - _alias.definition_id - '_cell_length_b_su' - '_cell.length_b_esd' +save_reflns.limit_k_min - _name.category_id cell - _name.object_id length_b_su - _name.linked_item_id '_cell.length_b' + _definition.id '_reflns.limit_k_min' + _alias.definition_id '_reflns_limit_k_min' + _name.category_id reflns + _name.object_id limit_k_min - _import.get - [{'file':templ_attr.cif 'save':cell_length_su}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.length_c +save_reflns.limit_l_max - _definition.id '_cell.length_c' - _alias.definition_id '_cell_length_c' - _name.category_id cell - _name.object_id length_c + _definition.id '_reflns.limit_l_max' + _alias.definition_id '_reflns_limit_l_max' + _name.category_id reflns + _name.object_id limit_l_max - _import.get [{'file':templ_attr.cif 'save':cell_length}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.length_c_su - - _definition.id '_cell.length_c_su' - - loop_ - _alias.definition_id - '_cell_length_c_su' - '_cell.length_c_esd' +save_reflns.limit_l_min - _name.category_id cell - _name.object_id length_c_su - _name.linked_item_id '_cell.length_c' + _definition.id '_reflns.limit_l_min' + _alias.definition_id '_reflns_limit_l_min' + _name.category_id reflns + _name.object_id limit_l_min - _import.get - [{'file':templ_attr.cif 'save':cell_length_su}] + _import.get [{'file':templ_attr.cif 'save':Miller_index}] save_ -save_cell.metric_tensor +save_reflns.limit_max - _definition.id '_cell.metric_tensor' - _definition.update 2021-07-07 + _definition.id '_reflns.limit_max' + _definition.update 2013-01-15 _description.text ; - The direct space (covariant) metric tensor used to transform - vectors and coordinates from real (direct) to reciprocal space. + Maximum Miller indices of refined diffraction reflections. ; - _name.category_id cell - _name.object_id metric_tensor + _name.category_id reflns + _name.object_id limit_max _type.purpose Number - _type.source Derived + _type.source Assigned _type.container Matrix - _type.dimension '[3,3]' + _type.dimension '[3]' _type.contents Real - _units.code angstrom_squared + _units.code none _method.purpose Evaluation _method.expression ; - with c as cell + With t as reflns - _cell.metric_tensor = [[ c.vector_a*c.vector_a, - c.vector_a*c.vector_b, c.vector_a*c.vector_c ], - [ c.vector_b*c.vector_a, c.vector_b*c.vector_b, c.vector_b*c.vector_c ], - [ c.vector_c*c.vector_a, c.vector_c*c.vector_b, - c.vector_c*c.vector_c ]] + _reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max] ; save_ -save_cell.orthogonal_matrix +save_reflns.limit_min - _definition.id '_cell.orthogonal_matrix' - _definition.update 2021-07-07 + _definition.id '_reflns.limit_min' + _definition.update 2013-01-15 _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. + Minimum Miller indices of refined diffraction reflections. ; - _name.category_id cell - _name.object_id orthogonal_matrix + _name.category_id reflns + _name.object_id limit_min _type.purpose Number - _type.source Derived + _type.source Assigned _type.container Matrix - _type.dimension '[3,3]' - _type.contents Real - _units.code angstroms + _type.dimension '[3]' + _type.contents Integer + _units.code none _method.purpose Evaluation _method.expression ; - With c as cell - _cell.orthogonal_matrix = [ - [ c.length_a*Sind(c.angle_beta)*Sind(c.reciprocal_angle_gamma), 0, - 0 ], [ - -c.length_a*Sind(c.angle_beta)*Cosd(c.reciprocal_angle_gamma), - c.length_b*Sind(c.angle_alpha), 0 ], [ - c.length_a*Cosd(c.angle_beta), - c.length_b*Cosd(c.angle_alpha), c.length_c ]] + With t as reflns + + _reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min] ; save_ -save_cell.reciprocal_angle_alpha +save_reflns.number_gt - _definition.id '_cell.reciprocal_angle_alpha' - _alias.definition_id '_cell_reciprocal_angle_alpha' - _definition.update 2013-01-18 + _definition.id '_reflns.number_gt' + + loop_ + _alias.definition_id + '_reflns_number_gt' + '_reflns_number_observed' + '_reflns_number_obs' + '_reflns.number_obs' + + _definition.update 2023-01-13 _description.text ; - Reciprocal of the angle between _cell.length_b and _cell.length_c. - Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. - New York: John Wiley & Sons Inc. + Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which + are significantly intense (see _reflns.threshold_expression). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending on the nature of the structure and the procedures used. ; - _name.category_id cell - _name.object_id reciprocal_angle_alpha - _type.purpose Measurand - _type.source Derived + _name.category_id reflns + _name.object_id number_gt + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.:180. - _units.code degrees - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.reciprocal_angle_alpha = - Acosd((Cosd(c.angle_beta)*Cosd(c.angle_gamma)-Cosd(c.angle_alpha))/ - (Sind(c.angle_beta)*Sind(c.angle_gamma))) -; + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell.reciprocal_angle_alpha_su +save_reflns.number_total - _definition.id '_cell.reciprocal_angle_alpha_su' + _definition.id '_reflns.number_total' loop_ _alias.definition_id - '_cell_reciprocal_angle_alpha_su' - '_cell.reciprocal_angle_alpha_esd' + '_reflns_number_total' + '_reflns_number_all' + '_reflns.number_all' - _definition.update 2021-03-03 + _definition.update 2023-01-13 _description.text ; - Standard uncertainty of the reciprocal of the angle - between _cell.length_b and _cell.length_c. + Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending on the nature of the structure and the procedures used. ; - _name.category_id cell - _name.object_id reciprocal_angle_alpha_su - _name.linked_item_id '_cell.reciprocal_angle_alpha' - _type.purpose SU - _type.source Related + _name.category_id reflns + _name.object_id number_total + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _units.code degrees + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell.reciprocal_angle_beta +save_reflns.special_details - _definition.id '_cell.reciprocal_angle_beta' - _alias.definition_id '_cell_reciprocal_angle_beta' - _definition.update 2013-01-18 + _definition.id '_reflns.special_details' + + loop_ + _alias.definition_id + '_reflns_special_details' + '_reflns.details' + + _definition.update 2012-11-26 _description.text ; - Reciprocal of the angle between _cell.length_a and _cell.length_c. - Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. - New York: John Wiley & Sons Inc. + 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. ; - _name.category_id cell - _name.object_id reciprocal_angle_beta - _type.purpose Measurand - _type.source Derived + _name.category_id reflns + _name.object_id special_details + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.:180. - _units.code degrees - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.reciprocal_angle_beta = - Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_gamma)-Cosd(c.angle_beta))/ - (Sind(c.angle_alpha)*Sind(c.angle_gamma))) -; + _type.contents Text save_ -save_cell.reciprocal_angle_beta_su +save_reflns.threshold_expression - _definition.id '_cell.reciprocal_angle_beta_su' + _definition.id '_reflns.threshold_expression' loop_ _alias.definition_id - '_cell_reciprocal_angle_beta_su' - '_cell.reciprocal_angle_beta_esd' + '_reflns_threshold_expression' + '_reflns_observed_criterion' + '_reflns.observed_criterion' - _definition.update 2021-03-03 + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of the reciprocal of the angle - between _cell.length_a and _cell.length_c. + 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. ; - _name.category_id cell - _name.object_id reciprocal_angle_beta_su - _name.linked_item_id '_cell.reciprocal_angle_beta' - _type.purpose SU - _type.source Related + _name.category_id reflns + _name.object_id threshold_expression + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _units.code degrees + _type.contents Text + _description_example.case I>2u(I) save_ -save_cell.reciprocal_angle_gamma +save_REFLNS_CLASS - _definition.id '_cell.reciprocal_angle_gamma' - _alias.definition_id '_cell_reciprocal_angle_gamma' - _definition.update 2016-09-09 + _definition.id REFLNS_CLASS + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Reciprocal of the angle between _cell.length_a and _cell.length_b. - Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. - New York: John Wiley & Sons Inc. -; - _name.category_id cell - _name.object_id reciprocal_angle_gamma - _type.purpose Measurand - _type.source Derived - _type.container Single - _type.contents Real - _enumeration.range 0.:180. - _units.code degrees - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.reciprocal_angle_gamma = - Acosd((Cosd(c.angle_alpha)*Cosd(c.angle_beta)-Cosd(c.angle_gamma))/ - (Sind(c.angle_alpha)*Sind(c.angle_beta))) + The CATEGORY of data items which specify the properties of reflections + in specific classes of reflections. ; + _name.category_id REFLNS + _name.object_id REFLNS_CLASS + _category_key.name '_reflns_class.code' -save_ - -save_cell.reciprocal_angle_gamma_su - - _definition.id '_cell.reciprocal_angle_gamma_su' - - loop_ - _alias.definition_id - '_cell_reciprocal_angle_gamma_su' - '_cell.reciprocal_angle_gamma_esd' - - _definition.update 2021-03-03 +save_ + +save_reflns_class.code + + _definition.id '_reflns_class.code' + _alias.definition_id '_reflns_class_code' + _definition.update 2021-10-27 _description.text ; - Standard uncertainty of the reciprocal of the angle - between _cell.length_a and _cell.length_b. + Code identifying a reflection class. ; - _name.category_id cell - _name.object_id reciprocal_angle_gamma_su - _name.linked_item_id '_cell.reciprocal_angle_gamma' - _type.purpose SU - _type.source Derived + _name.category_id reflns_class + _name.object_id code + _type.purpose Encode + _type.source Assigned _type.container Single - _type.contents Real - _units.code degrees + _type.contents Word + _description_example.case c1 save_ -save_cell.reciprocal_length_a +save_reflns_class.d_res_high - _definition.id '_cell.reciprocal_length_a' - _alias.definition_id '_cell_reciprocal_length_a' - _definition.update 2012-11-22 + _definition.id '_reflns_class.d_res_high' + _alias.definition_id '_reflns_class_d_res_high' + _definition.update 2021-03-03 _description.text ; - Reciprocal of the _cell.length_a. + Highest resolution for the reflections in this class. + This corresponds to the smallest interplanar d value. ; - _name.category_id cell - _name.object_id reciprocal_length_a - _type.purpose Measurand - _type.source Derived + _name.category_id reflns_class + _name.object_id d_res_high + _type.purpose Number + _type.source Assigned _type.container Single _type.contents Real - _enumeration.range 0.: - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - _cell.reciprocal_length_a = Norm ( _cell.reciprocal_vector_a ) -; + _enumeration.range 0.0: + _units.code angstroms save_ -save_cell.reciprocal_length_a_su - - _definition.id '_cell.reciprocal_length_a_su' - - loop_ - _alias.definition_id - '_cell_reciprocal_length_a_su' - '_cell.reciprocal_length_a_esd' +save_reflns_class.d_res_low + _definition.id '_reflns_class.d_res_low' + _alias.definition_id '_reflns_class_d_res_low' _definition.update 2021-03-03 _description.text ; - Standard uncertainty of the reciprocal of the _cell.length_a. + Lowest resolution for the reflections in this class. + This corresponds to the largest interplanar d value. ; - _name.category_id cell - _name.object_id reciprocal_length_a_su - _name.linked_item_id '_cell.reciprocal_length_a' - _type.purpose SU - _type.source Related + _name.category_id reflns_class + _name.object_id d_res_low + _type.purpose Number + _type.source Assigned _type.container Single _type.contents Real - _units.code reciprocal_angstroms + _enumeration.range 0.0: + _units.code angstroms save_ -save_cell.reciprocal_length_b +save_reflns_class.description - _definition.id '_cell.reciprocal_length_b' - _alias.definition_id '_cell_reciprocal_length_b' - _definition.update 2012-11-22 + _definition.id '_reflns_class.description' + _alias.definition_id '_reflns_class_description' + _definition.update 2012-11-26 _description.text ; - Reciprocal of the _cell.length_b. + Description of a reflection class. ; - _name.category_id cell - _name.object_id reciprocal_length_b - _type.purpose Measurand - _type.source Derived + _name.category_id reflns_class + _name.object_id description + _type.purpose Describe + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.: - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - _cell.reciprocal_length_b = Norm ( _cell.reciprocal_vector_b ) -; + _type.contents Text + _description_example.case 'H0L0 common projection reflections' save_ -save_cell.reciprocal_length_b_su +save_reflns_class.number_gt - _definition.id '_cell.reciprocal_length_b_su' + _definition.id '_reflns_class.number_gt' loop_ _alias.definition_id - '_cell_reciprocal_length_b_su' - '_cell.reciprocal_length_b_esd' + '_reflns_class_number_observed' + '_reflns_class_number_gt' - _definition.update 2021-03-03 + _definition.update 2023-01-13 _description.text ; - Standard uncertainty of the reciprocal of the _cell.length_b. + Count of reflections in this REFLN class (not the DIFFRN_REFLN set) + which are significantly intense (see _reflns.threshold_expression). It may + include Friedel equivalent reflections (i.e. those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending on the nature of the structure and the procedures used. ; - _name.category_id cell - _name.object_id reciprocal_length_b_su - _name.linked_item_id '_cell.reciprocal_length_b' - _type.purpose SU - _type.source Related + _name.category_id reflns_class + _name.object_id number_gt + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _units.code reciprocal_angstroms + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell.reciprocal_length_c +save_reflns_class.number_total - _definition.id '_cell.reciprocal_length_c' - _alias.definition_id '_cell_reciprocal_length_c' - _definition.update 2012-11-22 + _definition.id '_reflns_class.number_total' + _alias.definition_id '_reflns_class_number_total' + _definition.update 2023-01-13 _description.text ; - Reciprocal of the _cell.length_c. + Count of reflections in this REFLN class (not the DIFFRN_REFLN set). It + may include Friedel equivalent reflections (those which are equivalent + under the Laue symmetry but inequivalent under the crystal class), + depending on the nature of the structure and the procedures used. ; - _name.category_id cell - _name.object_id reciprocal_length_c - _type.purpose Measurand - _type.source Derived + _name.category_id reflns_class + _name.object_id number_total + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.: - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - _cell.reciprocal_length_c = Norm ( _cell.reciprocal_vector_c ) -; + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell.reciprocal_length_c_su - - _definition.id '_cell.reciprocal_length_c_su' - - loop_ - _alias.definition_id - '_cell_reciprocal_length_c_su' - '_cell.reciprocal_length_c_esd' +save_reflns_class.r_factor_all - _definition.update 2021-03-03 + _definition.id '_reflns_class.R_factor_all' + _alias.definition_id '_reflns_class_R_factor_all' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of the reciprocal of the _cell.length_c. + Residual factor for reflections in this class used in refinement. + + sum | F(meas) - F(calc) | + R(F all) = ------------------------ + sum | F(meas) | + + F(meas) = the measured structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + + and the sum is taken over the specified reflections ; - _name.category_id cell - _name.object_id reciprocal_length_c_su - _name.linked_item_id '_cell.reciprocal_length_c' - _type.purpose SU + _name.category_id reflns_class + _name.object_id R_factor_all + _type.purpose Number _type.source Derived _type.container Single _type.contents Real - _units.code reciprocal_angstroms + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_metric_tensor +save_reflns_class.r_factor_gt - _definition.id '_cell.reciprocal_metric_tensor' - _definition.update 2021-07-07 + _definition.id '_reflns_class.R_factor_gt' + + loop_ + _alias.definition_id + '_reflns_class_R_factor_gt' + '_reflns_class_R_factor_observed' + + _definition.update 2012-11-26 _description.text ; - The reciprocal (contravariant) metric tensor used to transform - vectors and coordinates from reciprocal space to real (direct) - space. + Residual factor for the reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. + + sum | F(meas_gt) - F(calc) | + R(F gt) = -------------------------------- + sum | F(meas_gt) | + + F(meas) = the measured structure-factor amplitudes + F(calc) = the calculated structure-factor amplitudes + + and the sum is taken over the specified reflections ; - _name.category_id cell - _name.object_id reciprocal_metric_tensor - _type.purpose Measurand + _name.category_id reflns_class + _name.object_id R_factor_gt + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstrom_squared - _method.purpose Evaluation - _method.expression -; - with c as cell - _cell.reciprocal_metric_tensor = [ - [ c.reciprocal_vector_a*c.reciprocal_vector_a, - c.reciprocal_vector_a*c.reciprocal_vector_b, - c.reciprocal_vector_a*c.reciprocal_vector_c ], [ - c.reciprocal_vector_b*c.reciprocal_vector_a, - c.reciprocal_vector_b*c.reciprocal_vector_b, - c.reciprocal_vector_b*c.reciprocal_vector_c ], [ - c.reciprocal_vector_c*c.reciprocal_vector_a, - c.reciprocal_vector_c*c.reciprocal_vector_b, - c.reciprocal_vector_c*c.reciprocal_vector_c ]] -; + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_metric_tensor_su +save_reflns_class.r_fsqd_factor - _definition.id '_cell.reciprocal_metric_tensor_su' - _definition.update 2021-09-23 + _definition.id '_reflns_class.R_Fsqd_factor' + _alias.definition_id '_reflns_class_R_Fsqd_factor' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _cell.reciprocal_metric_tensor. + Residual factor R(F^2^) for reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. + + sum | F(meas_gt)^2^ - F(calc)^2^ | + R(Fsqd gt) = ------------------------------------ + sum F(meas_gt)^2^ + + F(meas_gt)^2^ = square of the 'observed' structure-factor + F(calc )^2^ = square of the calculated structure-factor + + and the sum is taken over the specified reflections ; - _name.category_id cell - _name.object_id reciprocal_metric_tensor_su - _name.linked_item_id '_cell.reciprocal_metric_tensor' - _type.purpose SU + _name.category_id reflns_class + _name.object_id R_Fsqd_factor + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstrom_squared + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_orthogonal_matrix +save_reflns_class.r_i_factor - _definition.id '_cell.reciprocal_orthogonal_matrix' - _definition.update 2021-07-07 + _definition.id '_reflns_class.R_I_factor' + _alias.definition_id '_reflns_class_R_I_factor' + _definition.update 2012-11-26 _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) + Residual factor R(I) for reflections in this class judged + significantly intense (i.e. greater than required by the + _reflns.threshold_expression) and included in the refinement. - M h = p + sum | I(meas_gt) - I(calc) | + R(I gt) = ---------------------------- + sum | I(meas_gt) | + + I(meas_gt) = the net 'observed' intensity + I(calc ) = the net calculated intensity + + and the sum is taken over the specified reflections ; - _name.category_id cell - _name.object_id reciprocal_orthogonal_matrix - _type.purpose Measurand + _name.category_id reflns_class + _name.object_id R_I_factor + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - _cell.reciprocal_orthogonal_matrix = Inverse( - - Transpose( _cell.orthogonal_matrix )) -; + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_orthogonal_matrix_su +save_reflns_class.wr_factor_all - _definition.id '_cell.reciprocal_orthogonal_matrix_su' - _definition.update 2021-09-23 + _definition.id '_reflns_class.wR_factor_all' + _alias.definition_id '_reflns_class_wR_factor_all' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _cell.reciprocal_orthogonal_matrix. + For each reflection class, the weighted residual factors for all + reflections included in the refinement. The reflections also + satisfy the resolution limits established by + _reflns_class.d_res_high and _reflns_class.d_res_low. + + ( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^ + wR = ( ------------------------------- ) + ( sum w Y(meas)^2^ ) + + Y(meas) = the measured amplitudes specified by + _refine_ls.structure_factor_coef + Y(calc) = the calculated amplitudes specified by + _refine_ls.structure_factor_coef + w = the least-squares weights + + and the sum is taken over the reflections of this class. ; - _name.category_id cell - _name.object_id reciprocal_orthogonal_matrix_su - _name.linked_item_id '_cell.reciprocal_orthogonal_matrix' - _type.purpose SU + _name.category_id reflns_class + _name.object_id wR_factor_all + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3,3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_vector_a +save_REFLNS_SCALE - _definition.id '_cell.reciprocal_vector_a' - _definition.update 2021-07-07 + _definition.id REFLNS_SCALE + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - Reciprocal of the _cell.vector_a. -; - _name.category_id cell - _name.object_id reciprocal_vector_a - _type.purpose Measurand - _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Real - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.reciprocal_vector_a = c.vector_b ^ c.vector_c / _cell.volume + The CATEGORY of data items which specify the scales needed to place + measured structure factor coefficients on the same absolute scale. ; + _name.category_id REFLNS + _name.object_id REFLNS_SCALE + _category_key.name '_reflns_scale.group_code' save_ -save_cell.reciprocal_vector_a_su +save_reflns_scale.group_code - _definition.id '_cell.reciprocal_vector_a_su' - _definition.update 2021-09-23 + _definition.id '_reflns_scale.group_code' + _alias.definition_id '_reflns_scale_group_code' + _definition.update 2021-11-04 _description.text ; - Standard uncertainty of _cell.reciprocal_vector_a. + Code identifying a reflection scale group. These names need not + correspond to _diffrn_scale_group.code names. ; - _name.category_id cell - _name.object_id reciprocal_vector_a_su - _name.linked_item_id '_cell.reciprocal_vector_a' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Real - _units.code reciprocal_angstroms + _name.category_id reflns_scale + _name.object_id group_code + _type.purpose Encode + _type.source Assigned + _type.container Single + _type.contents Word save_ -save_cell.reciprocal_vector_b +save_reflns_scale.meas_f - _definition.id '_cell.reciprocal_vector_b' - _definition.update 2021-07-07 + _definition.id '_reflns_scale.meas_F' + _alias.definition_id '_reflns_scale_meas_F' + _definition.update 2012-11-26 _description.text ; - Reciprocal of the _cell.vector_b. + Structure factor scale for this scale group. ; - _name.category_id cell - _name.object_id reciprocal_vector_b + _name.category_id reflns_scale + _name.object_id meas_F _type.purpose Measurand _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - With c as cell - - _cell.reciprocal_vector_b = c.vector_c ^ c.vector_a / _cell.volume -; + _enumeration.range 0.0: + _units.code none save_ -save_cell.reciprocal_vector_b_su +save_reflns_scale.meas_f_su - _definition.id '_cell.reciprocal_vector_b_su' + _definition.id '_reflns_scale.meas_F_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _cell.reciprocal_vector_b. + Standard uncertainty of _reflns_scale.meas_F. ; - _name.category_id cell - _name.object_id reciprocal_vector_b_su - _name.linked_item_id '_cell.reciprocal_vector_b' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Real - _units.code reciprocal_angstroms + _name.category_id reflns_scale + _name.object_id meas_F_su + _name.linked_item_id '_reflns_scale.meas_F' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_cell.reciprocal_vector_c +save_reflns_scale.meas_f_squared - _definition.id '_cell.reciprocal_vector_c' - _definition.update 2021-07-07 + _definition.id '_reflns_scale.meas_F_squared' + _alias.definition_id '_reflns_scale_meas_F_squared' + _definition.update 2012-11-26 _description.text ; - Reciprocal of the _cell.vector_c. + Structure factor squared scale for this scale group. ; - _name.category_id cell - _name.object_id reciprocal_vector_c + _name.category_id reflns_scale + _name.object_id meas_F_squared _type.purpose Measurand _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms - _method.purpose Evaluation - _method.expression -; - With c as cell + _enumeration.range 0.0: + _units.code none - _cell.reciprocal_vector_c = c.vector_a ^ c.vector_b / _cell.volume +save_ + +save_reflns_scale.meas_f_squared_su + + _definition.id '_reflns_scale.meas_F_squared_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _reflns_scale.meas_F_squared. ; + _name.category_id reflns_scale + _name.object_id meas_F_squared_su + _name.linked_item_id '_reflns_scale.meas_F_squared' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_cell.reciprocal_vector_c_su +save_reflns_scale.meas_intensity - _definition.id '_cell.reciprocal_vector_c_su' - _definition.update 2021-09-23 + _definition.id '_reflns_scale.meas_intensity' + _alias.definition_id '_reflns_scale_meas_intensity' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _cell.reciprocal_vector_c. + Net intensity scale for this scale group. ; - _name.category_id cell - _name.object_id reciprocal_vector_c_su - _name.linked_item_id '_cell.reciprocal_vector_c' - _type.purpose SU + _name.category_id reflns_scale + _name.object_id meas_intensity + _type.purpose Measurand _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _type.container Single _type.contents Real - _units.code reciprocal_angstroms + _enumeration.range 0.0: + _units.code none save_ -save_cell.special_details - - _definition.id '_cell.special_details' - - loop_ - _alias.definition_id - '_cell_special_details' - '_cell.details' +save_reflns_scale.meas_intensity_su - _definition.update 2012-11-22 + _definition.id '_reflns_scale.meas_intensity_su' + _definition.update 2021-09-23 _description.text ; - Description of special aspects of the cell choice, noting - possible alternative settings. + Standard uncertainty of _reflns_scale.meas_intensity. ; - _name.category_id cell - _name.object_id special_details - _type.purpose Describe - _type.source Recorded - _type.container Single - _type.contents Text + _name.category_id reflns_scale + _name.object_id meas_intensity_su + _name.linked_item_id '_reflns_scale.meas_intensity' + _units.code none + + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_cell.vector_a +save_REFLNS_SHELL - _definition.id '_cell.vector_a' - _definition.update 2021-07-07 + _definition.id REFLNS_SHELL + _definition.scope Category + _definition.class Loop + _definition.update 2021-06-29 _description.text ; - The cell vector along the x axis. -; - _name.category_id cell - _name.object_id vector_a - _type.purpose Measurand - _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Real - _units.code angstroms - _method.purpose Evaluation - _method.expression -; - _cell.vector_a = _cell.orthogonal_matrix * Matrix([1,0,0]) + The CATEGORY of data items which specify the information about + reflections divided into shells bounded by d resolution limits. ; + _name.category_id REFLNS + _name.object_id REFLNS_SHELL + + loop_ + _category_key.name + '_reflns_shell.d_res_low' + '_reflns_shell.d_res_high' save_ -save_cell.vector_a_su +save_reflns_shell.d_res_high - _definition.id '_cell.vector_a_su' - _definition.update 2021-09-23 + _definition.id '_reflns_shell.d_res_high' + _alias.definition_id '_reflns_shell_d_res_high' + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _cell.vector_a. + Highest resolution for the reflections in this shell. + This corresponds to the smallest interplanar d value. ; - _name.category_id cell - _name.object_id vector_a_su - _name.linked_item_id '_cell.vector_a' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _name.category_id reflns_shell + _name.object_id d_res_high + _type.purpose Number + _type.source Assigned + _type.container Single _type.contents Real + _enumeration.range 0.0: _units.code angstroms save_ -save_cell.vector_b +save_reflns_shell.d_res_limits - _definition.id '_cell.vector_b' - _definition.update 2021-07-07 + _definition.id '_reflns_shell.d_res_limits' + _definition.update 2012-11-26 _description.text ; - The cell vector along the y axis. + Resolution for the reflections in this shell stored as + the list of lowest and highest values. This is the + category key. ; - _name.category_id cell - _name.object_id vector_b - _type.purpose Measurand + _name.category_id reflns_shell + _name.object_id d_res_limits + _type.purpose Number _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _type.container List + _type.dimension '[2]' _type.contents Real _units.code angstroms _method.purpose Evaluation _method.expression ; - _cell.vector_b = _cell.orthogonal_matrix * Matrix([0,1,0]) + With s as reflns_shell + + _reflns_shell.d_res_limits = [ s.d_res_low, s.d_res_high ] ; save_ -save_cell.vector_b_su +save_reflns_shell.d_res_low - _definition.id '_cell.vector_b_su' - _definition.update 2021-09-23 + _definition.id '_reflns_shell.d_res_low' + _alias.definition_id '_reflns_shell_d_res_low' + _definition.update 2021-03-03 _description.text ; - Standard uncertainty of _cell.vector_b. + Lowest resolution for the reflections in this shell. + This corresponds to the largest interplanar d value. ; - _name.category_id cell - _name.object_id vector_b_su - _name.linked_item_id '_cell.vector_b' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _name.category_id reflns_shell + _name.object_id d_res_low + _type.purpose Number + _type.source Assigned + _type.container Single _type.contents Real + _enumeration.range 0.0: _units.code angstroms save_ -save_cell.vector_c +save_reflns_shell.meani_over_sui_all - _definition.id '_cell.vector_c' - _definition.update 2021-07-07 + _definition.id '_reflns_shell.meanI_over_suI_all' + + loop_ + _alias.definition_id + '_reflns_shell_meanI_over_uI_all' + '_reflns_shell_meanI_over_sigI_all' + '_reflns_shell.meanI_over_sigI_all' + '_reflns_shell.meanI_over_uI_all' + + _definition.update 2012-11-26 _description.text ; - The cell vector along the z axis. + Ratio of the mean intensity in a shell to the mean standard uncertainty + of the intensities in the shell. ; - _name.category_id cell - _name.object_id vector_c - _type.purpose Measurand - _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _name.category_id reflns_shell + _name.object_id meanI_over_suI_all + _type.purpose Number + _type.source Recorded + _type.container Single _type.contents Real - _units.code angstroms - _method.purpose Evaluation - _method.expression -; - _cell.vector_c = _cell.orthogonal_matrix * Matrix([0,0,1]) -; + _enumeration.range 0: + _units.code none save_ -save_cell.vector_c_su +save_reflns_shell.meani_over_sui_gt - _definition.id '_cell.vector_c_su' - _definition.update 2021-09-23 + _definition.id '_reflns_shell.meanI_over_suI_gt' + + loop_ + _alias.definition_id + '_reflns_shell_meanI_over_sigI_obs' + '_reflns_shell.meanI_over_sigI_obs' + '_reflns_shell.meanI_over_sigI_gt' + '_reflns_shell_meanI_over_sigI_gt' + '_reflns_shell.meanI_over_uI_gt' + '_reflns_shell_meanI_over_uI_gt' + + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of _cell.vector_c. + 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. ; - _name.category_id cell - _name.object_id vector_c_su - _name.linked_item_id '_cell.vector_c' - _type.purpose SU - _type.source Derived - _type.container Matrix - _type.dimension '[3]' + _name.category_id reflns_shell + _name.object_id meanI_over_suI_gt + _type.purpose Number + _type.source Recorded + _type.container Single _type.contents Real - _units.code angstroms + _enumeration.range 0: + _units.code none save_ -save_cell.volume +save_reflns_shell.number_measured_all - _definition.id '_cell.volume' - _alias.definition_id '_cell_volume' - _definition.update 2013-03-07 + _definition.id '_reflns_shell.number_measured_all' + _alias.definition_id '_reflns_shell_number_measured_all' + _definition.update 2021-03-01 _description.text ; - Volume of the crystal unit cell. + Total count of reflections measured for this resolution shell. ; - _name.category_id cell - _name.object_id volume - _type.purpose Measurand - _type.source Derived + _name.category_id reflns_shell + _name.object_id number_measured_all + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstrom_cubed - _method.purpose Evaluation - _method.expression -; - With c as cell + _type.contents Integer + _enumeration.range 0: + _units.code none + +save_ + +save_reflns_shell.number_measured_gt + + _definition.id '_reflns_shell.number_measured_gt' + + loop_ + _alias.definition_id + '_reflns_shell_number_measured_obs' + '_reflns_shell.number_measured_obs' + '_reflns_shell_number_measured_gt' - _cell.volume = c.vector_a * ( c.vector_b ^ c.vector_c ) + _definition.update 2021-03-01 + _description.text +; + Number of reflections measured for this resolution shell which are + significantly intense (see _reflns.threshold_expression). ; + _name.category_id reflns_shell + _name.object_id number_measured_gt + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell.volume_su +save_reflns_shell.number_possible - _definition.id '_cell.volume_su' + _definition.id '_reflns_shell.number_possible' loop_ _alias.definition_id - '_cell_volume_su' - '_cell.volume_esd' + '_reflns_shell_number_possible' + '_reflns_shell.number_possible_all' - _definition.update 2014-06-08 + _definition.update 2021-03-01 _description.text ; - Standard uncertainty of the volume of the crystal unit cell. + Count of symmetry-unique reflections possible in this reflection shell. ; - _name.category_id cell - _name.object_id volume_su - _name.linked_item_id '_cell.volume' - _type.purpose SU - _type.source Related + _name.category_id reflns_shell + _name.object_id number_possible + _type.purpose Number + _type.source Recorded _type.container Single - _type.contents Real - _units.code angstrom_cubed + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_CELL_MEASUREMENT +save_reflns_shell.number_unique_all - _definition.id CELL_MEASUREMENT - _definition.scope Category - _definition.class Set - _definition.update 2012-11-22 + _definition.id '_reflns_shell.number_unique_all' + _alias.definition_id '_reflns_shell_number_unique_all' + _definition.update 2021-03-01 _description.text ; - The CATEGORY of data items used to describe the angles between - the axes in the crystal unit cell. + Count of symmetry-unique reflections present in this reflection shell. ; - _name.category_id CELL - _name.object_id CELL_MEASUREMENT + _name.category_id reflns_shell + _name.object_id number_unique_all + _type.purpose Number + _type.source Recorded + _type.container Single + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell_measurement.pressure +save_reflns_shell.number_unique_gt - _definition.id '_cell_measurement.pressure' - _alias.definition_id '_cell_measurement_pressure' - _definition.update 2012-11-22 + _definition.id '_reflns_shell.number_unique_gt' + + loop_ + _alias.definition_id + '_reflns_shell_number_unique_gt' + '_reflns_shell_number_unique_obs' + '_reflns_shell.number_unique_obs' + + _definition.update 2021-03-01 _description.text ; - The pressure at which the unit-cell parameters were measured - (not the pressure used to synthesize the sample). + Number of symmetry-unique reflections present in this reflection shell + which are significantly intense (see _reflns.threshold_expression). ; - _name.category_id cell_measurement - _name.object_id pressure - _type.purpose Measurand + _name.category_id reflns_shell + _name.object_id number_unique_gt + _type.purpose Number _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code kilopascals + _type.contents Integer + _enumeration.range 0: + _units.code none save_ -save_cell_measurement.pressure_su - - _definition.id '_cell_measurement.pressure_su' - - loop_ - _alias.definition_id - '_cell_measurement_pressure_su' - '_cell_measurement.pressure_esd' +save_reflns_shell.percent_possible_all - _definition.update 2021-03-03 + _definition.id '_reflns_shell.percent_possible_all' + _alias.definition_id '_reflns_shell_percent_possible_all' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of the pressure at which - the unit-cell parameters were measured. + Percentage of reflections present in this shell over that possible. ; - _name.category_id cell_measurement - _name.object_id pressure_su - _name.linked_item_id '_cell_measurement.pressure' - _type.purpose SU - _type.source Related + _name.category_id reflns_shell + _name.object_id percent_possible_all + _type.purpose Number + _type.source Recorded _type.container Single _type.contents Real - _units.code kilopascals + _enumeration.range 0.0:100.0 + _units.code none save_ -save_cell_measurement.radiation +save_reflns_shell.percent_possible_gt - _definition.id '_cell_measurement.radiation' - _alias.definition_id '_cell_measurement_radiation' - _definition.update 2012-11-22 + _definition.id '_reflns_shell.percent_possible_gt' + + loop_ + _alias.definition_id + '_reflns_shell_percent_possible_gt' + '_reflns_shell_percent_possible_obs' + '_reflns_shell.percent_possible_obs' + + _definition.update 2012-11-26 _description.text ; - Description of the radiation used to measure the unit-cell data. + Percentage of reflections present in this shell which are significantly + intense (see _reflns.threshold_expression), over that possible. ; - _name.category_id cell_measurement - _name.object_id radiation - _type.purpose Describe + _name.category_id reflns_shell + _name.object_id percent_possible_gt + _type.purpose Number _type.source Recorded _type.container Single - _type.contents Text - - loop_ - _description_example.case - 'neutron' - 'X-ray tube' - 'synchrotron' + _type.contents Real + _enumeration.range 0.0:100.0 + _units.code none save_ -save_cell_measurement.reflns_used +save_reflns_shell.rmerge_f_all - _definition.id '_cell_measurement.reflns_used' - _alias.definition_id '_cell_measurement_reflns_used' - _definition.update 2021-03-01 + _definition.id '_reflns_shell.Rmerge_F_all' + _alias.definition_id '_reflns_shell_Rmerge_F_all' + _definition.update 2012-11-26 _description.text ; - Total number of reflections used to determine the unit cell. - The reflections may be specified as cell_measurement_refln items. + 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. ; - _name.category_id cell_measurement - _name.object_id reflns_used + _name.category_id reflns_shell + _name.object_id Rmerge_F_all _type.purpose Number - _type.source Assigned + _type.source Recorded _type.container Single - _type.contents Integer - _enumeration.range 3: + _type.contents Real + _enumeration.range 0.0: _units.code none save_ -save_cell_measurement.temperature +save_reflns_shell.rmerge_f_gt - _definition.id '_cell_measurement.temperature' + _definition.id '_reflns_shell.Rmerge_F_gt' loop_ _alias.definition_id - '_cell_measurement_temperature' - '_cell_measurement_temp' - '_cell_measurement.temp' + '_reflns_shell_Rmerge_F_obs' + '_reflns_shell.Rmerge_F_obs' + '_reflns_shell_Rmerge_F_gt' - _definition.update 2012-11-22 + _definition.update 2012-11-26 _description.text ; - The temperature at which the unit-cell parameters were measured - (not the temperature of synthesis). + 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. ; - _name.category_id cell_measurement - _name.object_id temperature - _type.purpose Measurand + _name.category_id reflns_shell + _name.object_id Rmerge_F_gt + _type.purpose Number _type.source Recorded _type.container Single _type.contents Real _enumeration.range 0.0: - _units.code kelvins + _units.code none save_ -save_cell_measurement.temperature_su - - _definition.id '_cell_measurement.temperature_su' - - loop_ - _alias.definition_id - '_cell_measurement_temp_su' - '_cell_measurement.temp_esd' +save_reflns_shell.rmerge_i_all - _definition.update 2021-03-03 + _definition.id '_reflns_shell.Rmerge_I_all' + _alias.definition_id '_reflns_shell_Rmerge_I_all' + _definition.update 2012-11-26 _description.text ; - Standard uncertainty of the temperature of at which - the unit-cell parameters were measured. + 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. ; - _name.category_id cell_measurement - _name.object_id temperature_su - _name.linked_item_id '_cell_measurement.temperature' - _type.purpose SU - _type.source Related + _name.category_id reflns_shell + _name.object_id Rmerge_I_all + _type.purpose Number + _type.source Recorded _type.container Single _type.contents Real - _units.code kelvins + _enumeration.range 0.0: + _units.code none save_ -save_cell_measurement.theta_max +save_reflns_shell.rmerge_i_gt + + _definition.id '_reflns_shell.Rmerge_I_gt' + + loop_ + _alias.definition_id + '_reflns_shell_Rmerge_I_obs' + '_reflns_shell.Rmerge_I_obs' + '_reflns_shell_Rmerge_I_gt' - _definition.id '_cell_measurement.theta_max' - _alias.definition_id '_cell_measurement_theta_max' - _definition.update 2012-11-22 + _definition.update 2012-11-26 _description.text ; - Maximum theta scattering angle of reflections used to measure - the crystal unit cell. + 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. ; - _name.category_id cell_measurement - _name.object_id theta_max + _name.category_id reflns_shell + _name.object_id Rmerge_I_gt _type.purpose Number _type.source Recorded _type.container Single _type.contents Real - _enumeration.range 0.0:90.0 - _units.code degrees + _enumeration.range 0.0: + _units.code none save_ -save_cell_measurement.theta_min +save_EXPTL - _definition.id '_cell_measurement.theta_min' - _alias.definition_id '_cell_measurement_theta_min' - _definition.update 2012-11-22 + _definition.id EXPTL + _definition.scope Category + _definition.class Set + _definition.update 2023-01-13 _description.text ; - Minimum theta scattering angle of reflections used to measure - the crystal unit cell. + The CATEGORY of data items used to specify the experimental work + prior to diffraction measurements. These include crystallization + crystal measurements and absorption-correction techniques used. ; - _name.category_id cell_measurement - _name.object_id theta_min - _type.purpose Number - _type.source Recorded - _type.container Single - _type.contents Real - _enumeration.range 0.0:90.0 - _units.code degrees + _name.category_id CIF_CORE + _name.object_id EXPTL save_ -save_cell_measurement.wavelength +save_exptl.crystals_number - _definition.id '_cell_measurement.wavelength' - _alias.definition_id '_cell_measurement_wavelength' - _definition.update 2012-11-22 + _definition.id '_exptl.crystals_number' + _alias.definition_id '_exptl_crystals_number' + _definition.update 2021-03-01 _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 + Total number of crystals used in the measurement of intensities. ; - _name.category_id cell_measurement - _name.object_id wavelength + _name.category_id exptl + _name.object_id crystals_number _type.purpose Number - _type.source Assigned + _type.source Recorded _type.container Single - _type.contents Real - _enumeration.range 0.0: - _units.code angstroms + _type.contents Integer + _enumeration.range 1: + _units.code none save_ -save_CELL_MEASUREMENT_REFLN +save_exptl.method - _definition.id CELL_MEASUREMENT_REFLN - _definition.scope Category - _definition.class Loop - _definition.update 2021-06-29 + _definition.id '_exptl.method' + _definition.update 2014-06-12 _description.text ; - The CATEGORY of data items used to describe the reflection data - used in the measurement of the crystal unit cell. + The method used in the experiment. ; - _name.category_id CELL_MEASUREMENT - _name.object_id CELL_MEASUREMENT_REFLN + _name.category_id exptl + _name.object_id method + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text loop_ - _category_key.name - '_cell_measurement_refln.index_h' - '_cell_measurement_refln.index_k' - '_cell_measurement_refln.index_l' + _description_example.case + 'single-crystal x-ray diffraction' + 'single-crystal neutron diffraction' + 'single-crystal electron diffraction' + 'fiber x-ray diffraction' + 'fiber neutron diffraction' + 'fiber electron diffraction' + 'single-crystal joint x-ray and neutron diffraction' + 'single-crystal joint x-ray and electron diffraction' + 'solution nmr' + 'solid-state nmr' + 'theoretical model' + 'other' save_ -save_cell_measurement_refln.hkl +save_exptl.method_details - _definition.id '_cell_measurement_refln.hkl' - _definition.update 2021-03-01 + _definition.id '_exptl.method_details' + _definition.update 2014-06-12 _description.text ; - Miller indices of a reflection used to measure the unit cell. -; - _name.category_id cell_measurement_refln - _name.object_id hkl - _type.purpose Number - _type.source Derived - _type.container Matrix - _type.dimension '[3]' - _type.contents Integer - _units.code none - _method.purpose Evaluation - _method.expression + A description of special aspects of the experimental method. ; - With c as cell_measurement_refln + _name.category_id exptl + _name.object_id method_details + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text - _cell_measurement_refln.hkl = [c.index_h, c.index_k, c.index_l] -; + loop_ + _description_example.case + '29 structures' + 'minimized average structure' save_ -save_cell_measurement_refln.index_h +save_exptl.special_details - _definition.id '_cell_measurement_refln.index_h' - _alias.definition_id '_cell_measurement_refln_index_h' - _name.category_id cell_measurement_refln - _name.object_id index_h + _definition.id '_exptl.special_details' - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + loop_ + _alias.definition_id + '_exptl_special_details' + '_exptl.details' -save_ + _definition.update 2012-11-22 + _description.text +; + Details of the experiment prior to intensity measurement. + See also _exptl_crystal.preparation +; + _name.category_id exptl + _name.object_id special_details + _type.purpose Describe + _type.source Recorded + _type.container Single + _type.contents Text -save_cell_measurement_refln.index_k +save_ - _definition.id '_cell_measurement_refln.index_k' - _alias.definition_id '_cell_measurement_refln_index_k' - _name.category_id cell_measurement_refln - _name.object_id index_k +save_exptl.transmission_factor_max - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _definition.id '_exptl.transmission_factor_max' + _alias.definition_id '_exptl_transmission_factor_max' + _definition.update 2013-04-11 + _description.text +; + The calculated maximum value of the transmission factor for + the specimen. Its value does not include the effects of + absorption in the specimen mount. The presence of this + item does not imply that the structure factors have been + corrected for absorption. For the applied correction see + _exptl_absorpt.correction_T_max. +; + _name.category_id exptl + _name.object_id transmission_factor_max + _type.purpose Measurand + _type.source Derived + _type.container Single + _type.contents Real + _enumeration.range 0.0:1.0 + _units.code none save_ -save_cell_measurement_refln.index_l +save_exptl.transmission_factor_max_su - _definition.id '_cell_measurement_refln.index_l' - _alias.definition_id '_cell_measurement_refln_index_l' - _name.category_id cell_measurement_refln - _name.object_id index_l + _definition.id '_exptl.transmission_factor_max_su' + _definition.update 2021-09-23 + _description.text +; + Standard uncertainty of _exptl.transmission_factor_max. +; + _name.category_id exptl + _name.object_id transmission_factor_max_su + _name.linked_item_id '_exptl.transmission_factor_max' + _units.code none - _import.get [{'file':templ_attr.cif 'save':Miller_index}] + _import.get [{'file':templ_attr.cif 'save':general_su}] save_ -save_cell_measurement_refln.theta +save_exptl.transmission_factor_min - _definition.id '_cell_measurement_refln.theta' - _alias.definition_id '_cell_measurement_refln_theta' - _definition.update 2012-11-22 + _definition.id '_exptl.transmission_factor_min' + _alias.definition_id '_exptl_transmission_factor_min' + _definition.update 2013-04-11 _description.text ; - Theta angle of reflection used to measure the crystal unit cell. + The calculated minimum value of the transmission factor for + the specimen. Its value does not include the effects of + absorption in the specimen mount. The presence of this + item does not imply that the structure factors have been + corrected for absorption. For the applied correction see + _exptl_absorpt.correction_T_min. ; - _name.category_id cell_measurement_refln - _name.object_id theta + _name.category_id exptl + _name.object_id transmission_factor_min _type.purpose Measurand - _type.source Recorded + _type.source Derived _type.container Single _type.contents Real - _enumeration.range 0.0:90.0 - _units.code degrees + _enumeration.range 0.0:1.0 + _units.code none save_ -save_cell_measurement_refln.theta_su +save_exptl.transmission_factor_min_su - _definition.id '_cell_measurement_refln.theta_su' + _definition.id '_exptl.transmission_factor_min_su' _definition.update 2021-09-23 _description.text ; - Standard uncertainty of _cell_measurement_refln.theta. + Standard uncertainty of _exptl.transmission_factor_min. ; - _name.category_id cell_measurement_refln - _name.object_id theta_su - _name.linked_item_id '_cell_measurement_refln.theta' - _units.code degrees + _name.category_id exptl + _name.object_id transmission_factor_min_su + _name.linked_item_id '_exptl.transmission_factor_min' + _units.code none _import.get [{'file':templ_attr.cif 'save':general_su}] @@ -9955,30 +10052,30 @@ save_exptl_absorpt.special_details _description_example.case _description_example.detail ; - X-ray beam inhomogeneity and goniometer imperfection account for much - of the difference between estimated values of Tmin and Tmax and the - _exptl_absorpt_correction_ values. + X-ray beam inhomogeneity and goniometer imperfection account for much + of the difference between estimated values of Tmin and Tmax and the + _exptl_absorpt_correction_ values. ; ; - Text modified from: - Petty, Anthony J. et al. Computationally aided design of a high- - performance organic semiconductor: the development of a universal - crystal engineering core. Chemical Science, 2019 - https://doi.org/10.1039/C9SC02930C - COD 1552381 + Text modified from: + Petty, Anthony J. et al. Computationally aided design of a high- + performance organic semiconductor: the development of a universal + crystal engineering core. Chemical Science, 2019 + https://doi.org/10.1039/C9SC02930C + COD 1552381 ; ; - Neutron linear absorption coefficient is wavelength dependent. The value - of 0.2216 (mm^-1^) shown in _exptl_absorpt_coefficient_mu is the sample - absorption coefficient for a neutron wavelength at 1.0 \%A. + Neutron linear absorption coefficient is wavelength dependent. The + value of 0.2216 (mm^-1^) shown in _exptl_absorpt_coefficient_mu is the + sample absorption coefficient for a neutron wavelength at 1.0 \%A. ; ; - Text modified from: - Lengyel, Jeff et al. Antiferroelectric Phase Transition in a Proton- - Transfer Salt of Squaric Acid and 2,3-Dimethylpyrazine. - Journal of the American Chemical Society, 2019, 141, 16279-16287 - https://doi.org/10.1021/jacs.9b04473 - COD 4127699 + Text modified from: + Lengyel, Jeff et al. Antiferroelectric Phase Transition in a Proton- + Transfer Salt of Squaric Acid and 2,3-Dimethylpyrazine. + Journal of the American Chemical Society, 2019, 141, 16279-16287 + https://doi.org/10.1021/jacs.9b04473 + COD 4127699 ; save_ @@ -19634,25 +19731,25 @@ save_ATOM_ANALYTICAL _category_key.name '_atom_analytical.id' _description_example.case ; - loop_ - _atom_analytical.id - _atom_analytical.analyte - _atom_analytical.meas_id - _atom_analytical.chemical_species - _atom_analytical.analyte_mass_percent - _atom_analytical.chemical_species_mass_percent - 1 Si a 'Si O2' ? 22.7 - 2 Al a 'Al2 O3' ? 27.4 - 3 Ti b 'Ti O2' ? 2.7 - 4 Si c . 10.5 . - 5 Si d Si 11.7 11.7 + loop_ + _atom_analytical.id + _atom_analytical.analyte + _atom_analytical.meas_id + _atom_analytical.chemical_species + _atom_analytical.analyte_mass_percent + _atom_analytical.chemical_species_mass_percent + 1 Si a 'Si O2' ? 22.7 + 2 Al a 'Al2 O3' ? 27.4 + 3 Ti b 'Ti O2' ? 2.7 + 4 Si c . 10.5 . + 5 Si d Si 11.7 11.7 ; _description_example.detail ; - There are three separate determinations of Si content, and one each - of Al and Ti. The amount of Al is reported as the mass percent of - Al2O3. The equivalent amount of Al is not given. There are four - different measurements presented in this table. + There are three separate determinations of Si content, and one each + of Al and Ti. The amount of Al is reported as the mass percent of + Al2O3. The equivalent amount of Al is not given. There are four + different measurements presented in this table. ; save_ @@ -19857,26 +19954,26 @@ save_ATOM_ANALYTICAL_MASS_LOSS _category_key.name '_atom_analytical_mass_loss.id' _description_example.case ; - loop_ - _atom_analytical_mass_loss.id - _atom_analytical_mass_loss.meas_id - _atom_analytical_mass_loss.percent - _atom_analytical_mass_loss.temperature - LOD1 a 2 328 - LOI1 a 5 623 - LOI2 a 10 1023 - LOI3 a 15 1373 - LOI4 b 5 673 - LOI5 b 10 1123 + loop_ + _atom_analytical_mass_loss.id + _atom_analytical_mass_loss.meas_id + _atom_analytical_mass_loss.percent + _atom_analytical_mass_loss.temperature + LOD1 a 2 328 + LOI1 a 5 623 + LOI2 a 10 1023 + LOI3 a 15 1373 + LOI4 b 5 673 + LOI5 b 10 1123 ; _description_example.detail ; - Four mass-loss percentages are given for measurement 'a', and two - for measurement 'b'. The mass losses were recorded after exposing - the specimen to the listed temperatures. The mass lost at a lower - temperature for the same measurement should be included in the - higher temperatures; that is, for measurement 'a', the total mass - loss after four measurements is 15 wt%, not (2+5+10+15) wt%. + Four mass-loss percentages are given for measurement 'a', and two + for measurement 'b'. The mass losses were recorded after exposing + the specimen to the listed temperatures. The mass lost at a lower + temperature for the same measurement should be included in the + higher temperatures; that is, for measurement 'a', the total mass + loss after four measurements is 15 wt%, not (2+5+10+15) wt%. ; save_ @@ -20053,18 +20150,18 @@ save_ATOM_ANALYTICAL_SOURCE _category_key.name '_atom_analytical_source.id' _description_example.case ; - loop_ - _atom_analytical_source.id - _atom_analytical_source.technique - _atom_analytical_source.equipment_make - a XRF 'Hitachi Lab-X5000' - b 'X-ray fluorescence EDS' 'Hitachi Lab-X5000' - c ICP . - d EDS . + loop_ + _atom_analytical_source.id + _atom_analytical_source.technique + _atom_analytical_source.equipment_make + a XRF 'Hitachi Lab-X5000' + b 'X-ray fluorescence EDS' 'Hitachi Lab-X5000' + c ICP . + d EDS . ; _description_example.detail ; - Four different measurements of elemental composition are enumerated. + Four different measurements of elemental composition are enumerated. ; save_ @@ -20134,15 +20231,15 @@ save_atom_analytical_source.special_details loop_ _description_example.case ; - XRF utilising a WDS detector system calibrated for the analysis - of iron ores. + XRF utilising a WDS detector system calibrated for the analysis + of iron ores. ; ; - Laser Induced Breakdown Spectroscopy. Measurements carried out - by commercial laboratory, report #P90. + Laser Induced Breakdown Spectroscopy. Measurements carried out + by commercial laboratory, report #P90. ; ; - Detector calibrated following Smith (2018). + Detector calibrated following Smith (2018). ; save_ @@ -20194,59 +20291,60 @@ save_ATOM_SITE _description_example.case _description_example.detail ; - loop_ - _atom_site.label - _atom_site.occupancy - _atom_site.disorder_assembly - _atom_site.disorder_group - C1 1 . . - H11A .5 M 1 - H12A .5 M 1 - H13A .5 M 1 - H11B .5 M 2 - H12B .5 M 2 - H13B .5 M 2 -; -; - A hypothetical example of a positional disorder description. Disorder - assembly 'M' describes a methyl group with two alternative configurations - '1' and '2': - - H11B H11A H13B - . | . - . | . - . | . - C1 --------C2--- - / . \ - / . \ - / . \ - H12A H12B H13A -; -; - loop_ - _atom_site.label - _atom_site.type_symbol - _atom_site.fract_x - _atom_site.fract_y - _atom_site.fract_z - _atom_site.occupancy - _atom_site.disorder_assembly - _atom_site.disorder_group - Cu1 Cu 0.78443(2) 0.88297(4) 0.37825(2) 1 . . - Co1 Co 0.77504(2) 0.66957(4) 0.54249(2) 0.78(3) A 1 - Mn1 Mn 0.77504(2) 0.66957(4) 0.54249(2) 0.22(3) A 2 - O1 O 0.85532(9) 0.95747(19) 0.28965(9) 1 . . - O2 O 0.84868(9) 0.94662(19) 0.14953(8) 1 . . - # ... -; -; - An example of a compositional disorder description. Disorder assembly 'A' - describes a site that is simultaneously occupied by Co and Mn atoms which - are assigned to disorder group '1' and disorder group '2' respectively. - - The example was created based on data from: - Li, Ang et al. (2021). Dalton Transactions, 50(2), 681-688. - https://doi.org/10.1039/d0dt03269g + loop_ + _atom_site.label + _atom_site.occupancy + _atom_site.disorder_assembly + _atom_site.disorder_group + C1 1 . . + H11A .5 M 1 + H12A .5 M 1 + H13A .5 M 1 + H11B .5 M 2 + H12B .5 M 2 + H13B .5 M 2 +; +; + A hypothetical example of a positional disorder description. Disorder + assembly 'M' describes a methyl group with two alternative + configurations '1' and '2': + + H11B H11A H13B + . | . + . | . + . | . + C1 --------C2--- + / . \ + / . \ + / . \ + H12A H12B H13A +; +; + loop_ + _atom_site.label + _atom_site.type_symbol + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + _atom_site.occupancy + _atom_site.disorder_assembly + _atom_site.disorder_group + Cu1 Cu 0.78443(2) 0.88297(4) 0.37825(2) 1 . . + Co1 Co 0.77504(2) 0.66957(4) 0.54249(2) 0.78(3) A 1 + Mn1 Mn 0.77504(2) 0.66957(4) 0.54249(2) 0.22(3) A 2 + O1 O 0.85532(9) 0.95747(19) 0.28965(9) 1 . . + O2 O 0.84868(9) 0.94662(19) 0.14953(8) 1 . . + # ... +; +; + An example of a compositional disorder description. Disorder assembly + 'A' describes a site that is simultaneously occupied by Co and Mn + atoms which are assigned to disorder group '1' and disorder group '2' + respectively. + + The example was created based on data from: + Li, Ang et al. (2021). Dalton Transactions, 50(2), 681-688. + https://doi.org/10.1039/d0dt03269g ; save_ @@ -27033,7 +27131,7 @@ save_ Changed the content type of the _journal.paper_doi data item from 'Code' to 'Text' and added an example case. ; - 3.2.0 2023-02-06 + 3.2.0 2023-03-02 ; Added data names to allow multi-data-block expression of data sets. @@ -27100,4 +27198,8 @@ save_ Updated several definitions with enumeration values to be case-sensitive. Removed the _citation_author.key and _citation_editor.id data items. + + Reparented CELL to DIFFRN category and added key data names to allow + multiple cells for different diffraction conditions. Deprecated + _cell_measurement.temperature,pressure data names. ; diff --git a/examples/cell-measurement-multi-block.cif b/examples/cell-measurement-multi-block.cif new file mode 100644 index 0000000..d1275f7 --- /dev/null +++ b/examples/cell-measurement-multi-block.cif @@ -0,0 +1,57 @@ +#\#CIF_2.0 +## +# Represents an experiment where the cell measurement was performed under +# different conditions to the data collection. +# +# In this case the measurements are presented in two separate data blocks. +# This file conveys slightly more information on the differences of measurement +# conditions than the single block 'cell-measurement-single-block.cif' example +# file that uses deprecated data items from the CELL_MEASUREMENT category. +## +data_main_collection + +_cell.length_a 11.520(12) +_cell.length_b 11.210(11) +_cell.length_c 4.920(5) +_cell.angle_alpha 90.00000 +_cell.angle_beta 90.8331(5) +_cell.angle_gamma 90.00000 +_cell.volume 635.3(11) +_cell.formula_units_Z 4 +## +# Cell measurement details are provided in another data block. +## +_cell_measurement.condition_id 2 +_cell_measurement.theta_max 50.5 +_cell_measurement.theta_min 10.1 +_cell_measurement.reflns_used 20 + +_diffrn.id 1 +_diffrn.ambient_temperature 293 +_diffrn.ambient_pressure 10 +_diffrn_radiation.type 'Cu K\a' +_diffrn_radiation_wavelength.value 1.5418 +_diffrn_radiation.probe x-ray + +# Atom site coordinates and results would be provided in this data block, +# but are removed for brevity in this example. + +# ... + +data_cell_measurement + +_diffrn.id 2 +_diffrn.ambient_temperature 290 # Different temperature. +_diffrn.ambient_pressure 10 + +_diffrn_radiation.type 'Mo K\a' # Different radiation type. +_diffrn_radiation_wavelength.value 0.701 +_diffrn_radiation.probe x-ray + +# Any _cell_measurement items in this data block would relate to the +# determination of a unit cell used for any diffraction data presented +# in this data block. +_cell_measurement.condition_id 2 # Default value. +_cell_measurement.theta_max 50.4 +_cell_measurement.theta_min 10.0 +_cell_measurement.reflns_used 30 diff --git a/examples/cell-measurement-single-block.cif b/examples/cell-measurement-single-block.cif new file mode 100644 index 0000000..91911b1 --- /dev/null +++ b/examples/cell-measurement-single-block.cif @@ -0,0 +1,53 @@ +#\#CIF_2.0 +## +# Represents an experiment where the cell measurement was performed under +# different conditions to the data collection. +# +# In this case certain cell measurement conditions that differ from the data +# collection conditions are recorded using a very limited set of data items +# from the CELL_MEASUREMENT category. As a result, this file simply cannot fully +# convey the information provided in the 'cell-measurement-multi-block.cif' +# example file. +# +# Most items from the CELL_MEASUREMENT category have now been deprecated and +# the multi-block approach should be used in newly created files as it allows +# to describe cell measurements in more detail using data items from various +# categories such as DIFFR, DIFFRN_SOURCE and DIFFR_RADIATION. However, the +# deprecated data items may still be encountered in archival copies of older +# CIF files. +## +data_main_collection + +_cell.length_a 11.520(12) +_cell.length_b 11.210(11) +_cell.length_c 4.920(5) +_cell.angle_alpha 90.00000 +_cell.angle_beta 90.8331(5) +_cell.angle_gamma 90.00000 +_cell.volume 635.3(11) +_cell.formula_units_Z 4 +## +# The CELL_MEASUREMENT category is only capable of conveying differences in +# measurement temperature, pressure, radiation type and wavelength, but no +# other aspects of the experiment that may also differ. +## +# BEGIN DEPRECATED ITEMS +_cell_measurement.temperature 290 +_cell_measurement.pressure 10.1 +_cell_measurement.radiation 'Mo K\a' +_cell_measurement.wavelength 0.701 +# END DEPRECATED ITEMS +_cell_measurement.theta_max 50.4 +_cell_measurement.theta_min 10.0 +_cell_measurement.reflns_used 30 + +_diffrn.ambient_temperature 293 +_diffrn.ambient_pressure 10 +_diffrn_radiation.type 'Cu K\a' +_diffrn_radiation_wavelength.value 1.5418 +_diffrn_radiation.probe x-ray + +# Atom site coordinates and results would be provided in this data block, +# but are removed for brevity in this example. + +# ...