############################################################################## # # # CIF CORE DEFINITIONS # # -------------------- # # # # This dictionary contains the names and definitions of the Core data items # # recognised by the International Union of Crystallography for the exchange # # of data between laboratories and submissions to journals and databases. # # # # The STAR/DDL dictionary is available as the file "ddl_core.dic" # # located at URL ftp://ftp.iucr.org/pub/ddl_core.dic # # # # Copyright 2007 International Union of Crystallography # ############################################################################## data_on_this_dictionary _dictionary_name cif_core.dic _dictionary_version 2.3.2 _dictionary_update 2007-03-27 _dictionary_history ; 1991-05-27 Created from CIF Dictionary text. SRH 1991-05-30 Validated with CYCLOPS & CIF ms. SRH 1991-06-03 Adjustments to some definitions. SRH 1991-06-06 Adjustments a la B. McMahon. SRH 1991-06-18 Additions & some redefinitions. SRH 1991-07-04 Corrected 90:0 in *_detect_slit_. SRH 1991-09-20 Additions & some redefinitions. SRH 1991-09-20 Final published version. IUCr 1991-11-12 Add _diffrn_ambient_environment. SRH 1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH 1993-02-23 Apply global_ and 'unknown' -> '?' SRH 1993-03-05 Changes resulting from MM dictionary. SRH 1993-05-20 Changes arising from new DDL commands. SRH 1993-08-05 Additional finetuning pre-Beijing. SRH 1993-12-22 Introductory sections added to categories. BMcM 1993-12-22 Additional categories from mm work: audit_author, citation, atom_sites_fract_tran_matrix. BMcM 1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM 1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM 1994-03-01 Add 'atom_site_aniso_ratio'. BMcM 1994-04-15 Comments from IDB on draft version for circulation. BMcM 1994-04-15 Added _publ_section_exptl_solution. BMcM 1994-07-14 Added B. H. Toby's suggested _diffrn_radiation_xray_symbol and _diffrn_radiation_xray_target. BMcM 1994-08-05 Revised definition for _diffrn_reflns_number (S.R. Hall). BMcM 1994-08-05 Added _atom_type_scat_length_neutron (B.H. Toby). BMcM 1994-10-13 Reworded _diffrn_standards_ a la S.R. Hall. BMcM 1994-10-13 Added _diffrn_radiation_probe for non-X-ray experiments. BMcM 1995-01-17 Rewording of definition of _chemical_melting_point. BMcM 1995-02-24 Changed text references to e.s.d to 'standard uncertainty'. BMcM 1995-07-08 Added _chemical_formula_iupac. BMcM 1995-07-09 Finally added _symmetry_equiv_pos_id. BMcM 1995-07-09 _units_extension, _units_conversion and _units_description superseded by _units and _units_detail. Suffixed datanames retained as separate entries. BMcM 1995-10-23 Added _refine_ls_R_Fsqd_factor and _refine_ls_R_I_factor BMcM 1996-03-25 Correlated with mmCIF release 0.8 BMcM 1996-05-16 Added some extra datanames for use by Acta: _publ_section_synopsis, _publ_section_title_footnote, _publ_author_footnote, _journal_paper_category, and various _journal_index_ categories BMcM 1996-05-20 Added geom_hbond category BMcM 1996-06-10 Datanames with suffixes to indicate units moved to a new compatibility dictionary cif_compat.dic BMcM 1996-06-10 Embarrassing _units_ stuff removed from geom_hbond BMcM 1996-06-10 _list_mandatory and _list_reference added to _publ_author_ datanames (where _list was given as "both") BMcM 1996-06-10 Added audit_conform category BMcM 1996-06-11 Added audit_link category BMcM 1996-06-11 Reworded _exptl_crystal_F_000 definition BMcM 1996-06-11 Added _atom_site_U_equiv_geom BMcM 1996-06-11 Added publ_body category BMcM 1996-06-27 Added examples for most of the remaining category overviews BMcM 1996-06-27 Added _journal_language BMcM 1996-06-28 Added area-detector definitions from mmCIF dictionary: _diffrn_measurement_device_details, *_specific and *_type; _diffrn_radiation_detector_details, *_specific, *_type; _diffrn_radiation_source_details, *_power, *_specific, *_target, *_type; reflns_shell category BMcM Added _refine_ls_d_res_high and *_low and changed wording of definitions for R factors to include these. BMcM Added 'h' and 'f' flags to _refln_observed_status. BMcM 1996-07-05 Some typos fixed and examples modified as suggested by P.Strickland and I.D.Brown. BMcM 1996-07-27 BMcM: Added example for _diffrn_orient_refln_[] from G. Madariaga U~ij~ changed to U^ij^ a la Nomenclature Commission Definition of _diffrn_ambient_environment changed to omit vacuum as a possible default environment Changed definitions of *_site_symmetry_* items to I.D.Brown's suggested wording. Compressed various journal indexing categories into one Changed upper enumeration values for _refln_symmetry_epsilon and _refln_symmetry_multiplicity to 48. Added references to deprecated use of B values. Modified descriptions of phone, fax number conventions _publ_manuscript_incl_ entries reworded for greater clarity and given individual data blocks Added _list_reference to _symmetry_equiv_pos_id and changed _list value to 'both' for *_as_xyz to allow the P1 case Added _atom_site_B_equiv_geom for completeness Modified definitions of _atom_sites_[Cartn,fract]_tran_vector_ Added _units stuff to _chemical_formula_weight_* and _exptl_crystal_density_ items Added *_theta, *_omega to _diffrn_orient_refln_angle_ Added 'q' to enumeration list for _diffrn_refln_scan_mode Reworded definition in _diffrn_scale_group_[] Permitted esd for _refln_phase_meas (necessitates splitting _refln_phase_ datablock in two) Added _type_conditions esd for _reflns_scale_meas_ 1996-07-28 BMcM: Added example for refln_scale_[] and second example for _refln_[] from Xtal test data set. Changed references to category names to CAPITALS. Merged CELL and CELL_MEASUREMENT categories. Added _units deg to all angle quantities. Renamed _citation_journal_coden_CAS as _citation_journal_abstract_id_CAS Removed _diffrn_measurement_device_details, *_specific, *_type, _diffrn_radiation_detector_details, *_specific, *_type, _diffrn_radiation_source_power, *_specific, *_target, *_type, pending full analysis of requirements for describing diffraction apparatus. Reworded _exptl_crystal_F_000 definition again 1996-08-03 Reworded _refine_ls_number_reflns definition a la S.R.Hall BMcM 1996-09-10 BMcM: Clarified _diffrn_attenuator_scale definition with help from SRH In _refln_symmetry_multiplicity, changed 'structure-factor value' to 'structure-factor magnitudes' Slight modification to _diffrn_reflns_number to exclude all systematic absences, not just those due to centring Removed footnote markers from example of _publ_section_title_footnote Added new example to SYMMETRY_EQUIV category to explain the use of _symmetry_equiv_pos_id Reworking of DIFFRN_RADIATION and DIFFRN_MEASUREMENT categories and introduction of DIFFRN_DETECTOR and DIFFRN_SOURCE a la I.D.Brown 1996-09-11 Corrected category assignment for _diffrn_standards_ items BMcM 1996-09-12 BMcM: Added _cell_id and _cell_measurement_refln_id Changed the term "id" to "identifier" in definitions Renamed _citation_journal_abstract_id_CAS as _citation_abstract_id_CAS Added _audit_block_code and changed definition of _audit_link_block_code to refer to it 1996-09-18 BMcM: Fine tuning of IDB's new DIFFRN categories: in DIFFRN_DETECTOR changed *_type to *_device and added *_device_type. Moved _diffrn_radiation_detector back to DIFFRN_RADIATION category with expanded definition. Reworded definitions of _diffrn_measurement_device and *_device_type. In DIFFRN_RADIATION changed enumeration range for *_polarisn_norm to -180:180 and added 'as viewed from the specimen' to the definition; also added 'Cu K-L~2,3~' to examples for *_type. Reworded definitions for _diffrn_refln_index and _diffrn_source_target, and changed _type of _diffrn_source_power to "numb". Introduced _diffrn_detector_dtime in the DIFFRN_DETECTOR category and restored _diffrn_radiation_detector_dtime to DIFFRN_RADIATION 1996-09-25 BMcM: Reworded definitions of _atom_site_disorder_assembly and *_group 1996-10-02 BMcM: Changed _symmetry_equiv_pos_id to _symmetry_equiv_pos_site_id in recognition of the technical meaning of 'position' in International Tables Addition of the names of the relevant units to definitions of _atom_type_scat_length_neutron, _exptl_crystal_size_, _geom_hbond_distance_, _refine_ls_d_res_high and *_low, _reflns_shell_d_res_high and *_low; and cosmetic expansion of units listed in the definitions for _diffrn_source_current, *_power and *_voltage Addition of '_related_function conversion' to _atom_site_B_equiv_geom and *_U_equiv_geom and _atom_site_B_iso_or_equiv and *_U_iso_or_equiv Examples for CELL_MEASUREMENT_REFLN and DIFFRN_REFLN from Gotzon Madariaga Renamed _atom_site_U_equiv_geom as _atom_site_U_equiv_geom_mean and likewise for *_B_* to increase the consistency of abbreviations, as suggested by I.D. Brown Added disorder example to the ATOM_SITE category description 1996-10-15 BMcM: Modified description of example for DIFFRN_REFLN Changed _enumeration_range of _atom_site_attached_hydrogens from 0:4 to 0:8 (cf CSD entry with refcode DUTMAG01) (PRE) Added '_enumeration_default cif' to _publ_body_format Changed underscores to spaces in the example for the Hall spacegroup symbol in data_symmetry_[] Deleted extraneous '_' in data_(_)citation_abstract_id_CAS 1996-10-27 BMcM: Changed psiscan to psi-scan at request of SRH 1996-11-05 BMcM: Changed _citation_book_coden_ISBN to _citation_book_id_ISBN, _citation_journal_coden_ASTM to _citation_journal_id_ASTM, _citation_journal_coden_CSD to _citation_journal_id_CSD, _citation_journal_coden_ISSN to _citation_journal_id_ISSN, and _citation_Medline_AN to _citation_database_id_Medline. Also modified description of CODEN in _citation_journal_id_ASTM and _database_journal_ASTM (suggested by PMDF) The phrase 'diffraction data' modified to 'intensities' in several places, some other cosmetic commas and enforcement of consistent lower-case units names (PMDF) Clarification of the definition for _diffrn_radiation_polarisn_norm (PMDF) Added 'constr' to _refine_ls_hydrogen_treatment (SRH) Corrected misassignment of category of _diffrn_radiation_detector_dtime (H.J.Bernstein) 1996-11-06 BMcM: Added "_list yes" to items in the REFLNS_SHELL category (IDB) Added "measured" to definition of _reflns_shell_number_unique_all Changed enumeration range for _diffrn_standards_decay_% to ":100" and added statement about negative values (PMDF/SRH) 1996-11-08 BMcM: _diffrn_radiation_detector, _diffrn_radiation_detector_dtime and _diffrn_radiation_source removed (these will be transferred to cif_compat.dic for compatibility with files conforming to the original dictionary) _diffrn_radiation_wavelength_* items moved to new category 1996-11-12 BMcM: Deleted _cell_id and _cell_measurement_refln_id, and clarified the intent of the CELL category in _cell_[] (PMDF) Some small rewordings of various _diffrn_* items due to B.H.Toby 1996-11-14 BMcM: Imposed consistency on the nomenclature of diffraction device data names: _diffrn_detector_device_type -> *_detector_type, _diffrn_measurement_device_details -> *_measurement_details, *_measurement_device_type -> *_measurement_type; introduction of _diffrn_source_device and parallel definitions. Existing *_measurement_details example moved to *_special_details (PMDF) 1996-11-21 BMcM: Reintroduced _diffrn_measurement_device_details, further tidying of data names thus: _diffrn_measurement_type -> *_device_type; _diffrn_detector_device and _diffrn_source_device both drop "_device" (PMDF) Added _journal_data_validation_number and _publ_requested_category to enable handling of CIF-access submissions by Acta Cryst. C 1996-11-23 A few typos fixed. BMcM 1996-11-24 BMcM: Added 'gaussian', 'multi-scan' and 'numerical' to enumeration list for _exptl_absorpt_correction_type (SRH) Added 'mixed' to enumeration list for _refine_ls_hydrogen_treatment (SRH) 1996-11-25 A few typos fixed (BMcM) 1996-11-27 BMcM: Removed looped _related_item from _publ_contact_author and reintroduced _diffrn_radiation_detector, *_dtime and _diffrn_radiation_source (see 1996-11-08) with "_related_function replace" as a preparation for using this mechanism further in version 2.1. 1996-11-27 Release version 2.0. IUCr 1997-01-20 BMcM: Some small changes thanks to PMDF. Double space after period at end of sentence changed to single space throughout; _citation_database_id_Medline _diffrn_detector_type moved to correct alphabetic sequence; space introduced between sentences in definition of _citation_journal_id_CSD; some other minor grammatical changes 1997-10-30 BMcM: (changes to align with Acta C Notes for Authors) Obsoleted *_obs_* entries in REFLNS and REFINE_LS categories and replaced with *_gt_*; obsoleted _refine_ls_shift/esd_ by _refine_ls_shift/su_; obsoleted _atom_site_thermal_displace_type by *_adp_type 1997-11-05 BMcM: (changes to align with Acta C Notes for Authors) Added _diffrn_detector_area_resol_mean, _diffrn_measured_fraction_theta_max and *_full, _diffrn_reflns_theta_full 1997-11-05 BMcM: Added _reflns_number_Friedel; changed various *_obs items in examples to *_gt equivalents and likewise for other obsoleted items 1997-11-24 BMcM: Slightly changed wording of _reflns_number_Friedel and _reflns_threshold_expression at suggestion of I.D.Brown. Modified definition of _refine_ls_abs_structure_Flack and changed the text of the example in category REFINE at the request of H.D.Flack. 1997-12-08 BMcM: Removed the phrase "(enantiomorph or polarity)" from _refine_ls_abs_structure_Flack and *_Rogers because "absolute structure" is a phrase uniquely defined (H.D.Flack) 1997-12-08 BMcM: Several instances of \s changed to u 1997-12-08 BMcM: Modified definitions of _reflns_number_total and *_Friedel (after H.D.Flack) to clarify the distinction between crystal-class and Laue-symmetry independent reflection sets 1997-12-08 BMcM: Added _chemical_absolute_configuration and _chemical_optical_rotation (H.D.Flack) 1998-08-04 BMcM: Moved _diffrn_pressure_history and _diffrn_thermal_history from draft msCIF dictionary to core as _exptl_crystal_pressure_history and _exptl_crystal_thermal_history (G. Madariaga/I.D.Brown) Moved _diffrn_symmetry_description and REFINE_LS_CLASS from draft msCIF dictionary to core (G. Madariaga/I.D.Brown) 1998-08-04 BMcM: Minor rewordings of _refine_ls_R_Fsqd_factor, _refine_ls_R_I_factor, various definitions referring to F_calc in electrons, and _reflns_shell_number_unique_* (I.D.Brown) 1998-08-04 BMcM: added _reflns_Friedel_coverage (H.D.Flack/S.R.Hall) 1998-08-04 BMcM: changed formula for F(000) (from F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ to F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ ) (H.D.Flack) 1998-08-04 BMcM: added 'syn' and 'unk' as enumerations to _chemical_absolute_configuration (H.D.Flack/A.Linden) 1998-09-02 BMcM: added _exptl_crystal_size_length and modified slightly the definition of _exptl_crystal_size_ (W.Clegg/I.D.Brown) Added _diffrn_attenuator_material (I.D.Brown) Added sentence explaining the physical meaning of the _enumeration_range to _refine_ls_abs_structure_Flack (H.D.Flack) Some rewording in _chemical_absolute_configuration implying that for absolute configuration determination the measurement and reporting of the optical rotation in solution are considered mandatory. (H.D.Flack) Some rewording in _reflns_number_total and *_gt to clarify the inclusion of Friedel reflections; addition of _reflns_Friedel_coverage; deletion of _reflns_number_Friedel (H.D.Flack/S.R.Hall) Further minor rewording to _reflns_shell_number_unique_all, *_gt, *_obs (H.D.Flack) 1998-09-10 BMcM: transferred _diffrn_reflns_number_of_classes and the categories DIFFRN_REFLNS_CLASS, REFLNS_CLASS and REFLNS_SHELL_CLASS from the draft msCIF dictionary; added _diffrn_refln_class_code and _refln_class_code to link individual reflections to their related categories. 1998-12-08 BMcM: implemented H.D. Flack's reworking of DIFFRN_REFLNS_CLASS, REFLNS_CLASS, REFLNS_SHELL_CLASS and REFINE_LS_CLASS, deleting the latter two; removed _diffrn_reflns_number_of_classes. 1998-12-15 BMcM: completed the above reworking; fixed embarrassing typo for _related_function 1999-01-16 BMcM: coreDMG review of version 2.1beta5. Numerous small changes from I.D.Brown, the most significant being: _atom_site_occupancy definition clarifies how to impose an experimental uncertainty on the _enumeration_range; _atom_site_U_iso_or_equiv enumeration range set to infinity; _atom_type_analytical_mass_% enumeration range set as 0:100; expanded definitions of _diffrn_radiation_probe and *_type to clarify the distinction between these two items; added reference to _exptl_crystal_size to the definition of _exptl_crystal_description, and modified the definition of _exptl_crystal_face_diffr_ ; new data item _refln_d_spacing; clarified the role of _reflns_special_details in specifying whether Friedel pairs have been averaged; Numerous small changes from H.D.Flack, most significantly: removed enumeration range from _diffrn_refln_counts_ because *_net can go negative; fixed various typos in equations for wR and S; removed reference to Friedel reflections from _refln_symmetry_multiplicity 1999-01-24 BMcM: further revision to wording of _refln_symmetry_multiplicity following discussions by HDF and IDB Numerous small changes from G.Madariaga, most significantly: a instead of A for real-space cell lengths (_atom_site_B_iso_or_equiv and _atom_site_U_iso_or_equiv); _related_function alternate for _atom_site_Cartn_ & _fract_; "or scattering lengths" added to _atom_type_scat_source; deleted incorrect _list_reference in DIFFRN_RADIATION; added rtf to enumeration in _publ_body_format; added enumeration range to _refine_ls_abs_structure_Rogers 1999-02-04 BMcM: fixed some long lines 1999-02-06 BMcM: data names using sigma as an indicator of experimental standard uncertainty replaced by equivalents using the preferred 'u' notation (HDF): _diffrn_refln_intensity_sigma _diffrn_reflns_av_sigmaI/netI _diffrn_reflns_class_av_sgI/I _diffrn_standards_scale_sigma _reflns_shell_meanI_over_sigI_all _reflns_shell_meanI_over_sigI_gt (_reflns_shell_meanI_over_sigI_obs already replaced by *_gt) addition of '_related function alternate' to new data items corresponding to old items with '_related_function replace' (SRH) Example for _citation_journal_id_CSD changed to 0070 to reflect current practice at PDB (F.C.Bernstein) Added _atom_type_scat_dispersion_source (GM) 1999-03-24 Some minor cosmetic modifications (BMcM) 1999-03-24 Release version 2.1. IUCr 2001-01-09 BMcM: simplified entry for _chemical_absolute_configuration (H.D.Flack) Added _geom_bond_valence and the new categories VALENCE_PARAM and VALENCE_REF (I.D.Brown) 2001-01-11 BMcM: Categories EI, EO, EM added to _publ_requested_category 2001-01-11 Release version 2.2. IUCr 2003-09-28 BMcM: incorporated changes approved by COMCIFS following discussions of the core Dictionary Management Group: _atom_site_fract_ nonsense enumeration default value removed _atom_site_refinement_flags deprecated in favour of new *_flags_posn, *_adp and *_occupancy items _atom_sites_special_details added _cell_reciprocal_angle_ and *_length_ added '_type_conditions esd' added to _chemical_melting_point _chemical_melting_point_gt and *_lt added Added several new items describing chemical properties to the CHEMICAL category: _chemical_properties_biological and *_physical, _chemical_temperature_decomposition_* and *_sublimation_*, at the request of CCDC _citation_database_id_CSD added at request of CCDC Several additional tags storing deposition numbers of database entries and record revision history at request of CCDC: _database_code_depnum_ccdc_fiz, *_journal, *_archive and _database_CSD_history Added _diffrn_ambient_pressure_gt,lt and *_temperature_gt,lt Added _diffrn_source_take-off_angle Added _diffrn_standards_decay_%_lt _diffrn_reflns_measured_fraction_resolution_full and *_max introduced as replacements for _diffrn_measured_fraction_theta_full and *_max, moved to a more appropriate category and defined in terms of resolution rather than angle which depends on the radiation used. Likewise for _diffrn_reflns_resolution_full and *_max as replacements for _diffrn_reflns_theta_full and *_max More specific parsable tags for crystal colour introduced as _exptl_crystal_colour_primary, *_modifier and *_lustre Added _exptl_crystal_density_meas_gt,lt and *_meas_temp_gt,lt Added _exptl_crystal_recrystallization_method Added _publ_contact_author_id_iucr and _publ_author_id_iucr to allow unique author identification by IUCr database reference identifier More datanames for recording imprecise quantities: _refine_ls_shift/su_max_lt and _refine_ls_shift/su_mean_lt Added the categories SPACE_GROUP and SPACE_GROUP_SYMOP as imports from the symmetry dictionary cif_sym.dic Added _related_function 'replace' to a number of items in the old SYMMETRY category pointing to the preferred items from the new SPACE_GROUP category 2003-08-19 BMcM: formal approval for COMCIFS for the additions and contingent changes discussed on the coreDMG discussion list from June 2002 2003-09-29 BMcM: second round of changes from coreDMG discussions: Added _enumeration_range to new _chemical_temperature_* items; Expanded definition of _space_group_symop_operation_xyz to make explicit the need for inclusion of centring translations (HDF/IDB) Removed _diffrn_reflns_measured_fraction_resolution_full and *_max for reconsideration following suggestion by Curt Haltiwanger that terms are needed that do not refer to resolution or theta Likewise removed _diffrn_standards_decay_%_lt for further consideration, and added _type_conditions esd to _diffrn_standards_decay_% as a measurable quantity (CH/HDF) Modified _example_detail for _space_group_symop_operation_xyz to use a full and unambiguous wording in accordance with International Tables A (CH/IDB/HDF) 2003-09-29 Removed "_type_conditions esd" from the remaining *_gt and *_lt items at the suggestion of Gotzon Madariaga: since these are ceiling/floor values a measurable uncertainty is pointless (BMcM) 2003-10-01 Fixed some typos following checking by IDB (BMcM) 2003-10-03 BMcM: Final editorial pass. Added _related_function alternate to _exptl_crystal_colour. Also added this flag to the new items which replace existing ones: _atom_site_refinement_flags_* and the _space_group_ items 2003-10-04 Release version 2.3. IUCr 2004-06-06 BMcM: minor editorial changes for International Tables Volume G. Text of _atom_sites_*_tran_* definitions changed to ATOM_SITE from STOM_SITES. Some realignment of examples to fit column width. 2004-09-11 BMcM: corrected related item error in _atom_site_refinement_flags_posn, *_adp and *_occupancy 2004-11-26 NJA: updated reference to IT Vol A from 1987 to 2002 2004-12-22 NJA: minor corrections to hyphenation, spelling and punctuation atom_site definition: ', and so on' removed _atom_site_aniso_B_: 1/4 in formula replaced by (1/4) _atom_site_aniso_label: '...atom coordinate list' changed to '...atom in the atom coordinate list' _atom_site_B_iso_or_equiv: 'anisotropic temperature factor parameters' changed to 'anisotropic displacement components' _atom_site_label: 'Each label may have...' changed to 'Different labels may have...' _atom_site_type_symbol: '...atom specie(s)...' changed to 'atom species (singular or plural)...' _atom_type_scat_Cromer_Mann_: reference to Volume C updated to 2004 _atom_type_symbol: 'atom specie(s)' changed to 'atom species (singular or plural)' _audit_conform_dict_location: 'where the conformant dictionary resides' changed to 'for the dictionary to which the current data block conforms' _audit_conform_dict_version: 'conformant dictionary' changed to 'dictionary to which the current data block conforms' 2004-12-23 NJA: minor corrections to hyphenation, spelling and punctuation _audit_contact_author_fax,_audit_contact_author_phone: edited slightly _cell_angle_: 'in degrees of the reported structure' changed to 'of the reported structure in degrees' _cell_measurement_pressure: 'pressure used to synthesize the sample' changed to 'pressure at which the sample was synthesized' _cell_measurement_theta_: 'angles in degrees of reflections used to measure the unit cell' changed to 'angles of reflections used to measure the unit cell in degrees' _cell_reciprocal_angle_: 'angles in degrees defining the reciprocal cell' changed to 'angles defining the reciprocal cell in degrees' _chemical_[]: 'compounds' changed to 'compound' _chemical_optical_rotation: 'c is the value of CONC in g' changed to 'c is the value of CONC as defined above'. _chemical_properties_physical, _biological: 'free description' changed to 'free-text description' _chemical_conn_atom_display_: 'if absent...staff.' deleted _citation_[]: 'literature cited relevant' changed to 'literature cited as being relevant' _citation_*: 'book chapters' changed to 'books or book chapters' _citation_country: 'both journal articles and' deleted _citation_database_id_CSD: 'containing' changed to 'that contains' _citation_language: 'citation appears' changed to 'cited article is written' _diffrn_crystal_treatment: 'intensity measurement' changed to 'the intensity measurements' _diffrn_special_details: 'diffraction measurement' changed to 'intensity-measurement' _diffrn_attenuator_scale: 'This scale must be multiplied by the measured intensity to convert it...' changed to 'The measured intensity must be multiplied by this scale to convert it...' _diffrn_orient_matrix_[]: 'used in data measurement' changed to 'used in the measurement of the diffraction intensities' _diffrn_orient_refln_angle_: 'in degrees of a reflection... matrix' changed to 'of a reflection...matrix in degrees' _diffrn_radiation_probe,_diffrn_radiation_type: definitions reworded slightly _diffrn_refln_angle_: 'in degrees of a reflection' changed to 'of a reflection in degrees' _diffrn_refln_elapsed_time: 'diffraction measurement' changed to 'the diffraction experiment' _diffrn_refln_scale_group_code: 'applying' changed to 'applicable' _diffrn_refln_scan_mode: 'with a diffractometer' changed to 'for measurements using a diffractometer' _diffrn_refln_scan_rate: 'to measure the intensity in degrees per minute' changed to 'in degrees per minute to measure the intensity' _diffrn_refln_standard_code: 'identifying' changed to 'indicating'; 'intensity' changed to 'reflection' _diffrn_reflns_class_d_res_high,_low: defintions rephrased. _diffrn_source_details: 'used' deleted. _diffrn_source_target: 'for generation of' changed to 'to generate' _diffrn_standards_decay_%: 'at the start of the measurement process and at the finish' changed to 'from the start of the measurement process to the end' _diffrn_standards_number: 'used in the diffraction measurements' changed to 'used during the measurement of the diffraction intensities' _exptl_absorpt_correction_type: 'no more detailed information is' changed to 'more detailed information is not'. _exptl_crystal_[]: 'and so on' deleted _exptl_crystal_face_perp_dist: 'millimetres of the face' changed to 'millimetres from the face' _geom_[], _geom_angle_[], _geom_bond_[], _geom_contact_[], _geom_hbond_[], _geom_torsion_[]: 'contents of the' deleted _geom_contact_[], _geom_torsion_[]: year for reference for example 1 corrected from 1991 to 1992 _geom_hbond_angle_DHA: 'Site at *_D' changed to 'Site at *_H' _publ_contact_author_fax: definition rephrased slightly _publ_requested_category: Cif-access codes marked as '(no longer in use)' 2005-01-05 NJA: minor corrections to hyphenation, spelling and punctuation _refine_ls_*: 'least squares' changed to 'least-squares refinement' _refine_ls_restrained_S_all: `Y(calc) = the observed coefficients` changed to `Y(calc) = the calculated coefficients` _refine_ls_restrained_S_gt: `Y(calc) = the observed coefficients` changed to `Y(calc) = the calculated coefficients` _refine_ls_restrained_S_obs: `Y(calc) = the observed coefficients` changed to `Y(calc) = the calculated coefficients` _refine_ls_shift/esd_*: 'divided by' changed to 'to' _refine_ls_shift/su_*: 'divided by' changed to 'to' _refine_ls_class_d_res_*: edited slightly _refine_ls_d_res_*: edited slightly _refln_intensity_*: edited slightly _refln_symmetry_multiplicity: reference to Volume A updated to (2002), Chapter 10.1 _reflns_d_resolution_*: edited slightly _reflns_class_d_res_*: edited slightly _reflns_shell_d_res_*: edited slightly _space_group_name_Hall: erratum added to reference to Hall (1981); reference to Volume B updated to 2001. _space_group_name_H-M_alt: reference to Volume A updated to (2002) _symmetry_Int_Tables_number: reference to Volume A updated to (2002) _symmetry_space_group_name_Hall: erratum added to reference to Hall (1981) _symmetry_space_group_name_H-M: reference to Volume A updated to (2002) _symmetry_equiv_pos_as_xyz: reference to Volume A updated to (2002) 2005-01-11 NJA: more minor corrections to hyphenation, spelling and punctuation 2005-01-21 NJA: _reflns_shell_Rmerge_I_obs: related item changed from _reflns_shell_Rmerge_I_obs to _reflns_shell_Rmerge_I_gt 2005-06-21 NJA: corrections to proofs of Intl Tables G Chapter 4.1 included. New data name _publ_author_email added. 2005-06-27 BMcM: Removed _list_mandatory yes from _atom_site_aniso_label in response to cif-developers list discussion 2007-03-27 BMcM: Added _publ_section_related_literature; added new categories (QI, QM, QO) to _publ_requested_category ; ############### ## ATOM_SITE ## ############### data_atom_site_[] _name '_atom_site_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_calc_attached_atom O1 .4154(4) .5699(1) .3026(0) .060(1) Uani ? ? C2 .5630(5) .5087(2) .3246(1) .060(2) Uani ? ? C3 .5350(5) .4920(2) .3997(1) .048(1) Uani ? ? N4 .3570(3) .5558(1) .4167(0) .039(1) Uani ? ? C5 .3000(5) .6122(2) .3581(1) .045(1) Uani ? ? O21 .6958(5) .4738(2) .2874(1) .090(2) Uani ? ? C31 .4869(6) .3929(2) .4143(2) .059(2) Uani ? ? # - - - - data truncated for brevity - - - - H321C .04(1) .318(3) .320(2) .14000 Uiso ? ? H322A .25(1) .272(4) .475(3) .19000 Uiso ? ? H322B .34976 .22118 .40954 .19000 Uiso calc C322 H322C .08(1) .234(4) .397(3) .19000 Uiso ? ? ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_site_aniso_label _atom_site_aniso_B_11 _atom_site_aniso_B_22 _atom_site_aniso_B_33 _atom_site_aniso_B_12 _atom_site_aniso_B_13 _atom_site_aniso_B_23 _atom_site_aniso_type_symbol O1 .071(1) .076(1) .0342(9) .008(1) .0051(9) -.0030(9) O C2 .060(2) .072(2) .047(1) .002(2) .013(1) -.009(1) C C3 .038(1) .060(2) .044(1) .007(1) .001(1) -.005(1) C N4 .037(1) .048(1) .0325(9) .0025(9) .0011(9) -.0011(9) N C5 .043(1) .060(1) .032(1) .001(1) -.001(1) .001(1) C # - - - - data truncated for brevity - - - - O21 .094(2) .109(2) .068(1) .023(2) .038(1) -.010(1) O C51 .048(2) .059(2) .049(1) .002(1) -.000(1) .007(1) C C511 .048(2) .071(2) .097(3) -.008(2) -.003(2) .010(2) C C512 .078(2) .083(2) .075(2) .009(2) -.005(2) .033(2) C C513 .074(2) .055(2) .075(2) .004(2) .001(2) -.010(2) C # - - - - data truncated for brevity - - - - ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_site_label _atom_site_chemical_conn_number _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv S1 1 0.74799(9) -0.12482(11) 0.27574(9) 0.0742(3) S2 2 1.08535(10) 0.16131(9) 0.34061(9) 0.0741(3) N1 3 1.0650(2) -0.1390(2) 0.2918(2) 0.0500(5) C1 4 0.9619(3) -0.0522(3) 0.3009(2) 0.0509(6) # - - - - data truncated for brevity - - - - ; ; Example 3 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_site_label # *_assembly 'M' is a disordered methyl _atom_site_occupancy # with configurations 'A' and 'B': _atom_site_disorder_assembly # _atom_site_disorder_group # H11B H11A H13B # . | . C1 1 . . # . | . H11A .5 M A # . | . H12A .5 M A # C1 --------C2--- H13A .5 M A # / . \ H11B .5 M B # / . \ H12B .5 M B # / . \ H13B .5 M B # H12A H12B H13A ; ; Example 4 - hypothetical example to illustrate the description of a disordered methyl group. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the ATOM_SITE category record details about the atom sites in a crystal structure, such as the positional coordinates, atomic displacement parameters, and magnetic moments and directions. ; data_atom_site_adp_type _name '_atom_site_adp_type' _category atom_site _type char _related_item '_atom_site_thermal_displace_type' _related_function alternate _list yes _list_reference '_atom_site_label' loop_ _enumeration _enumeration_detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' _definition ; A standard code used to describe the type of atomic displacement parameters used for the site. ; data_atom_site_aniso_B_ loop_ _name '_atom_site_aniso_B_11' '_atom_site_aniso_B_12' '_atom_site_aniso_B_13' '_atom_site_aniso_B_22' '_atom_site_aniso_B_23' '_atom_site_aniso_B_33' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_aniso_label' _related_item '_atom_site_aniso_U_' _related_function conversion _units A^2^ _units_detail 'angstroms squared' _definition ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term T = exp{-(1/4) sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; data_atom_site_aniso_label _name '_atom_site_aniso_label' _category atom_site _type char _list yes _list_link_parent '_atom_site_label' _definition ; Anisotropic atomic displacement parameters are usually looped in a separate list. If this is the case, this code must match the _atom_site_label of the associated atom in the atom coordinate list and conform with the same rules described in _atom_site_label. ; data_atom_site_aniso_ratio _name '_atom_site_aniso_ratio' _category atom_site _type numb _list yes _list_reference '_atom_site_aniso_label' _enumeration_range 1.0: _definition ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; data_atom_site_aniso_type_symbol _name '_atom_site_aniso_type_symbol' _category atom_site _type char _list yes _list_reference '_atom_site_aniso_label' _list_link_parent '_atom_site_type_symbol' _definition ; This _atom_type_symbol code links the anisotropic atom parameters to the atom-type data associated with this site and must match one of the _atom_type_symbol codes in this list. ; data_atom_site_aniso_U_ loop_ _name '_atom_site_aniso_U_11' '_atom_site_aniso_U_12' '_atom_site_aniso_U_13' '_atom_site_aniso_U_22' '_atom_site_aniso_U_23' '_atom_site_aniso_U_33' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_aniso_label' _related_item '_atom_site_aniso_B_' _related_function conversion _units A^2^ _units_detail 'angstroms squared' _definition ; These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row. ; data_atom_site_attached_hydrogens _name '_atom_site_attached_hydrogens' _category atom_site _type numb _list yes _list_reference '_atom_site_label' _enumeration_range 0:8 _enumeration_default 0 loop_ _example _example_detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen' _definition ; The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. ; data_atom_site_B_equiv_geom_mean _name '_atom_site_B_equiv_geom_mean' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_label' _enumeration_range 0.0: loop_ _related_item _related_function '_atom_site_B_iso_or_equiv' alternate '_atom_site_U_equiv_geom_mean' conversion _units A^2^ _units_detail 'angstroms squared' _definition ; Equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B(equiv) = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; data_atom_site_B_iso_or_equiv _name '_atom_site_B_iso_or_equiv' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_label' _enumeration_range 0.0: loop_ _related_item _related_function '_atom_site_B_equiv_geom_mean' alternate '_atom_site_U_iso_or_equiv' conversion _units A^2^ _units_detail 'angstroms squared' _definition ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated from anisotropic displacement components. B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)] a = the real-space cell lengths a* = the reciprocal-space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; data_atom_site_calc_attached_atom _name '_atom_site_calc_attached_atom' _category atom_site _type char _list yes _list_reference '_atom_site_label' _enumeration_default '.' _definition ; The _atom_site_label of the atom site to which the 'geometry- calculated' atom site is attached. ; data_atom_site_calc_flag _name '_atom_site_calc_flag' _category atom_site _type char _list yes _list_reference '_atom_site_label' loop_ _enumeration _enumeration_detail d 'determined from diffraction measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates' _enumeration_default d _definition ; A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy coordinates. The abbreviation 'c' may be used in place of 'calc'. ; data_atom_site_Cartn_ loop_ _name '_atom_site_Cartn_x' '_atom_site_Cartn_y' '_atom_site_Cartn_z' _category atom_site _type numb _type_conditions esd _related_item '_atom_site_fract_' _related_function alternate _list yes _list_reference '_atom_site_label' _units A _units_detail 'angstroms' _definition ; The atom-site coordinates in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the _atom_sites_Cartn_transform_axes description. ; data_atom_site_chemical_conn_number _name '_atom_site_chemical_conn_number' _category atom_site _type numb _list yes _list_link_parent '_chemical_conn_atom_number' _list_reference '_atom_site_label' _enumeration_range 1: _definition ; This number links an atom site to the chemical connectivity list. It must match a number specified by _chemical_conn_atom_number. ; data_atom_site_constraints _name '_atom_site_constraints' _category atom_site _type char _list yes _list_reference '_atom_site_label' _enumeration_default '.' _example 'pop=1.0-pop(Zn3)' _definition ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site_refinement_flags and _refine_ls_number_constraints. ; data_atom_site_description _name '_atom_site_description' _category atom_site _type char _list yes _list_reference '_atom_site_label' _example 'Ag/Si disordered' _definition ; A description of special aspects of this site. See also _atom_site_refinement_flags. ; data_atom_site_disorder_assembly _name '_atom_site_disorder_assembly' _category atom_site _type char _list yes _list_reference '_atom_site_label' loop_ _example _example_detail A 'disordered methyl assembly with groups 1 and 2' B 'disordered sites related by a mirror' S 'disordered sites independent of symmetry' _definition ; A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site_disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. ; data_atom_site_disorder_group _name '_atom_site_disorder_group' _category atom_site _type char _list yes _list_reference '_atom_site_label' loop_ _example _example_detail 1 'unique disordered site in group 1' 2 'unique disordered site in group 2' -1 'symmetry-independent disordered site' _definition ; A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. "-1") is used to indicate sites disordered about a special position. ; data_atom_site_fract_ loop_ _name '_atom_site_fract_x' '_atom_site_fract_y' '_atom_site_fract_z' _category atom_site _type numb _type_conditions esd _related_item '_atom_site_Cartn_' _related_function alternate _list yes _list_reference '_atom_site_label' _definition ; Atom-site coordinates as fractions of the _cell_length_ values. ; data_atom_site_label _name '_atom_site_label' _category atom_site _type char _list yes _list_mandatory yes loop_ _list_link_child '_atom_site_aniso_label' '_geom_angle_atom_site_label_1' '_geom_angle_atom_site_label_2' '_geom_angle_atom_site_label_3' '_geom_bond_atom_site_label_1' '_geom_bond_atom_site_label_2' '_geom_contact_atom_site_label_1' '_geom_contact_atom_site_label_2' '_geom_hbond_atom_site_label_D' '_geom_hbond_atom_site_label_H' '_geom_hbond_atom_site_label_A' '_geom_torsion_atom_site_label_1' '_geom_torsion_atom_site_label_2' '_geom_torsion_atom_site_label_3' '_geom_torsion_atom_site_label_4' loop_ _example C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0 _definition ; The _atom_site_label is a unique identifier for a particular site in the crystal. This code is made up of a sequence of up to seven components, _atom_site_label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type_symbol codes. This is not mandatory if an _atom_site_type_symbol item is included in the atom-site list. The _atom_site_type_symbol always takes precedence over an _atom_site_label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underscore. Underscores are only used if higher-order components exist. If an intermediate component is not used, it may be omitted provided the underscore separators are inserted. For example, the label 'C233__ggg' is acceptable and represents the components C, 233, '' and ggg. Different labels may have a different number of components. ; data_atom_site_label_component_ loop_ _name '_atom_site_label_component_0' '_atom_site_label_component_1' '_atom_site_label_component_2' '_atom_site_label_component_3' '_atom_site_label_component_4' '_atom_site_label_component_5' '_atom_site_label_component_6' _category atom_site _type char _list yes _list_reference '_atom_site_label' _definition ; Component 0 is normally a code which matches identically with one of the _atom_type_symbol codes. If this is the case, then the rules governing the _atom_type_symbol code apply. If, however, the data item _atom_site_type_symbol is also specified in the atom-site list, component 0 need not match this symbol or adhere to any of the _atom_type_symbol rules. Component 1 is referred to as the "atom number". When component 0 is the atom-type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components 2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underscore. ; data_atom_site_occupancy _name '_atom_site_occupancy' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_label' _enumeration_range 0.0:1.0 _enumeration_default 1.0 _definition ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. The value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u. The _enumeration_range of 0.0:1.0 is thus correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). ; data_atom_site_refinement_flags _name '_atom_site_refinement_flags' _category atom_site _type char _list yes _list_reference '_atom_site_label' loop_ _related_item _related_function '_atom_site_refinement_flags_posn' replace '_atom_site_refinement_flags_adp' replace '_atom_site_refinement_flags_occupancy' replace loop_ _enumeration _enumeration_detail . 'no refinement constraints' S 'special-position constraint on site' G 'rigid-group refinement of site' R 'riding-atom site attached to non-riding atom' D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint' _definition ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by _atom_site_refinement_flags_posn, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with legacy CIFs. ; data_atom_site_refinement_flags_adp _name '_atom_site_refinement_flags_adp' _category atom_site _type char _list yes _list_reference '_atom_site_label' _related_item '_atom_site_refinement_flags' _related_function alternate loop_ _enumeration _enumeration_detail . 'no constraints on atomic displacement parameters' T 'special-position constraints on atomic displacement parameters' U 'Uiso or Uij restraint (rigid bond)' TU 'both constraints applied' _definition ; A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. ; data_atom_site_refinement_flags_occupancy _name '_atom_site_refinement_flags_occupancy' _category atom_site _type char _list yes _list_reference '_atom_site_label' _related_item '_atom_site_refinement_flags' _related_function alternate loop_ _enumeration _enumeration_detail . 'no constraints on site-occupancy parameters' P 'site-occupancy constraint' _definition ; A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. ; data_atom_site_refinement_flags_posn _name '_atom_site_refinement_flags_posn' _category atom_site _type char _list yes _list_reference '_atom_site_label' _related_item '_atom_site_refinement_flags' _related_function alternate loop_ _enumeration _enumeration_detail . 'no constraints on positional coordinates' D 'distance or angle restraint on positional coordinates' G 'rigid-group refinement of positional coordinates' R 'riding-atom site attached to non-riding atom' S 'special-position constraint on positional coordinates' DG 'combination of the above constraints' DR 'combination of the above constraints' DS 'combination of the above constraints' GR 'combination of the above constraints' GS 'combination of the above constraints' RS 'combination of the above constraints' DGR 'combination of the above constraints' DGS 'combination of the above constraints' DRS 'combination of the above constraints' GRS 'combination of the above constraints' DGRS 'combination of the above constraints' _definition ; A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. ; data_atom_site_restraints _name '_atom_site_restraints' _category atom_site _type char _list yes _list_reference '_atom_site_label' _example 'restrained to planar ring' _definition ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site_refinement_flags and _refine_ls_number_restraints. ; data_atom_site_symmetry_multiplicity _name '_atom_site_symmetry_multiplicity' _category atom_site _type numb _list yes _list_reference '_atom_site_label' _enumeration_range 1:192 _definition ; The multiplicity of a site due to the space-group symmetry as given in International Tables for Crystallography Vol. A (2002). ; data_atom_site_thermal_displace_type _name '_atom_site_thermal_displace_type' _category atom_site _type char _related_item '_atom_site_adp_type' _related_function replace _list yes _list_reference '_atom_site_label' loop_ _enumeration _enumeration_detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' _definition ; A standard code used to describe the type of atomic displacement parameters used for the site. ; data_atom_site_type_symbol _name '_atom_site_type_symbol' _category atom_site _type char _list yes _list_reference '_atom_site_label' _list_link_parent '_atom_type_symbol' _list_link_child '_atom_site_aniso_type_symbol' loop_ _example Cu Cu2+ dummy Fe3+Ni2+ S- H* H(SDS) _definition ; A code to identify the atom species (singular or plural) occupying this site. This code must match a corresponding _atom_type_symbol. The specification of this code is optional if component 0 of the _atom_site_label is used for this purpose. See _atom_type_symbol. ; data_atom_site_U_equiv_geom_mean _name '_atom_site_U_equiv_geom_mean' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_label' _enumeration_range 0.0: loop_ _related_item _related_function '_atom_site_U_iso_or_equiv' alternate '_atom_site_B_equiv_geom_mean' conversion _units A^2^ _units_detail 'angstroms squared' _definition ; Equivalent isotropic atomic displacement parameter, U(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U(equiv) = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ ; data_atom_site_U_iso_or_equiv _name '_atom_site_U_iso_or_equiv' _category atom_site _type numb _type_conditions esd _list yes _list_reference '_atom_site_label' _enumeration_range 0.0: loop_ _related_item _related_function '_atom_site_U_equiv_geom_mean' alternate '_atom_site_B_iso_or_equiv' conversion _units A^2^ _units_detail 'angstroms squared' _definition ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U(equiv), in angstroms squared, calculated from anisotropic atomic displacement parameters. U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)] a = the real-space cell lengths a* = the reciprocal-space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. ; data_atom_site_Wyckoff_symbol _name '_atom_site_Wyckoff_symbol' _category atom_site _type char _list yes _list_reference '_atom_site_label' _definition ; The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography Vol. A (2002). ; ################ ## ATOM_SITES ## ################ data_atom_sites_[] _name '_atom_sites_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _atom_sites_Cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites_Cartn_tran_matrix_11 58.39 _atom_sites_Cartn_tran_matrix_12 0.00 _atom_sites_Cartn_tran_matrix_13 0.00 _atom_sites_Cartn_tran_matrix_21 0.00 _atom_sites_Cartn_tran_matrix_22 86.70 _atom_sites_Cartn_tran_matrix_23 0.00 _atom_sites_Cartn_tran_matrix_31 0.00 _atom_sites_Cartn_tran_matrix_32 0.00 _atom_sites_Cartn_tran_matrix_33 46.27 ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. ; data_atom_sites_Cartn_tran_matrix_ loop_ _name '_atom_sites_Cartn_tran_matrix_11' '_atom_sites_Cartn_tran_matrix_12' '_atom_sites_Cartn_tran_matrix_13' '_atom_sites_Cartn_tran_matrix_21' '_atom_sites_Cartn_tran_matrix_22' '_atom_sites_Cartn_tran_matrix_23' '_atom_sites_Cartn_tran_matrix_31' '_atom_sites_Cartn_tran_matrix_32' '_atom_sites_Cartn_tran_matrix_33' _category atom_sites _type numb _definition ; Matrix elements used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. The 3 x 1 translation is defined in _atom_sites_Cartn_tran_vector_. x' |11 12 13| x | 1 | ( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 | z' |31 32 33| z | 3 | ; data_atom_sites_Cartn_transform_axes _name '_atom_sites_Cartn_transform_axes' _category atom_sites _type char _example 'a parallel to x; b in the plane of y and z' _definition ; A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites_Cartn_tran_matrix_. ; data_atom_sites_Cartn_tran_vector_ loop_ _name '_atom_sites_Cartn_tran_vector_1' '_atom_sites_Cartn_tran_vector_2' '_atom_sites_Cartn_tran_vector_3' _category atom_sites _type numb _definition ; Elements of a 3 x 1 translation vector used in the transformation of fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. x' |11 12 13| x | 1 | ( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 | z' |31 32 33| z | 3 | ; data_atom_sites_fract_tran_matrix_ loop_ _name '_atom_sites_fract_tran_matrix_11' '_atom_sites_fract_tran_matrix_12' '_atom_sites_fract_tran_matrix_13' '_atom_sites_fract_tran_matrix_21' '_atom_sites_fract_tran_matrix_22' '_atom_sites_fract_tran_matrix_23' '_atom_sites_fract_tran_matrix_31' '_atom_sites_fract_tran_matrix_32' '_atom_sites_fract_tran_matrix_33' _category atom_sites _type numb _definition ; Matrix elements used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. The 3 x 1 translation is defined in _atom_sites_fract_tran_vector_. x' |11 12 13| x | 1 | ( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 | z' |31 32 33| z | 3 | ; data_atom_sites_fract_tran_vector_ loop_ _name '_atom_sites_fract_tran_vector_1' '_atom_sites_fract_tran_vector_2' '_atom_sites_fract_tran_vector_3' _category atom_sites _type numb _definition ; Elements of a 3 x 1 translation vector used in the transformation of Cartesian coordinates in the ATOM_SITE category to fractional coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. x' |11 12 13| x | 1 | ( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 | z' |31 32 33| z | 3 | ; data_atom_sites_solution_ loop_ _name '_atom_sites_solution_primary' '_atom_sites_solution_secondary' '_atom_sites_solution_hydrogens' _category atom_sites _type char loop_ _enumeration _enumeration_detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' _definition ; Codes which identify the methods used to locate the initial atom sites. The *_primary code identifies how the first atom sites were determined; the *_secondary code identifies how the remaining non-hydrogen sites were located; and the *_hydrogens code identifies how the hydrogen sites were located. ; data_atom_sites_special_details _name '_atom_sites_special_details' _category atom_sites _type char _definition ; Additional information about the atomic coordinates not coded elsewhere in the CIF. ; ############### ## ATOM_TYPE ## ############### data_atom_type_[] _name '_atom_type_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _atom_type_symbol _atom_type_oxidation_number _atom_type_number_in_cell _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the ATOM_TYPE category record details about properties of the atoms that occupy the atom sites, such as the atomic scattering factors. ; data_atom_type_analytical_mass_% _name '_atom_type_analytical_mass_%' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_range 0.0:100.0 _definition ; Mass percentage of this atom type derived from chemical analysis. ; data_atom_type_description _name '_atom_type_description' _category atom_type _type char _list yes _list_reference '_atom_type_symbol' loop_ _example deuterium 0.34Fe+0.66Ni _definition ; A description of the atom(s) designated by this atom type. In most cases, this will be the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. ; data_atom_type_number_in_cell _name '_atom_type_number_in_cell' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_range 0: _definition ; Total number of atoms of this atom type in the unit cell. ; data_atom_type_oxidation_number _name '_atom_type_oxidation_number' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_range -8:8 _enumeration_default 0 _definition ; Formal oxidation state of this atom type in the structure. ; data_atom_type_radius_ loop_ _name '_atom_type_radius_bond' '_atom_type_radius_contact' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_range 0.0:5.0 _units A _units_detail 'angstroms' _definition ; The effective intra- and intermolecular bonding radii in angstroms of this atom type. ; data_atom_type_scat_Cromer_Mann_ loop_ _name '_atom_type_scat_Cromer_Mann_a1' '_atom_type_scat_Cromer_Mann_a2' '_atom_type_scat_Cromer_Mann_a3' '_atom_type_scat_Cromer_Mann_a4' '_atom_type_scat_Cromer_Mann_b1' '_atom_type_scat_Cromer_Mann_b2' '_atom_type_scat_Cromer_Mann_b3' '_atom_type_scat_Cromer_Mann_b4' '_atom_type_scat_Cromer_Mann_c' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _definition ; The Cromer-Mann scattering-factor coefficients used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5 ; data_atom_type_scat_dispersion_ loop_ _name '_atom_type_scat_dispersion_imag' '_atom_type_scat_dispersion_real' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_default 0.0 _definition ; The imaginary and real components of the anomalous-dispersion scattering factor, f'' and f', in electrons for this atom type and the radiation given in _diffrn_radiation_wavelength. ; data_atom_type_scat_dispersion_source _name '_atom_type_scat_dispersion_source' _category atom_type _type char _list yes _list_reference '_atom_type_symbol' _example 'International Tables Vol. IV Table 2.3.1' _definition ; Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type. ; data_atom_type_scat_length_neutron _name '_atom_type_scat_length_neutron' _category atom_type _type numb _list yes _list_reference '_atom_type_symbol' _enumeration_default 0.0 _units fm _units_detail 'femtometres' _definition ; The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. ; data_atom_type_scat_source _name '_atom_type_scat_source' _category atom_type _type char _list yes _list_reference '_atom_type_symbol' _example 'International Tables Vol. IV Table 2.4.6B' _definition ; Reference to source of scattering factors or scattering lengths used for this atom type. ; data_atom_type_scat_versus_stol_list _name '_atom_type_scat_versus_stol_list' _category atom_type _type char _list yes _list_reference '_atom_type_symbol' _definition ; A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. ; data_atom_type_symbol _name '_atom_type_symbol' _category atom_type _type char _list yes _list_mandatory yes _list_link_child '_atom_site_type_symbol' loop_ _example C Cu2+ H(SDS) dummy FeNi _definition ; The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; ########### ## AUDIT ## ########### data_audit_[] _name '_audit_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _audit_block_code TOZ_1991-03-20 _audit_creation_date 1991-03-20 _audit_creation_method from_xtal_archive_file_using_CIFIO _audit_update_record ; 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec'd by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report. ; ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the AUDIT category record details about the creation and subsequent updating of the data block. ; data_audit_block_code _name '_audit_block_code' _category audit _type char _example TOZ_1991-03-20 _definition ; A code intended to identify uniquely the current data block. ; data_audit_creation_date _name '_audit_creation_date' _category audit _type char _example 1990-07-12 _definition ; The date that the data block was created. The date format is yyyy-mm-dd. ; data_audit_creation_method _name '_audit_creation_method' _category audit _type char _example 'spawned by the program QBEE' _definition ; A description of how data were entered into the data block. ; data_audit_update_record _name '_audit_update_record' _category audit _type char _example '1990-07-15 Updated by the Co-editor' _definition ; A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. ; ################## ## AUDIT_AUTHOR ## ################## data_audit_author_[] _name '_audit_author_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_author_name _audit_author_address 'Fitzgerald, Paula M. D.' ; Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway New Jersey 07065 USA ; 'Van Middlesworth, J. F.' ; Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway New Jersey 07065 USA ; ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. ; data_audit_author_address _name '_audit_author_address' _category audit_author _type char _list yes _list_reference '_audit_author_name' _example ; Department Institute Street City and postcode COUNTRY ; _definition ; The address of an author of this data block. If there are multiple authors, _audit_author_address is looped with _audit_author_name. ; data_audit_author_name _name '_audit_author_name' _category audit_author _type char _list yes _list_mandatory yes loop_ _example 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' 'M\"uller, H.A.' 'Ross II, C.R.' _definition ; The name of an author of this data block. If there are multiple authors, _audit_author_name is looped with _audit_author_address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; ################### ## AUDIT_CONFORM ## ################### data_audit_conform_[] _name '_audit_conform_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _audit_conform_dict_name cif_core.dic _audit_conform_dict_version 2.3.1 _audit_conform_dict_location ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic ; ; Example 1 - any file conforming to the current CIF core dictionary. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. ; data_audit_conform_dict_location _name '_audit_conform_dict_location' _category audit_conform _type char _list both _list_reference '_audit_conform_dict_name' _definition ; A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. ; data_audit_conform_dict_name _name '_audit_conform_dict_name' _category audit_conform _type char _list both _list_mandatory yes _definition ; The string identifying the highest-level dictionary defining data names used in this file. ; data_audit_conform_dict_version _name '_audit_conform_dict_version' _category audit_conform _type char _list both _list_reference '_audit_conform_dict_name' _definition ; The version number of the dictionary to which the current data block conforms. ; ########################## ## AUDIT_CONTACT_AUTHOR ## ########################## data_audit_contact_author_[] _name '_audit_contact_author_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_contact_author_name _audit_contact_author_address _audit_contact_author_email _audit_contact_author_fax _audit_contact_author_phone 'Fitzgerald, Paula M. D.' ; Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway New Jersey 07065 USA ; 'paula_fitzgerald@merck.com' '1(908)5945510' '1(908)5945510' ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. ; data_audit_contact_author_address _name '_audit_contact_author_address' _category audit_contact_author _type char _example ; Department Institute Street City and postcode COUNTRY ; _definition ; The mailing address of the author of the data block to whom correspondence should be addressed. ; data_audit_contact_author_email _name '_audit_contact_author_email' _category audit_contact_author _type char loop_ _example name@host.domain.country bm@iucr.org _definition ; The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; data_audit_contact_author_fax _name '_audit_contact_author_fax' _category audit_contact_author _type char loop_ _example '12(34)9477334' '12()349477334' _definition ; The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. ; data_audit_contact_author_name _name '_audit_contact_author_name' _category audit_contact_author _type char loop_ _example 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' 'M\"uller, H.A.' 'Ross II, C.R.' _definition ; The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; data_audit_contact_author_phone _name '_audit_contact_author_phone' _category audit_contact_author _type char loop_ _example '12(34)9477330' '12()349477330' '12(34)9477330x5543' _definition ; The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. ; ################ ## AUDIT_LINK ## ################ data_audit_link_[] _name '_audit_link_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link_block_code _audit_link_block_description . 'discursive text of paper with two structures' morA_(1) 'structure 1 of 2' morA_(2) 'structure 2 of 2' ; ; Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link_block_code _audit_link_block_description . 'publication details' KSE_COM 'experimental data common to ref./mod. structures' KSE_REF 'reference structure' KSE_MOD 'modulated structure' ; ; Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. ; data_audit_link_block_code _name '_audit_link_block_code' _category audit_link _type char _list yes _list_mandatory yes _definition ; The value of _audit_block_code associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. ; data_audit_link_block_description _name '_audit_link_block_description' _category audit_link _type char _list yes _list_reference '_audit_link_block_code' _definition ; A textual description of the relationship of the referenced data block to the current one. ; ########## ## CELL ## ########## data_cell_[] _name '_cell_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _cell_length_a 5.959(1) _cell_length_b 14.956(1) _cell_length_c 19.737(3) _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 1759.0(3) _cell_measurement_temperature 293 _cell_measurement_reflns_used 25 _cell_measurement_theta_min 25 _cell_measurement_theta_max 31 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CELL category record details about the crystallographic cell parameters and their measurement. ; data_cell_angle_ loop_ _name '_cell_angle_alpha' '_cell_angle_beta' '_cell_angle_gamma' _category cell _type numb _type_conditions esd _enumeration_range 0.0:180.0 _enumeration_default 90.0 _units deg _units_detail 'degrees' _definition ; Unit-cell angles of the reported structure in degrees. The values of _refln_index_h, *_k, *_l must correspond to the cell defined by these values and _cell_length_a, *_b and *_c. The values of _diffrn_refln_index_h, *_k, *_l may not correspond to these values if a cell transformation took place following the measurement of the diffraction intensities. See also _diffrn_reflns_transf_matrix_. ; data_cell_formula_units_Z _name '_cell_formula_units_Z' _category cell _type numb _enumeration_range 1: _definition ; The number of the formula units in the unit cell as specified by _chemical_formula_structural, _chemical_formula_moiety or _chemical_formula_sum. ; data_cell_length_ loop_ _name '_cell_length_a' '_cell_length_b' '_cell_length_c' _category cell _type numb _type_conditions esd _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Unit-cell lengths in angstroms corresponding to the structure reported. The values of _refln_index_h, *_k, *_l must correspond to the cell defined by these values and _cell_angle_ values. The values of _diffrn_refln_index_h, *_k, *_l may not correspond to these values if a cell transformation took place following the measurement of the diffraction intensities. See also _diffrn_reflns_transf_matrix_. ; data_cell_measurement_pressure _name '_cell_measurement_pressure' _category cell _type numb _type_conditions esd _enumeration_range 0.0: _units kPa _units_detail 'kilopascals' _definition ; The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). ; data_cell_measurement_radiation _name '_cell_measurement_radiation' _category cell _type char loop_ _example 'neutron' 'Cu K\a' 'synchrotron' _definition ; Description of the radiation used to measure the unit-cell data. See also _cell_measurement_wavelength. ; data_cell_measurement_reflns_used _name '_cell_measurement_reflns_used' _category cell _type numb _definition ; The total number of reflections used to determine the unit cell. These reflections may be specified as _cell_measurement_refln_ data items. ; data_cell_measurement_temperature _name '_cell_measurement_temperature' _category cell _type numb _type_conditions esd _enumeration_range 0.0: _units K _units_detail kelvin _definition ; The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). ; data_cell_measurement_theta_ loop_ _name '_cell_measurement_theta_max' '_cell_measurement_theta_min' _category cell _type numb _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; The maximum and minimum theta angles of reflections used to measure the unit cell in degrees. ; data_cell_measurement_wavelength _name '_cell_measurement_wavelength' _category cell _type numb _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The wavelength in angstroms 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. ; data_cell_reciprocal_angle_ loop_ _name '_cell_reciprocal_angle_alpha' '_cell_reciprocal_angle_beta' '_cell_reciprocal_angle_gamma' _category cell _type numb _type_conditions esd _enumeration_range 0.0:180.0 _enumeration_default 90.0 _units deg _units_detail 'degrees' _definition ; The angles defining the reciprocal cell in degrees. These are related to those in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; data_cell_reciprocal_length_ loop_ _name '_cell_reciprocal_length_a' '_cell_reciprocal_length_b' '_cell_reciprocal_length_c' _category cell _type numb _type_conditions esd _enumeration_range 0.0: _units A^-1^ _units_detail 'reciprocal angstroms' _definition ; The reciprocal-cell lengths in inverse angstroms. These are related to the real cell by: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; data_cell_special_details _name '_cell_special_details' _category cell _type char loop_ _example 'pseudo-orthorhombic' 'standard setting from 45 deg rotation around c' _definition ; A description of special aspects of the cell choice, noting possible alternative settings. ; data_cell_volume _name '_cell_volume' _category cell _type numb _type_conditions esd _enumeration_range 0.0: _units A^3^ _units_detail 'cubic angstroms' _definition ; Cell volume V in angstroms cubed. V = a b c [1 - cos^2^(alpha) - cos^2^(beta) - cos^2^(gamma) + 2 cos(alpha) cos(beta) cos(gamma) ] ^1/2^ a = _cell_length_a b = _cell_length_b c = _cell_length_c alpha = _cell_angle_alpha beta = _cell_angle_beta gamma = _cell_angle_gamma ; ############################ ## CELL_MEASUREMENT_REFLN ## ############################ data_cell_measurement_refln_[] _name '_cell_measurement_refln_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _cell_measurement_refln_index_h _cell_measurement_refln_index_k _cell_measurement_refln_index_l _cell_measurement_refln_theta -2 4 1 8.67 0 3 2 9.45 3 0 2 9.46 -3 4 1 8.93 -2 1 -2 7.53 10 0 0 23.77 0 10 0 23.78 -5 4 1 11.14 # - - - - data truncated for brevity - - - - ; ; Example 1 - extracted from the CAD-4 listing for Rb~2~S~2~O~6~ at room temperature (unpublished). ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used in the determination of the crystallographic cell parameters. The _cell_measurement_refln_ data items would in general be used only for diffractometer measurements. ; data_cell_measurement_refln_index_ loop_ _name '_cell_measurement_refln_index_h' '_cell_measurement_refln_index_k' '_cell_measurement_refln_index_l' _category cell_measurement_refln _type numb _list yes _list_mandatory yes _definition ; Miller indices of a reflection used for measurement of the unit cell. ; data_cell_measurement_refln_theta _name '_cell_measurement_refln_theta' _category cell_measurement_refln _type numb _list yes _list_reference '_cell_measurement_refln_index_' _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; Theta angle in degrees for the reflection used for measurement of the unit cell with the indices _cell_measurement_refln_index_. ; ############## ## CHEMICAL ## ############## data_chemical_[] _name '_chemical_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _chemical_name_systematic trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0) ; ; Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CHEMICAL category record details about the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. ; data_chemical_absolute_configuration _name '_chemical_absolute_configuration' _category chemical _type char loop_ _enumeration _enumeration_detail rm ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration ; ad ; absolute configuration established by anomalous-dispersion effects in diffraction measurements on the crystal ; rmad ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous-dispersion effects in diffraction measurements on the crystal ; syn ; absolute configuration has not been established by anomalous-dispersion effects in diffraction measurements on the crystal. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure ; unk ; absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous-dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made ; . 'inapplicable' _definition ; Necessary conditions for the assignment of _chemical_absolute_configuration are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) ; data_chemical_compound_source _name '_chemical_compound_source' _category chemical _type char loop_ _example 'From Norilsk (USSR)' 'Extracted from the bark of Cinchona Naturalis' _definition ; Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. ; data_chemical_melting_point _name '_chemical_melting_point' _category chemical _type numb _type_conditions esd _enumeration_range 0.0: _units K _units_detail kelvin _definition ; The temperature in kelvins at which the crystalline solid changes to a liquid. ; data_chemical_melting_point_ loop_ _name '_chemical_melting_point_gt' '_chemical_melting_point_lt' _category chemical _type numb _related_item '_chemical_melting_point' _related_function alternate _enumeration_range 0.0: _units K _units_detail kelvin _definition ; A temperature in kelvins below which (*_lt) or above which (*_gt) the melting point (the temperature at which the crystalline solid changes to a liquid) lies. These items allow a range of temperatures to be given. _chemical_melting_point should always be used in preference to these items whenever possible. ; data_chemical_name_common _name '_chemical_name_common' _category chemical _type char _example '1-bromoestradiol' _definition ; Trivial name by which the compound is commonly known. ; data_chemical_name_mineral _name '_chemical_name_mineral' _category chemical _type char _example chalcopyrite _definition ; Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical_compound_source. ; data_chemical_name_structure_type _name '_chemical_name_structure_type' _category chemical _type char loop_ _example perovskite sphalerite A15 _definition ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; data_chemical_name_systematic _name '_chemical_name_systematic' _category chemical _type char _example '1-bromoestra-1,3,5(10)-triene-3,17\b-diol' _definition ; IUPAC or Chemical Abstracts full name of the compound. ; data_chemical_optical_rotation _name '_chemical_optical_rotation' _category chemical _type char _example '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)' _definition ; The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g per 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. ; data_chemical_properties_biological _name '_chemical_properties_biological' _category chemical _type char loop_ _example ; diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) ; ; antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) ; ; weakly potent lipoxygenase nonredox inhibitor ; ; no influenza A virus sialidase inhibitory and plaque reduction activities ; ; low toxicity against Drosophila melanogaster ; _definition ; A free-text description of the biological properties of the material. ; data_chemical_properties_physical _name '_chemical_properties_physical' _category chemical _type char loop_ _example air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor 'ferromagnetic at low temperature' 'paramagnetic and thermochromic' _definition ; A free-text description of the physical properties of the material. ; data_chemical_temperature_decomposition _name '_chemical_temperature_decomposition' _category chemical _type numb _type_conditions esd _enumeration_range 0.0: _units K _units_detail kelvin _example 350 _definition ; The temperature in kelvins at which the solid decomposes. ; data_chemical_temperature_decomposition_ loop_ _name '_chemical_temperature_decomposition_gt' '_chemical_temperature_decomposition_lt' _category chemical _type numb _enumeration_range 0.0: _units K _units_detail kelvin _related_item '_chemical_temperature_decomposition' _related_function alternate _example 350 _definition ; A temperature in kelvins below which (*_lt) or above which (*_gt) the solid is known to decompose. These items allow a range of temperatures to be given. _chemical_temperature_decomposition should always be used in preference to these items whenever possible. ; data_chemical_temperature_sublimation _name '_chemical_temperature_sublimation' _category chemical _type numb _type_conditions esd _enumeration_range 0.0: _units K _units_detail kelvin _example 350 _definition ; The temperature in kelvins at which the solid sublimes. ; data_chemical_temperature_sublimation_ loop_ _name '_chemical_temperature_sublimation_gt' '_chemical_temperature_sublimation_lt' _category chemical _type numb _enumeration_range 0.0: _units K _units_detail kelvin _related_item '_chemical_temperature_sublimation' _related_function alternate _example 350 _definition ; A temperature in kelvins below which (*_lt) or above which (*_gt) the solid is known to sublime. These items allow a range of temperatures to be given. _chemical_temperature_sublimation should always be used in preference to these items whenever possible. ; ######################## ## CHEMICAL_CONN_ATOM ## ######################## data_chemical_conn_atom_[] _name '_chemical_conn_atom_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _chemical_conn_atom_number _chemical_conn_atom_type_symbol _chemical_conn_atom_display_x _chemical_conn_atom_display_y _chemical_conn_atom_NCA _chemical_conn_atom_NH 1 S .39 .81 1 0 2 S .39 .96 2 0 3 N .14 .88 3 0 4 C .33 .88 3 0 5 C .11 .96 2 2 6 C .03 .96 2 2 7 C .03 .80 2 2 8 C .11 .80 2 2 9 S .54 .81 1 0 10 S .54 .96 2 0 11 N .80 .88 3 0 12 C .60 .88 3 0 13 C .84 .96 2 2 14 C .91 .96 2 2 15 C .91 .80 2 2 16 C .84 .80 2 2 ; ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_ categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The _chemical_conn_atom_ data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the _chemical_conn_atom_ and _chemical_conn_bond_ data items will always describe a complete chemical entity. ; data_chemical_conn_atom_charge _name '_chemical_conn_atom_charge' _category chemical_conn_atom _type numb _list yes _list_reference '_chemical_conn_atom_type_symbol' _enumeration_range -6:6 _enumeration_default 0 loop_ _example _example_detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' _definition ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; data_chemical_conn_atom_display_ loop_ _name '_chemical_conn_atom_display_x' '_chemical_conn_atom_display_y' _category chemical_conn_atom _type numb _list yes _list_reference '_chemical_conn_atom_type_symbol' _enumeration_range 0.0:1.0 _definition ; The 2D Cartesian coordinates (x,y) of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. ; data_chemical_conn_atom_NCA _name '_chemical_conn_atom_NCA' _category chemical_conn_atom _type numb _list yes _list_reference '_chemical_conn_atom_type_symbol' _enumeration_range 0: _definition ; The number of connected atoms excluding terminal hydrogen atoms. ; data_chemical_conn_atom_NH _name '_chemical_conn_atom_NH' _category chemical_conn_atom _type numb _list yes _list_reference '_chemical_conn_atom_type_symbol' _enumeration_range 0: _definition ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the _atom_site_ list. This number will be the same as _atom_site_attached_hydrogens only if none of the hydrogen atoms appear in the _atom_site_ list. ; data_chemical_conn_atom_number _name '_chemical_conn_atom_number' _category chemical_conn_atom _type numb _list yes loop_ _list_link_child '_atom_site_chemical_conn_number' '_chemical_conn_bond_atom_1' '_chemical_conn_bond_atom_2' _list_reference '_chemical_conn_atom_type_symbol' _enumeration_range 1: _definition ; The chemical sequence number to be associated with this atom. ; data_chemical_conn_atom_type_symbol _name '_chemical_conn_atom_type_symbol' _category chemical_conn_atom _type char _list yes _list_mandatory yes _definition ; A code identifying the atom type. This code must match an _atom_type_symbol code in the _atom_type_ list or be a recognizable element symbol. ; ######################## ## CHEMICAL_CONN_BOND ## ######################## data_chemical_conn_bond_[] _name '_chemical_conn_bond_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _chemical_conn_bond_atom_1 _chemical_conn_bond_atom_2 _chemical_conn_bond_type 4 1 doub 4 3 sing 4 2 sing 5 3 sing 6 5 sing 7 6 sing 8 7 sing 8 3 sing 10 2 sing 12 9 doub 12 11 sing 12 10 sing 13 11 sing 14 13 sing 15 14 sing 16 15 sing 16 11 sing 17 5 sing 18 5 sing 19 6 sing 20 6 sing 21 7 sing 22 7 sing 23 8 sing 24 8 sing 25 13 sing 26 13 sing 27 14 sing 28 14 sing 29 15 sing 30 15 sing 31 16 sing 32 16 sing ; ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_ categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The _chemical_conn_bond_ data items specify the connections between the atoms in the _chemical_conn_atom_ list and the nature of the chemical bond between these atoms. ; data_chemical_conn_bond_atom_ loop_ _name '_chemical_conn_bond_atom_1' '_chemical_conn_bond_atom_2' _category chemical_conn_bond _type numb _list yes _list_link_parent '_chemical_conn_atom_number' _enumeration_range 1: _definition ; Atom numbers which must match with chemical sequence numbers specified as _chemical_conn_atom_number values. These link the bond connection to the chemical numbering and atom sites. ; data_chemical_conn_bond_type _name '_chemical_conn_bond_type' _category chemical_conn_bond _type char _list yes _list_reference '_chemical_conn_bond_atom_' loop_ _enumeration _enumeration_detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' _enumeration_default sing _definition ; The chemical bond type associated with the connection between the two sites _chemical_conn_bond_atom_1 and *_2. ; ###################### ## CHEMICAL_FORMULA ## ###################### data_chemical_formula_[] _name '_chemical_formula_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _chemical_formula_moiety 'C18 H25 N O3' _chemical_formula_sum 'C18 H25 N O3' _chemical_formula_weight 303.40 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _chemical_formula_iupac '[Mo (C O)4 (C18 H33 P)2]' _chemical_formula_moiety 'C40 H66 Mo O4 P2' _chemical_formula_structural '((C O)4 (P (C6 H11)3)2)Mo' _chemical_formula_sum 'C40 H66 Mo O4 P2' _chemical_formula_weight 768.81 ; ; Example 2 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; _chemical_formula_ items specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula_analytical, *_structural and *_sum. For the data item *_moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula_moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for *_moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula_structural, the order of the elements within any group or moiety depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula_moiety and _chemical_formula_sum. ; data_chemical_formula_analytical _name '_chemical_formula_analytical' _category chemical_formula _type char _example 'Fe2.45(2) Ni1.60(3) S4' _definition ; Formula determined by standard chemical analysis including trace elements. See the _chemical_formula_[] category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (e.s.d.'s). ; data_chemical_formula_iupac _name '_chemical_formula_iupac' _category chemical_formula _type char _example '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' _definition ; Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other _chemical_formula_ entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other _chemical_formula_ data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. ; data_chemical_formula_moiety _name '_chemical_formula_moiety' _category chemical_formula _type char loop_ _example 'C7 H4 Cl Hg N O3 S' 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' 'C12 H16 N2 O6, 5(H2 O1)' "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)" _definition ; Formula with each discrete bonded residue or ion shown as a separate moiety. See the _chemical_formula_[] category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the _chemical_formula_[] category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. ; data_chemical_formula_structural _name '_chemical_formula_structural' _category chemical_formula _type char loop_ _example 'Ca ((Cl O3)2 O)2 (H2 O)6' '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' _definition ; See the _chemical_formula_[] category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site lists should not be included in this formula (see also _chemical_formula_analytical). ; data_chemical_formula_sum _name '_chemical_formula_sum' _category chemical_formula _type char loop_ _example 'C18 H19 N7 O8 S' _definition ; See the _chemical_formula_[] category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the _chemical_formula_[] category description. Parentheses are not normally used. ; data_chemical_formula_weight _name '_chemical_formula_weight' _category chemical_formula _type numb _enumeration_range 1.0: _units Da _units_detail 'daltons' _definition ; Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula_structural, *_iupac, *_moiety or *_sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal_density_diffrn. ; data_chemical_formula_weight_meas _name '_chemical_formula_weight_meas' _category chemical_formula _type numb _enumeration_range 1.0: _units Da _units_detail 'daltons' _definition ; Formula mass in daltons measured by a non-diffraction experiment. ; ############## ## CITATION ## ############## data_citation_[] _name '_citation_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _citation_id _citation_coordinate_linkage _citation_title _citation_country _citation_page_first _citation_page_last _citation_year _citation_journal_abbrev _citation_journal_volume _citation_journal_issue _citation_journal_id_ASTM _citation_journal_id_ISSN _citation_book_title _citation_book_publisher _citation_book_id_ISBN _citation_special_details primary yes ; Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution. ; US 14209 14219 1990 'J. Biol. Chem.' 265 . HBCHA3 0021-9258 . . . ; The publication that directly relates to this coordinate set. ; 2 no ; Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1. ; UK 615 619 1989 'Nature' 337 . NATUAS 0028-0836 . . . ; Determination of the structure of the unliganded enzyme. ; 3 no ; Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1. ; US 1919 1921 1989 'J. Biol. Chem.' 264 . HBCHA3 0021-9258 . . . ; Crystallization of the unliganded enzyme. ; ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. ; data_citation_abstract _name '_citation_abstract' _category citation _type char _list yes _list_reference '_citation_id' _definition ; Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. ; data_citation_abstract_id_CAS _name '_citation_abstract_id_CAS' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. ; data_citation_book_id_ISBN _name '_citation_book_id_ISBN' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. ; data_citation_book_publisher _name '_citation_book_publisher' _category citation _type char _list yes _list_reference '_citation_id' _example 'John Wiley' _definition ; The name of the publisher of the citation; relevant for books or book chapters. ; data_citation_book_publisher_city _name '_citation_book_publisher_city' _category citation _type char _list yes _list_reference '_citation_id' _example 'New York' _definition ; The location of the publisher of the citation; relevant for books or book chapters. ; data_citation_book_title _name '_citation_book_title' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The title of the book in which the citation appeared; relevant for books or book chapters. ; data_citation_coordinate_linkage _name '_citation_coordinate_linkage' _category citation _type char _list yes _list_reference '_citation_id' loop_ _enumeration _enumeration_detail no 'citation unrelated to current coordinates' n 'abbreviation for "no"' yes 'citation related to current coordinates' y 'abbreviation for "yes"' _definition ; _citation_coordinate_linkage states whether or not this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to creation of the data block, the value of this data item would be 'no'. ; data_citation_country _name '_citation_country' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The country of publication; relevant for books and book chapters. ; data_citation_database_id_CSD _name '_citation_database_id_CSD' _category citation _type char _list yes _list_reference '_citation_id' _example LEKKUH _definition ; Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. ; data_citation_database_id_Medline _name '_citation_database_id_Medline' _category citation _type numb _list yes _list_reference '_citation_id' _enumeration_range 1: _example 89064067 _definition ; Accession number used by Medline to categorize a specific bibliographic entry. ; data_citation_id _name '_citation_id' _category citation _type char _list yes _list_mandatory yes loop_ _list_link_child '_citation_author_citation_id' '_citation_editor_citation_id' loop_ _example primary 1 2 3 _definition ; The value of _citation_id must uniquely identify a record in the _citation_ list. The _citation_id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; data_citation_journal_abbrev _name '_citation_journal_abbrev' _category citation _type char _list yes _list_reference '_citation_id' _example 'J. Mol. Biol.' _definition ; Abbreviated name of the journal cited as given in the Chemical Abstracts Service Source Index. ; data_citation_journal_id_ASTM _name '_citation_journal_id_ASTM' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. ; data_citation_journal_id_CSD _name '_citation_journal_id_CSD' _category citation _type char _list yes _list_reference '_citation_id' _example '0070' _definition ; The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). ; data_citation_journal_id_ISSN _name '_citation_journal_id_ISSN' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; data_citation_journal_full _name '_citation_journal_full' _category citation _type char _list yes _list_reference '_citation_id' _example 'Journal of Molecular Biology' _definition ; Full name of the journal cited; relevant for journal articles. ; data_citation_journal_issue _name '_citation_journal_issue' _category citation _type char _list yes _list_reference '_citation_id' _example 2 _definition ; Issue number of the journal cited; relevant for journal articles. ; data_citation_journal_volume _name '_citation_journal_volume' _category citation _type char _list yes _list_reference '_citation_id' _example 174 _definition ; Volume number of the journal cited; relevant for journal articles. ; data_citation_language _name '_citation_language' _category citation _type char _list yes _list_reference '_citation_id' _example German _definition ; Language in which the cited article is written. ; data_citation_page_ loop_ _name '_citation_page_first' '_citation_page_last' _category citation _type char _list yes _list_reference '_citation_id' _definition ; The first and last pages of the citation; relevant for journal articles, books and book chapters. ; data_citation_special_details _name '_citation_special_details' _category citation _type char _list yes _list_reference '_citation_id' loop_ _example ; citation relates to this precise coordinate set ; ; citation relates to earlier low-resolution structure ; ; citation relates to further refinement of structure reported in citation 2 ; _definition ; A description of special aspects of the relationship of the contents of the data block to the literature item cited. ; data_citation_title _name '_citation_title' _category citation _type char _list yes _list_reference '_citation_id' _example ; Structure of diferric duck ovotransferrin at 2.35 \%A resolution. ; _definition ; The title of the citation; relevant for journal articles, books and book chapters. ; data_citation_year _name '_citation_year' _category citation _type numb _list yes _list_reference '_citation_id' _example 1984 _definition ; The year of the citation; relevant for journal articles, books and book chapters. ; ##################### ## CITATION_AUTHOR ## ##################### data_citation_author_[] _name '_citation_author_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _citation_author_citation_id _citation_author_name primary 'Fitzgerald, P.M.D.' primary 'McKeever, B.M.' primary 'Van Middlesworth, J.F.' primary 'Springer, J.P.' primary 'Heimbach, J.C.' primary 'Leu, C.-T.' primary 'Herber, W.K.' primary 'Dixon, R.A.F.' primary 'Darke, P.L.' 2 'Navia, M.A.' 2 'Fitzgerald, P.M.D.' 2 'McKeever, B.M.' 2 'Leu, C.-T.' 2 'Heimbach, J.C.' 2 'Herber, W.K.' 2 'Sigal, I.S.' 2 'Darke, P.L.' 2 'Springer, J.P.' 3 'McKeever, B.M.' 3 'Navia, M.A.' 3 'Fitzgerald, P.M.D.' 3 'Springer, J.P.' 3 'Leu, C.-T.' 3 'Heimbach, J.C.' 3 'Herber, W.K.' 3 'Sigal, I.S.' 3 'Darke, P.L.' ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the _citation_ list. ; data_citation_author_citation_id _name '_citation_author_citation_id' _category citation_author _type char _list yes _list_mandatory yes _list_link_parent '_citation_id' _definition ; The value of _citation_author_citation_id must match an identifier specified by _citation_id in the _citation_ list. ; data_citation_author_name _name '_citation_author_name' _category citation_author _type char _list yes _list_mandatory yes loop_ _example 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' 'M\"uller, H.A.' 'Ross II, C.R.' _definition ; Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; data_citation_author_ordinal _name '_citation_author_ordinal' _category citation_author _type char _list yes _definition ; This data name defines the order of the author's name in the list of authors of a citation. ; ##################### ## CITATION_EDITOR ## ##################### data_citation_editor_[] _name '_citation_editor_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _citation_editor_citation_id _citation_editor_name 5 'McKeever, B.M.' 5 'Navia, M.A.' 5 'Fitzgerald, P.M.D.' 5 'Springer, J.P.' ; ; Example 1 - hypothetical example. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the CITATION_EDITOR category record details about the editor associated with the book or book chapter citations in the _citation_ list. ; data_citation_editor_citation_id _name '_citation_editor_citation_id' _category citation_editor _type char _list yes _list_mandatory yes _list_link_parent '_citation_id' _definition ; The value of _citation_editor_citation_id must match an identifier specified by _citation_id in the _citation_ list. ; data_citation_editor_name _name '_citation_editor_name' _category citation_editor _type char _list yes _list_mandatory yes loop_ _example 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' 'M\"uller, H.A.' 'Ross II, C.R.' _definition ; Name of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; data_citation_editor_ordinal _name '_citation_editor_ordinal' _category citation_editor _type char _list yes _definition ; This data name defines the order of the editor's name in the list of editors of a citation. ; ############### ## COMPUTING ## ############### data_computing_[] _name '_computing_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _computing_data_collection 'CAD-4 (Enraf-Nonius, 1989)' _computing_cell_refinement 'CAD-4 (Enraf-Nonius, 1989)' _computing_data_reduction 'CFEO (Solans, 1978)' _computing_structure_solution 'SHELXS86 (Sheldrick, 1990)' _computing_structure_refinement 'SHELXL93 (Sheldrick, 1993)' _computing_molecular_graphics 'ORTEPII (Johnson, 1976)' _computing_publication_material 'PARST (Nardelli, 1983)' ; ; Example 1 - Rodr\'iguez-Romero, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. ; data_computing_ loop_ _name '_computing_cell_refinement' '_computing_data_collection' '_computing_data_reduction' '_computing_molecular_graphics' '_computing_publication_material' '_computing_structure_refinement' '_computing_structure_solution' _category computing _type char loop_ _example 'CAD-4 (Enraf-Nonius, 1989)' 'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)' 'FRODO (Jones, 1986), ORTEP (Johnson, 1965)' 'CRYSTALS (Watkin, 1988)' 'SHELX85 (Sheldrick, 1985)' _definition ; Software used in the processing of the data. Give the program or package name and a brief reference. ; ############## ## DATABASE ## ############## data_database_[] _name '_database_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _database_code_CSD 'VOBYUG' ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DATABASE category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a CIF if they originate from that source. ; data_database_code_ loop_ _name '_database_code_CAS' '_database_code_CSD' '_database_code_ICSD' '_database_code_MDF' '_database_code_NBS' '_database_code_PDB' '_database_code_PDF' _category database _type char _definition ; The codes are assigned by databases: Chemical Abstracts; Cambridge Structural Database (organic and metal-organic compounds); Inorganic Crystal Structure Database; Metals Data File (metal structures); NBS (NIST) Crystal Data Database (lattice parameters); Protein Data Bank; and the Powder Diffraction File (JCPDS/ICDD). ; data_database_code_depnum_ccdc_fiz _name '_database_code_depnum_ccdc_fiz' _category database _type char _definition ; Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; data_database_code_depnum_ccdc_journal _name '_database_code_depnum_ccdc_journal' _category database _type char _definition ; Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; data_database_code_depnum_ccdc_archive _name '_database_code_depnum_ccdc_archive' _category database _type char _definition ; Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. ; data_database_CSD_history _name '_database_CSD_history' _category database _type char _definition ; A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). ; data_database_journal_ loop_ _name '_database_journal_ASTM' '_database_journal_CSD' _category database _type char _definition ; The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service, and the journal code used in the Cambridge Structural Database. ; ############ ## DIFFRN ## ############ data_diffrn_[] _name '_diffrn_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_special_details ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% min^-1^. Background counts for 5 s on each side every scan. ; _diffrn_ambient_temperature 293 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN category record details about the intensity measurements. ; data_diffrn_ambient_environment _name '_diffrn_ambient_environment' _category diffrn _type char loop_ _example He vacuum 'mother liquor' _definition ; The gas or liquid surrounding the sample, if not air. ; data_diffrn_ambient_pressure _name '_diffrn_ambient_pressure' _category diffrn _type numb _type_conditions esd _enumeration_range 0.0: _units kPa _units_detail 'kilopascals' _definition ; The mean hydrostatic pressure in kilopascals at which the intensities were measured. ; data_diffrn_ambient_pressure_ loop_ _name '_diffrn_ambient_pressure_gt' '_diffrn_ambient_pressure_lt' _category diffrn _type numb _related_item '_diffrn_ambient_pressure' _related_function alternate _enumeration_range 0.0: _units kPa _units_detail 'kilopascals' _definition ; The mean hydrostatic pressure in kilopascals above which (*_gt) or below which (*_lt) the intensities were measured. These items allow for a pressure range to be given. _diffrn_ambient_pressure should always be used in preference to these items whenever possible. ; data_diffrn_ambient_temperature _name '_diffrn_ambient_temperature' _category diffrn _type numb _type_conditions esd _enumeration_range 0.0: _units K _units_detail kelvin _definition ; The mean temperature in kelvins at which the intensities were measured. ; data_diffrn_ambient_temperature_ loop_ _name '_diffrn_ambient_temperature_gt' '_diffrn_ambient_temperature_lt' _category diffrn _type numb _related_item '_diffrn_ambient_temperature' _related_function alternate _enumeration_range 0.0: _units K _units_detail kelvin _definition ; The mean temperature in kelvins above which (*_gt) or below which (*_lt) the intensities were measured. These items allow a range of temperatures to be given. _diffrn_ambient_temperature should always be used in preference to these items whenever possible. ; data_diffrn_crystal_treatment _name '_diffrn_crystal_treatment' _category diffrn _type char loop_ _example 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream' _definition ; Remarks about how the crystal was treated prior to the intensity measurements. Particularly relevant when intensities were measured at low temperature. ; data_diffrn_measured_fraction_theta_full _name '_diffrn_measured_fraction_theta_full' _category diffrn _type numb _enumeration_range 0:1.0 _definition ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_full. ; data_diffrn_measured_fraction_theta_max _name '_diffrn_measured_fraction_theta_max' _category diffrn _type numb _enumeration_range 0:1.0 _definition ; Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_max. ; data_diffrn_special_details _name '_diffrn_special_details' _category diffrn _type char _example ; The results may not be entirely reliable as the measurement was made during a heat wave when the air-conditioning had failed. ; _definition ; Special details of the intensity-measurement process. Should include information about source instability, crystal motion, degradation and so on. ; data_diffrn_symmetry_description _name '_diffrn_symmetry_description' _category diffrn _type char _definition ; Observed diffraction point symmetry, systematic absences and possible space group(s) or superspace group(s) compatible with these. ; ####################### ## DIFFRN_ATTENUATOR ## ####################### data_diffrn_attenuator_[] _name '_diffrn_attenuator_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_attenuator_code _diffrn_attenuator_scale 0 1.00 1 16.97 2 33.89 ; ; Example 1 - hypothetical example. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. ; data_diffrn_attenuator_code _name '_diffrn_attenuator_code' _category diffrn_attenuator _type char _list yes _list_mandatory yes _list_link_child '_diffrn_refln_attenuator_code' _definition ; A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln_attenuator_code which is stored with the intensities. See _diffrn_attenuator_scale. ; data_diffrn_attenuator_material _name '_diffrn_attenuator_material' _category diffrn_attenuator _type char _list yes _list_reference '_diffrn_attenuator_code' _definition ; Material from which the attenuator is made. ; data_diffrn_attenuator_scale _name '_diffrn_attenuator_scale' _category diffrn_attenuator _type numb _list yes _list_reference '_diffrn_attenuator_code' _enumeration_range 1.0: _definition ; The scale factor applied when an intensity measurement is reduced by an attenuator identified by _diffrn_attenuator_code. The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. ; ##################### ## DIFFRN_DETECTOR ## ##################### data_diffrn_detector_[] _name '_diffrn_detector_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_detector 'multiwire' _diffrn_detector_type 'Siemens' ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. ; data_diffrn_detector _name '_diffrn_detector' _category diffrn_detector _type char _related_item '_diffrn_radiation_detector' _related_function alternate loop_ _example 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' _definition ; The general class of the radiation detector. ; data_diffrn_detector_area_resol_mean _name '_diffrn_detector_area_resol_mean' _category diffrn_detector _type numb _enumeration_range 0.0: _units mm^-1^ _units_detail 'pixels per millimetre' _definition ; The resolution of an area detector, in pixels/mm. ; data_diffrn_detector_details _name '_diffrn_detector_details' _category diffrn_detector _type char _definition ; A description of special aspects of the radiation detector. ; data_diffrn_detector_dtime _name '_diffrn_detector_dtime' _category diffrn_detector _related_item '_diffrn_radiation_detector_dtime' _related_function alternate _type numb _enumeration_range 0.0: _definition ; The deadtime in microseconds of the detector used to measure the diffraction intensities. ; data_diffrn_detector_type _name '_diffrn_detector_type' _category diffrn_detector _type char _definition ; The make, model or name of the detector device used. ; data_diffrn_radiation_detector _name '_diffrn_radiation_detector' _category diffrn_detector _type char _related_item '_diffrn_detector' _related_function replace _definition ; The detector used to measure the diffraction intensities. ; data_diffrn_radiation_detector_dtime _name '_diffrn_radiation_detector_dtime' _category diffrn_detector _type numb _enumeration_range 0.0: _related_item '_diffrn_detector_dtime' _related_function replace _definition ; The deadtime in microseconds of the detector used to measure the diffraction intensities. ; ######################## ## DIFFRN_MEASUREMENT ## ######################## data_diffrn_measurement_[] _name '_diffrn_measurement_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_measurement_device_type 'Philips PW1100/20 diffractometer' _diffrn_measurement_method \q/2\q ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_MEASUREMENT category refer to the mounting of the sample and to the goniometer on which it is mounted. ; data_diffrn_measurement_details _name '_diffrn_measurement_details' _category diffrn_measurement _type char _example '440 frames of 0.25\%' _definition ; A description of special aspects of the intensity measurement. ; data_diffrn_measurement_device _name '_diffrn_measurement_device' _category diffrn_measurement _type char loop_ _example 'three-circle diffractometer' 'four-circle diffractometer' '\k-geometry diffractometer' 'oscillation camera' 'precession camera' _definition ; The general class of goniometer or device used to support and orient the specimen. ; data_diffrn_measurement_device_details _name '_diffrn_measurement_device_details' _category diffrn_measurement _type char _example ; commercial goniometer modified locally to allow for 90\% \t arc ; _definition ; A description of special aspects of the device used to measure the diffraction intensities. ; data_diffrn_measurement_device_type _name '_diffrn_measurement_device_type' _category diffrn_measurement _type char _definition ; The make, model or name of the measurement device (goniometer) used. ; data_diffrn_measurement_method _name '_diffrn_measurement_method' _category diffrn_measurement _type char _example 'profile data from \q/2\q scans' _definition ; Method used to measure the intensities. ; data_diffrn_measurement_specimen_support _name '_diffrn_measurement_specimen_support' _category diffrn_measurement _type char loop_ _example 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' _definition ; The physical device used to support the crystal during data collection. ; ########################## ## DIFFRN_ORIENT_MATRIX ## ########################## data_diffrn_orient_matrix_[] _name '_diffrn_orient_matrix_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_orient_matrix_UB_11 -0.04170 _diffrn_orient_matrix_UB_12 -0.01429 _diffrn_orient_matrix_UB_13 -0.02226 _diffrn_orient_matrix_UB_21 -0.00380 _diffrn_orient_matrix_UB_22 -0.05578 _diffrn_orient_matrix_UB_23 -0.05048 _diffrn_orient_matrix_UB_31 0.00587 _diffrn_orient_matrix_UB_32 -0.13766 _diffrn_orient_matrix_UB_33 0.02277 _diffrn_orient_matrix_type 'TEXSAN convention (MSC, 1989)' ; ; Example 1 - data set n-alkylation_C-4 of Hussain, Fleming, Norman & Chang [Acta Cryst. (1996), C52, 1010-1012]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction intensities. ; data_diffrn_orient_matrix_type _name '_diffrn_orient_matrix_type' _category diffrn_orient_matrix _type char _definition ; A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. ; data_diffrn_orient_matrix_UB_ loop_ _name '_diffrn_orient_matrix_UB_11' '_diffrn_orient_matrix_UB_12' '_diffrn_orient_matrix_UB_13' '_diffrn_orient_matrix_UB_21' '_diffrn_orient_matrix_UB_22' '_diffrn_orient_matrix_UB_23' '_diffrn_orient_matrix_UB_31' '_diffrn_orient_matrix_UB_32' '_diffrn_orient_matrix_UB_33' _category diffrn_orient_matrix _type numb _definition ; The elements of the diffractometer orientation matrix. These define the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See _diffrn_orient_matrix_type. ; ######################### ## DIFFRN_ORIENT_REFLN ## ######################### data_diffrn_orient_refln_[] _name '_diffrn_orient_refln_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_orient_refln_index_h _diffrn_orient_refln_index_k _diffrn_orient_refln_index_l _diffrn_orient_refln_angle_theta _diffrn_orient_refln_angle_phi _diffrn_orient_refln_angle_omega _diffrn_orient_refln_angle_kappa -3 2 3 7.35 44.74 2.62 17.53 -4 1 0 9.26 83.27 8.06 5.79 0 0 6 5.85 -43.93 -25.36 86.20 2 1 3 7.36 -57.87 6.26 5.42 0 0 -6 5.85 -161.59 36.96 -86.79 -3 1 0 6.74 80.28 5.87 2.60 2 0 3 5.86 -76.86 -0.17 21.34 0 0 12 11.78 -44.02 -19.51 86.41 0 0 -12 11.78 -161.67 42.81 -86.61 -5 1 0 11.75 86.24 9.16 7.44 0 4 6 11.82 -19.82 10.45 4.19 5 0 6 14.13 -77.28 10.17 15.34 8 0 0 20.79 -77.08 25.30 -13.96 ; ; Example 1 - typical output listing from an Enraf-Nonius CAD-4 diffractometer. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. ; data_diffrn_orient_refln_angle_ loop_ _name '_diffrn_orient_refln_angle_chi' '_diffrn_orient_refln_angle_kappa' '_diffrn_orient_refln_angle_omega' '_diffrn_orient_refln_angle_phi' '_diffrn_orient_refln_angle_psi' '_diffrn_orient_refln_angle_theta' _category diffrn_orient_refln _type numb _list yes _list_reference '_diffrn_orient_refln_index_' _units deg _units_detail 'degrees' _definition ; Diffractometer angles of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix_UB_ and _diffrn_orient_refln_index_h, *_k and *_l. ; data_diffrn_orient_refln_index_ loop_ _name '_diffrn_orient_refln_index_h' '_diffrn_orient_refln_index_k' '_diffrn_orient_refln_index_l' _category diffrn_orient_refln _type numb _list yes _list_mandatory yes _definition ; The indices of a reflection used to define the orientation matrix. See _diffrn_orient_matrix_. ; ###################### ## DIFFRN_RADIATION ## ###################### data_diffrn_radiation_[] _name '_diffrn_radiation_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_radiation_type 'Cu K\a' _diffrn_radiation_monochromator 'graphite' ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. ; data_diffrn_radiation_collimation _name '_diffrn_radiation_collimation' _category diffrn_radiation _type char loop_ _example '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' _definition ; The collimation or focusing applied to the radiation. ; data_diffrn_radiation_filter_edge _name '_diffrn_radiation_filter_edge' _category diffrn_radiation _type numb _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Absorption edge in angstroms of the radiation filter used. ; data_diffrn_radiation_inhomogeneity _name '_diffrn_radiation_inhomogeneity' _category diffrn_radiation _type numb _enumeration_range 0.0: _definition ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; data_diffrn_radiation_monochromator _name '_diffrn_radiation_monochromator' _category diffrn_radiation _type char loop_ _example 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' _definition ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. ; data_diffrn_radiation_polarisn_norm _name '_diffrn_radiation_polarisn_norm' _category diffrn_radiation _type numb _enumeration_range -180.0:180.0 _units deg _units_detail 'degrees' _definition ; The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See _diffrn_radiation_polarisn_ratio. ; data_diffrn_radiation_polarisn_ratio _name '_diffrn_radiation_polarisn_ratio' _category diffrn_radiation _type numb _enumeration_range 0.0: _definition ; Polarization ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarized to the parallel polarized components 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). ; data_diffrn_radiation_probe _name '_diffrn_radiation_probe' _category diffrn_radiation _type char loop_ _enumeration x-ray neutron electron gamma _definition ; The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information be given, so that the probe radiation can be simply determined. ; data_diffrn_radiation_type _name '_diffrn_radiation_type' _category diffrn_radiation _type char loop_ _example 'Cu K\a' 'Cu K\a~1~' 'Cu K-L~2,3~' white-beam _definition ; The type of the radiation. This is used to give a more detailed description than _diffrn_radiation_probe and is typically a description of the X-ray wavelength in Siegbahn notation. ; data_diffrn_radiation_xray_symbol _name '_diffrn_radiation_xray_symbol' _category diffrn_radiation _type char loop_ _enumeration _enumeration_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' _definition ; The IUPAC symbol for the X-ray wavelength for the probe radiation. ; ################################### ### DIFFRN_RADIATION_WAVELENGTH ### ################################### data_diffrn_radiation_wavelength_[] _name '_diffrn_radiation_wavelength_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_radiation_wavelength 1.5418 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used in measuring the diffraction intensities. Items may be looped to identify and assign weights to distinct wavelength components from a polychromatic beam. ; data_diffrn_radiation_wavelength _name '_diffrn_radiation_wavelength' _category diffrn_radiation_wavelength _type numb _list both _list_reference '_diffrn_radiation_wavelength_id' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The radiation wavelength in angstroms. ; data_diffrn_radiation_wavelength_id _name '_diffrn_radiation_wavelength_id' _category diffrn_radiation_wavelength _type char _list yes _list_mandatory yes _list_link_child '_diffrn_refln_wavelength_id' loop_ _example x1 x2 neut _definition ; An arbitrary code identifying each value of _diffrn_radiation_wavelength. Items in the DIFFRN_RADIATION category are looped when multiple wavelengths are used. This code is used to link with the _diffrn_refln_ list. It must match with one of the _diffrn_refln_wavelength_id codes. ; data_diffrn_radiation_wavelength_wt _name '_diffrn_radiation_wavelength_wt' _category diffrn_radiation_wavelength _type numb _list yes _list_reference '_diffrn_radiation_wavelength_id' _enumeration_range 0.0:1.0 _enumeration_default 1.0 _definition ; The relative weight of a wavelength identified by the code _diffrn_radiation_wavelength_id in the list of wavelengths. ; ################## ## DIFFRN_REFLN ## ################## data_diffrn_refln_[] _name '_diffrn_refln_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_refln_index_h _diffrn_refln_index_k _diffrn_refln_index_l _diffrn_refln_angle_chi _diffrn_refln_scan_rate _diffrn_refln_counts_bg_1 _diffrn_refln_counts_total _diffrn_refln_counts_bg_2 _diffrn_refln_angle_theta _diffrn_refln_angle_phi _diffrn_refln_angle_omega _diffrn_refln_angle_kappa _diffrn_refln_scan_width _diffrn_refln_elapsed_time 0 0 -16 0. 4.12 28 127 36 33.157 -75.846 16.404 50.170 1.516 19.43 0 0 -15 0. 4.12 38 143 28 30.847 -75.846 14.094 50.170 1.516 19.82 0 0 -14 0. 1.03 142 742 130 28.592 -75.846 11.839 50.170 1.516 21.32 0 0 -13 0. 4.12 26 120 37 26.384 -75.846 9.631 50.170 1.450 21.68 0 0 -12 0. 0.97 129 618 153 24.218 -75.846 7.464 50.170 1.450 23.20 0 0 -11 0. 4.12 33 107 38 22.087 -75.846 5.334 50.170 1.384 23.55 0 0 -10 0. 4.12 37 146 33 19.989 -75.846 3.235 50.170 1.384 23.90 0 0 -9 0. 4.12 50 179 49 17.918 -75.846 1.164 50.170 1.384 24.25 # - - - - data truncated for brevity - - - - 3 4 -4 0. 1.03 69 459 73 30.726 -53.744 46.543 -47.552 1.516 2082.58 3 4 -5 0. 1.03 91 465 75 31.407 -54.811 45.519 -42.705 1.516 2084.07 3 14 -6 0. 1.03 84 560 79 32.228 -55.841 44.745 -38.092 1.516 2085.57 # - - - - data truncated for brevity - - - - ; ; Example 1 - extracted from the CAD-4 listing for Tl~2~Cd~2~(SO~4~)~3~ at 85 K (unpublished). ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_REFLN category record details about the intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. (The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLNS data items are not looped.) ; data_diffrn_refln_angle_ loop_ _name '_diffrn_refln_angle_chi' '_diffrn_refln_angle_kappa' '_diffrn_refln_angle_omega' '_diffrn_refln_angle_phi' '_diffrn_refln_angle_psi' '_diffrn_refln_angle_theta' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _units deg _units_detail 'degrees' _definition ; The diffractometer angles of a reflection in degrees. These correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; data_diffrn_refln_attenuator_code _name '_diffrn_refln_attenuator_code' _category diffrn_refln _type char _list yes _list_reference '_diffrn_refln_index_' _list_link_parent '_diffrn_attenuator_code' _definition ; The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn_attenuator_code values. ; data_diffrn_refln_class_code _name '_diffrn_refln_class_code' _category diffrn_refln _type char _list yes _list_reference '_diffrn_refln_index_' _list_link_parent '_diffrn_reflns_class_code' _definition ; The code identifying the class to which this reflection has been assigned. This code must match a value of _diffrn_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. ; data_diffrn_refln_counts_ loop_ _name '_diffrn_refln_counts_bg_1' '_diffrn_refln_counts_bg_2' '_diffrn_refln_counts_net' '_diffrn_refln_counts_peak' '_diffrn_refln_counts_total' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _definition ; The diffractometer counts for the measurements: background before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak). ; data_diffrn_refln_crystal_id _name '_diffrn_refln_crystal_id' _category diffrn_refln _type char _list yes _list_reference '_diffrn_refln_index_' _list_link_parent '_exptl_crystal_id' _definition ; Code identifying each crystal if multiple crystals are used. Is used to link with _exptl_crystal_id in the _exptl_crystal_ list. ; data_diffrn_refln_detect_slit_ loop_ _name '_diffrn_refln_detect_slit_horiz' '_diffrn_refln_detect_slit_vert' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; Total slit apertures in degrees in the diffraction plane (*_horiz) and perpendicular to the diffraction plane (*_vert). ; data_diffrn_refln_elapsed_time _name '_diffrn_refln_elapsed_time' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0: _units min _units_detail 'minutes' _definition ; Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. ; data_diffrn_refln_index_ loop_ _name '_diffrn_refln_index_h' '_diffrn_refln_index_k' '_diffrn_refln_index_l' _category diffrn_refln _type numb _list yes _list_mandatory yes _definition ; Miller indices of a measured reflection. These need not match the _refln_index_h, *_k, *_l values if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns_reduction_process. See also _diffrn_reflns_transf_matrix_. ; data_diffrn_refln_intensity_net _name '_diffrn_refln_intensity_net' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0: _definition ; Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; data_diffrn_refln_intensity_sigma _name '_diffrn_refln_intensity_sigma' _category diffrn_refln _type numb _related_item '_diffrn_refln_intensity_u' _related_function replace _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0: _definition ; Standard uncertainty (e.s.d.) of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; data_diffrn_refln_intensity_u _name '_diffrn_refln_intensity_u' _category diffrn_refln _type numb _related_item '_diffrn_refln_intensity_sigma' _related_function alternate _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0: _definition ; Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; data_diffrn_refln_scale_group_code _name '_diffrn_refln_scale_group_code' _category diffrn_refln _type char _list yes _list_link_parent '_diffrn_scale_group_code' _list_reference '_diffrn_refln_index_' _definition ; The code identifying the scale applicable to this reflection. This code must match with a specified _diffrn_scale_group_code value. ; data_diffrn_refln_scan_mode _name '_diffrn_refln_scan_mode' _category diffrn_refln _type char _list yes _list_reference '_diffrn_refln_index_' loop_ _enumeration _enumeration_detail om 'omega scan' ot 'omega/2theta scan' q 'Q scans (arbitrary reciprocal directions)' _definition ; The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln_scan_width and _diffrn_refln_scan_mode_backgd. ; data_diffrn_refln_scan_mode_backgd _name '_diffrn_refln_scan_mode_backgd' _category diffrn_refln _type char _list yes _list_reference '_diffrn_refln_index_' loop_ _enumeration _enumeration_detail st 'stationary counter background' mo 'moving counter background' _definition ; The code identifying the mode of scanning a reflection to measure the background intensity. ; data_diffrn_refln_scan_rate _name '_diffrn_refln_scan_rate' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0: _units deg/min _units_detail 'degrees per minute' _definition ; The rate of scanning a reflection in degrees per minute to measure the intensity. ; data_diffrn_refln_scan_time_backgd _name '_diffrn_refln_scan_time_backgd' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0: _units sec _units_detail 'seconds' _definition ; The time spent measuring each background in seconds. ; data_diffrn_refln_scan_width _name '_diffrn_refln_scan_width' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; The scan width in degrees of the scan mode defined by the code _diffrn_refln_scan_mode. ; data_diffrn_refln_sint/lambda _name '_diffrn_refln_sint/lambda' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0: _units A^-1^ _units_detail 'reciprocal angstroms' _definition ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; data_diffrn_refln_standard_code _name '_diffrn_refln_standard_code' _category diffrn_refln _type char _list yes _list_link_parent '_diffrn_standard_refln_code' _list_reference '_diffrn_refln_index_' loop_ _example 1 2 3 s1 s2 s3 A B C _definition ; A code indicating that this reflection was measured as a standard reflection. The value must be '.' or match one of the _diffrn_standard_refln_code values. ; data_diffrn_refln_wavelength _name '_diffrn_refln_wavelength' _category diffrn_refln _type numb _list yes _list_reference '_diffrn_refln_index_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for reflections measured using energy-dispersive detectors or the Laue method. ; data_diffrn_refln_wavelength_id _name '_diffrn_refln_wavelength_id' _category diffrn_refln _type char _list yes _list_link_parent '_diffrn_radiation_wavelength_id' _list_reference '_diffrn_refln_index_' loop_ _example x1 x2 neut _definition ; Code identifying the wavelength in the _diffrn_radiation_ list. ; ################### ## DIFFRN_REFLNS ## ################### data_diffrn_reflns_[] _name '_diffrn_reflns_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_reflns_number 1592 _diffrn_reflns_av_R_equivalents 0 _diffrn_reflns_av_unetI/netI .027 _diffrn_reflns_limit_h_min 0 _diffrn_reflns_limit_h_max 6 _diffrn_reflns_limit_k_min -17 _diffrn_reflns_limit_k_max 0 _diffrn_reflns_limit_l_min 0 _diffrn_reflns_limit_l_max 22 _diffrn_reflns_theta_min 3.71 _diffrn_reflns_theta_max 61.97 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLNS data items are not looped. (The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists.) ; data_diffrn_reflns_av_R_equivalents _name '_diffrn_reflns_av_R_equivalents' _category diffrn_reflns _type numb _enumeration_range 0.0: _definition ; 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. ; data_diffrn_reflns_av_sigmaI/netI _name '_diffrn_reflns_av_sigmaI/netI' _category diffrn_reflns _type numb _related_item '_diffrn_reflns_av_unetI/netI' _related_function replace _enumeration_range 0.0: _definition ; Measure [sum u(net I)|/sum|net I|] for all measured reflections. ; data_diffrn_reflns_av_unetI/netI _name '_diffrn_reflns_av_unetI/netI' _category diffrn_reflns _type numb _related_item '_diffrn_reflns_av_sigmaI/netI' _related_function alternate _enumeration_range 0.0: _definition ; Measure [sum u(net I)|/sum|net I|] for all measured reflections. ; data_diffrn_reflns_limit_ loop_ _name '_diffrn_reflns_limit_h_max' '_diffrn_reflns_limit_h_min' '_diffrn_reflns_limit_k_max' '_diffrn_reflns_limit_k_min' '_diffrn_reflns_limit_l_max' '_diffrn_reflns_limit_l_min' _category diffrn_reflns _type numb _definition ; The limits on the Miller indices of the intensities specified by _diffrn_refln_index_h, *_k, *_l. ; data_diffrn_reflns_number _name '_diffrn_reflns_number' _category diffrn_reflns _type numb _enumeration_range 0: _definition ; The total number of measured intensities, excluding reflections that are classed as systematically absent arising from translational symmetry in the crystal unit cell. ; data_diffrn_reflns_reduction_process _name '_diffrn_reflns_reduction_process' _category diffrn_reflns _type char _example 'data averaged using Fisher test' _definition ; A description of the process used to reduce the intensities into structure-factor magnitudes. ; data_diffrn_reflns_resolution_full _name '_diffrn_reflns_resolution_full' _category diffrn_reflns _type numb _enumeration_range 0.0: _units A^-1^ _units_detail 'reciprocal angstroms' _related_item '_diffrn_reflns_theta_full' _related_function alternate _definition ; The resolution in reciprocal angstroms at which the measured reflection count is close to complete. ; data_diffrn_reflns_resolution_max _name '_diffrn_reflns_resolution_max' _category diffrn_reflns _type numb _enumeration_range 0.0: _units A^-1^ _units_detail 'reciprocal angstroms' _related_item '_diffrn_reflns_theta_max' _related_function alternate _definition ; Maximum resolution in reciprocal angstroms of the measured diffraction pattern. ; data_diffrn_reflns_theta_full _name '_diffrn_reflns_theta_full' _category diffrn_reflns _type numb _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; The theta angle (in degrees) 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. ; data_diffrn_reflns_theta_max _name '_diffrn_reflns_theta_max' _category diffrn_reflns _type numb _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; Maximum theta angle in degrees for the measured intensities. ; data_diffrn_reflns_theta_min _name '_diffrn_reflns_theta_min' _category diffrn_reflns _type numb _enumeration_range 0.0:90.0 _units deg _units_detail 'degrees' _definition ; Minimum theta angle in degrees for the measured intensities. ; data_diffrn_reflns_transf_matrix_ loop_ _name '_diffrn_reflns_transf_matrix_11' '_diffrn_reflns_transf_matrix_12' '_diffrn_reflns_transf_matrix_13' '_diffrn_reflns_transf_matrix_21' '_diffrn_reflns_transf_matrix_22' '_diffrn_reflns_transf_matrix_23' '_diffrn_reflns_transf_matrix_31' '_diffrn_reflns_transf_matrix_32' '_diffrn_reflns_transf_matrix_33' _category diffrn_reflns _type numb _definition ; Elements of the matrix used to transform the diffraction reflection indices _diffrn_refln_index_h, *_k, *_l into the _refln_index_h, *_k, *_l indices. |11 12 13| (h k l) diffraction |21 22 23| = (h' k' l') |31 32 33| ; ######################### ## DIFFRN_REFLNS_CLASS ## ######################### data_diffrn_reflns_class_[] _name '_diffrn_reflns_class_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_reflns_class_number _diffrn_reflns_class_d_res_high _diffrn_reflns_class_d_res_low _diffrn_reflns_class_av_R_eq _diffrn_reflns_class_code _diffrn_reflns_class_description 1580 0.551 6.136 0.015 'Main' 'm=0; main reflections' 1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites' ; ; Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is 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. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. ; data_diffrn_reflns_class_av_R_eq _name '_diffrn_reflns_class_av_R_eq' _category diffrn_reflns_class _type numb _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, 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 intensities. ; data_diffrn_reflns_class_av_sgI/I _name '_diffrn_reflns_class_av_sgI/I' _category diffrn_reflns_class _type numb _related_item '_diffrn_reflns_class_av_uI/I' _related_function replace _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0.0: _definition ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. ; data_diffrn_reflns_class_av_uI/I _name '_diffrn_reflns_class_av_uI/I' _category diffrn_reflns_class _type numb _related_item '_diffrn_reflns_class_av_sgI/I' _related_function alternate _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0.0: _definition ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. ; data_diffrn_reflns_class_code _name '_diffrn_reflns_class_code' _category diffrn_reflns_class _type char _list yes _list_mandatory yes _list_link_child '_diffrn_refln_class_code' loop_ _example '1' 'm1' 's2' _definition ; The code identifying a certain reflection class. ; data_diffrn_reflns_class_description _name '_diffrn_reflns_class_description' _category diffrn_reflns_class _type char _list yes _list_reference '_diffrn_reflns_class_code' loop_ _example 'm=1 first order satellites' 'H0L0 common projection reflections' _definition ; Description of each reflection class. ; data_diffrn_reflns_class_d_res_high _name '_diffrn_reflns_class_d_res_high' _category diffrn_reflns_class _type numb _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; The smallest value in angstroms of the interplanar spacings of the reflections in each reflection class. This is called the highest resolution for this reflection class. ; data_diffrn_reflns_class_d_res_low _name '_diffrn_reflns_class_d_res_low' _category diffrn_reflns_class _type numb _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; The highest value in angstroms of the interplanar spacings of the reflections in each reflection class. This is called the lowest resolution for this reflection class. ; data_diffrn_reflns_class_number _name '_diffrn_reflns_class_number' _category diffrn_reflns_class _type numb _list yes _list_reference '_diffrn_reflns_class_code' _enumeration_range 0: _definition ; The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. ; ######################## ## DIFFRN_SCALE_GROUP ## ######################## data_diffrn_scale_group_[] _name '_diffrn_scale_group_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_scale_group_code _diffrn_scale_group_I_net 1 .86473 2 1.0654 ; ; Example 1 - hypothetical example. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for instance, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. ; data_diffrn_scale_group_code _name '_diffrn_scale_group_code' _category diffrn_scale_group _type char _list yes _list_mandatory yes _list_link_child '_diffrn_refln_scale_group_code' loop_ _example 1 2 3 s1 A B c1 c2 c3 _definition ; The code identifying a specific measurement group (e.g. for multi-film or multi-crystal data). The code must match a _diffrn_refln_scale_group_code in the reflection list. ; data_diffrn_scale_group_I_net _name '_diffrn_scale_group_I_net' _category diffrn_scale_group _type numb _list yes _list_reference '_diffrn_scale_group_code' _enumeration_range 0.0: _definition ; The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the _diffrn_refln_ or _refln_ list on a common scale. ; ################### ## DIFFRN_SOURCE ## ################### data_diffrn_source_[] _name '_diffrn_source_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_source 'rotating anode X-ray tube' _diffrn_source_type 'Rigaku RU-200' _diffrn_source_power 50 _diffrn_source_current 180 _diffrn_source_size '8 mm x 0.4 mm broad focus' ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. ; data_diffrn_radiation_source _name '_diffrn_radiation_source' _category diffrn_source _type char _related_item '_diffrn_source' _related_function replace _definition ; The source of radiation. ; data_diffrn_source _name '_diffrn_source' _category diffrn_source _type char _related_item '_diffrn_radiation_source' _related_function alternate loop_ _example 'sealed X-ray tube' 'nuclear reactor' 'spallation source' 'electron microscope' 'rotating-anode X-ray tube' 'synchrotron' _definition ; The general class of the source of radiation. ; data_diffrn_source_current _name '_diffrn_source_current' _category diffrn_source _type numb _enumeration_range 0.0: _units mA _units_detail 'milliamperes' _definition ; The current in milliamperes at which the radiation source was operated. ; data_diffrn_source_details _name '_diffrn_source_details' _category diffrn_source _type char _definition ; A description of special aspects of the source. ; data_diffrn_source_power _name '_diffrn_source_power' _category diffrn_source _type numb _enumeration_range 0.0: _units kW _units_detail 'kilowatts' _definition ; The power in kilowatts at which the radiation source was operated. ; data_diffrn_source_size _name '_diffrn_source_size' _category diffrn_source _type char loop_ _example '8mm x 0.4 mm fine-focus' 'broad focus' _definition ; The dimensions of the source as viewed from the sample. ; data_diffrn_source_take-off_angle _name '_diffrn_source_take-off_angle' _category diffrn_source _type numb _enumeration_range 0:90 _units degrees _example 1.53 _definition ; 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. ; data_diffrn_source_target _name '_diffrn_source_target' _category diffrn_source _type char loop_ _enumeration H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr _definition ; The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. ; data_diffrn_source_type _name '_diffrn_source_type' _category diffrn_source _type char loop_ _example 'NSLS beamline X8C' 'Rigaku RU200' _definition ; The make, model or name of the source of radiation. ; data_diffrn_source_voltage _name '_diffrn_source_voltage' _category diffrn_source _type numb _enumeration_range 0.0: _units kV _units_detail 'kilovolts' _definition ; The voltage in kilovolts at which the radiation source was operated. ; ########################### ## DIFFRN_STANDARD_REFLN ## ########################### data_diffrn_standard_refln_[] _name '_diffrn_standard_refln_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_standard_refln_index_h _diffrn_standard_refln_index_k _diffrn_standard_refln_index_l 3 2 4 1 9 1 3 0 10 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of the diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. ; data_diffrn_standard_refln_code _name '_diffrn_standard_refln_code' _category diffrn_standard_refln _type char _list yes _list_link_child '_diffrn_refln_standard_code' _list_reference '_diffrn_standard_refln_index_' loop_ _example 1 2 3 s1 A B _definition ; The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln_index_. This is the same code as the _diffrn_refln_standard_code in the _diffrn_refln_ list. ; data_diffrn_standard_refln_index_ loop_ _name '_diffrn_standard_refln_index_h' '_diffrn_standard_refln_index_k' '_diffrn_standard_refln_index_l' _category diffrn_standard_refln _type numb _list yes _list_mandatory yes _definition ; Miller indices of standard reflections used in the diffraction measurement process. ; ###################### ## DIFFRN_STANDARDS ## ###################### data_diffrn_standards_[] _name '_diffrn_standards_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _diffrn_standards_number 3 _diffrn_standards_interval_time 120 _diffrn_standards_decay_% 0 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. ; data_diffrn_standards_decay_% _name '_diffrn_standards_decay_%' _category diffrn_standards _type numb _type_conditions esd _enumeration_range :100 _definition ; The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. ; data_diffrn_standards_interval_ loop_ _name '_diffrn_standards_interval_count' '_diffrn_standards_interval_time' _category diffrn_standards _type numb _enumeration_range 0: _definition ; The number of reflection intensities, or the time in minutes, between the measurement of standard reflection intensities. ; data_diffrn_standards_number _name '_diffrn_standards_number' _category diffrn_standards _type numb _enumeration_range 0: _definition ; The number of unique standard reflections used during the measurement of the diffraction intensities. ; data_diffrn_standards_scale_sigma _name '_diffrn_standards_scale_sigma' _category diffrn_standards _type numb _related_item '_diffrn_standards_scale_u' _related_function replace _enumeration_range 0.0: _definition ; The standard uncertainty (e.s.d.) of the individual mean standard scales applied to the intensity data. ; data_diffrn_standards_scale_u _name '_diffrn_standards_scale_u' _category diffrn_standards _type numb _related_item '_diffrn_standards_scale_sigma' _related_function alternate _enumeration_range 0.0: _definition ; The standard uncertainty of the individual mean standard scales applied to the intensity data. ; ########### ## EXPTL ## ########### data_exptl_[] _name '_exptl_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _exptl_absorpt_coefficient_mu 0.962 _exptl_absorpt_correction_type psi-scan _exptl_absorpt_process_details 'North, Phillips & Mathews (1968)' _exptl_absorpt_correction_T_min 0.929 _exptl_absorpt_correction_T_max 0.997 ; ; Example 1 - based on a paper by Steiner [Acta Cryst. (1996), C52, 2554-2556]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. ; data_exptl_absorpt_coefficient_mu _name '_exptl_absorpt_coefficient_mu' _category exptl _type numb _enumeration_range 0.0: _units mm^-1^ _units_detail 'reciprocal millimetres' _definition ; The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. ; data_exptl_absorpt_correction_T_ loop_ _name '_exptl_absorpt_correction_T_max' '_exptl_absorpt_correction_T_min' _category exptl _type numb _enumeration_range 0.0:1.0 _definition ; The maximum and minimum transmission factors for the crystal and radiation. These factors are also referred to as the absorption correction A or 1/A*. ; data_exptl_absorpt_correction_type _name '_exptl_absorpt_correction_type' _category exptl _type char loop_ _enumeration _enumeration_detail analytical 'analytical from crystal shape' cylinder 'cylindrical' empirical 'empirical from intensities' gaussian 'Gaussian from crystal shape' integration 'integration from crystal shape' multi-scan 'symmetry-related measurements' none 'no absorption correction applied' numerical 'numerical from crystal shape' psi-scan 'psi-scan corrections' refdelf 'refined from delta-F' sphere 'spherical' _definition ; The absorption-correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. ; data_exptl_absorpt_process_details _name '_exptl_absorpt_process_details' _category exptl _type char loop_ _example 'Tompa analytical' 'MolEN (Fair, 1990)' '(North, Phillips & Mathews, 1968)' _definition ; Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. ; data_exptl_crystals_number _name '_exptl_crystals_number' _category exptl _type numb _enumeration_range 1: _definition ; The total number of crystals used for the measurement of intensities. ; data_exptl_special_details _name '_exptl_special_details' _category exptl _type char _definition ; Any special information about the experimental work prior to the intensity measurements. See also _exptl_crystal_preparation. ; ################### ## EXPTL_CRYSTAL ## ################### data_exptl_crystal_[] _name '_exptl_crystal_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _exptl_crystal_description prism _exptl_crystal_colour colourless _exptl_crystal_size_max 0.32 _exptl_crystal_size_mid 0.27 _exptl_crystal_size_min 0.10 _exptl_crystal_density_diffrn 1.146 _exptl_crystal_density_meas ? _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 656 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _exptl_crystal_density_meas_gt 2.5 _exptl_crystal_density_meas_lt 5.0 ; ; Example 2 - using separate items to define upper and lower limits for a value. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _exptl_crystal_density_meas_temp_lt 300 ; ; Example 3 - here the density was measured at some unspecified temperature below room temperature. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the EXPTL_CRYSTAL category record details about experimental measurements on the crystal or crystals used, such as shape, size or density. ; data_exptl_crystal_colour _name '_exptl_crystal_colour' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' loop_ _related_item _related_function '_exptl_crystal_colour_lustre' alternate '_exptl_crystal_colour_modifier' alternate '_exptl_crystal_colour_primary' alternate _example 'dark green' _definition ; The colour of the crystal. ; data_exptl_crystal_colour_lustre _name '_exptl_crystal_colour_lustre' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' loop_ _enumeration metallic dull clear _related_item '_exptl_crystal_colour' _related_function alternate _definition ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal_colour_modifier with _exptl_crystal_colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal_colour_lustre, as in 'metallic-green'. ; data_exptl_crystal_colour_modifier _name '_exptl_crystal_colour_modifier' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' loop_ _enumeration light dark whitish blackish grayish brownish reddish pinkish orangish yellowish greenish bluish _related_item '_exptl_crystal_colour' _related_function alternate _definition ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal_colour_modifier with _exptl_crystal_colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal_colour_lustre, as in 'metallic-green'. ; data_exptl_crystal_colour_primary _name '_exptl_crystal_colour_primary' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' loop_ _enumeration colourless white black gray brown red pink orange yellow green blue violet _related_item '_exptl_crystal_colour' _related_function alternate _definition ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal_colour_modifier with _exptl_crystal_colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal_colour_lustre, as in 'metallic-green'. ; data_exptl_crystal_density_diffrn _name '_exptl_crystal_density_diffrn' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units Mgm^-3^ _units_detail 'megagrams per cubic metre' _definition ; Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). ; data_exptl_crystal_density_meas _name '_exptl_crystal_density_meas' _category exptl_crystal _type numb _type_conditions esd _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units Mgm^-3^ _units_detail 'megagrams per cubic metre' _definition ; Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). ; data_exptl_crystal_density_meas_gt _name '_exptl_crystal_density_meas_gt' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units Mg^-3^ _units_detail 'megagrams per cubic metre' _related_item '_exptl_crystal_density_meas' _related_function alternate loop_ _example _example_detail 2.5 ; lower limit for the density (only the range within which the density lies was given in the original paper) ; _definition ; The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal_density_meas_gt and _exptl_crystal_density_meas_lt should not be used to report new experimental work, for which _exptl_crystal_density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal_density_meas. ; data_exptl_crystal_density_meas_lt _name '_exptl_crystal_density_meas_lt' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units Mg^-3^ _units_detail 'megagrams per cubic metre' _related_item '_exptl_crystal_density_meas' _related_function alternate loop_ _example _example_detail 1.0 'specimen floats in water' 5.0 ; upper limit for the density (only the range within which the density lies was given in the original paper) ; _definition ; The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal_density_meas_gt and _exptl_crystal_density_meas_lt should not be used to report new experimental work, for which _exptl_crystal_density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal_density_meas. ; data_exptl_crystal_density_meas_temp _name '_exptl_crystal_density_meas_temp' _category exptl_crystal _type numb _type_conditions esd _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units K _units_detail kelvin _definition ; Temperature in kelvins at which _exptl_crystal_density_meas was determined. ; data_exptl_crystal_density_meas_temp_gt _name '_exptl_crystal_density_meas_temp_gt' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units K _units_detail kelvin _related_item '_exptl_crystal_density_meas_temp' _related_function alternate _definition ; Temperature in kelvins above which _exptl_crystal_density_meas was determined. _exptl_crystal_density_meas_temp_gt and _exptl_crystal_density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal_density_meas_temp. ; data_exptl_crystal_density_meas_temp_lt _name '_exptl_crystal_density_meas_temp_lt' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units K _units_detail kelvin _related_item '_exptl_crystal_density_meas_temp' _related_function alternate loop_ _example _example_detail 300 ; The density was measured at some unspecified temperature below room temperature. ; _definition ; Temperature in kelvins below which _exptl_crystal_density_meas was determined. _exptl_crystal_density_meas_temp_gt and _exptl_crystal_density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal_density_meas_temp. ; data_exptl_crystal_density_method _name '_exptl_crystal_density_method' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' loop_ _example 'flotation in aqueous KI' 'not measured' 'Berman density torsion balance' _definition ; The method used to measure _exptl_crystal_density_meas. ; data_exptl_crystal_description _name '_exptl_crystal_description' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' _definition ; A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead _exptl_crystal_size_ for the gross dimensions of the crystal and _exptl_crystal_face_ to describe the relationship between individual faces. ; data_exptl_crystal_F_000 _name '_exptl_crystal_F_000' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _definition ; The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 f~i~ = imaginary part of the scattering factors at theta = 0 the sum is taken over each atom in the unit cell ; data_exptl_crystal_id _name '_exptl_crystal_id' _category exptl_crystal _type char _list yes _list_mandatory yes loop_ _list_link_child '_diffrn_refln_crystal_id' '_refln_crystal_id' _definition ; Code identifying each crystal if multiple crystals are used. It is used to link with _diffrn_refln_crystal_id in the intensity measurements and with _refln_crystal_id in the _refln_ list. ; data_exptl_crystal_preparation _name '_exptl_crystal_preparation' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' _example 'mounted in an argon-filled quartz capillary' _definition ; Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. ; data_exptl_crystal_pressure_history _name '_exptl_crystal_pressure_history' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' _definition ; Relevant details concerning the pressure history of the sample. ; data_exptl_crystal_recrystallization_method _name '_exptl_crystal_recrystallization_method' _category exptl_crystal _type char _definition ; Describes the method used to recrystallize the sample. Sufficient details should be given for the procedure to be repeated. The temperature or temperatures should be given as well as details of the solvent, flux or carrier gas with concentrations or pressures and ambient atmosphere. ; data_exptl_crystal_size_ loop_ _name '_exptl_crystal_size_length' '_exptl_crystal_size_max' '_exptl_crystal_size_mid' '_exptl_crystal_size_min' '_exptl_crystal_size_rad' _category exptl_crystal _type numb _list both _list_reference '_exptl_crystal_id' _enumeration_range 0.0: _units mm _units_detail 'millimetres' _definition ; The maximum, medial and minimum dimensions in millimetres of the crystal. If the crystal is a sphere, then the *_rad item is its radius. If the crystal is a cylinder, then the *_rad item is its radius and the *_length item is its length. These may appear in a list with _exptl_crystal_id if multiple crystals are used in the experiment. ; data_exptl_crystal_thermal_history _name '_exptl_crystal_thermal_history' _category exptl_crystal _type char _list both _list_reference '_exptl_crystal_id' _definition ; Relevant details concerning the thermal history of the sample. ; ######################## ## EXPTL_CRYSTAL_FACE ## ######################## data_exptl_crystal_face_[] _name '_exptl_crystal_face_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist 0 -1 -2 .18274 1 0 -2 .17571 -1 1 -2 .17845 -2 1 0 .21010 -1 0 2 .18849 1 -1 2 .20605 2 -1 0 .24680 -1 2 0 .19688 0 1 2 .15206 ; ; Example 1 - based on structure PAWD2 of Vittal & Dean [Acta Cryst. (1996), C52, 1180-1182]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. ; data_exptl_crystal_face_diffr_ loop_ _name '_exptl_crystal_face_diffr_chi' '_exptl_crystal_face_diffr_kappa' '_exptl_crystal_face_diffr_phi' '_exptl_crystal_face_diffr_psi' _category exptl_crystal_face _type numb _list yes _list_reference '_exptl_crystal_face_index_' _units deg _units_detail 'degrees' _definition ; The goniometer angle settings in degrees when the perpendicular to the specified crystal face is aligned along a specified direction (e.g. the bisector of the incident and reflected beams in an optical goniometer). ; data_exptl_crystal_face_index_ loop_ _name '_exptl_crystal_face_index_h' '_exptl_crystal_face_index_k' '_exptl_crystal_face_index_l' _category exptl_crystal_face _type numb _list yes _list_mandatory yes _definition ; Miller indices of the crystal face associated with the value _exptl_crystal_face_perp_dist. ; data_exptl_crystal_face_perp_dist _name '_exptl_crystal_face_perp_dist' _category exptl_crystal_face _type numb _list yes _list_reference '_exptl_crystal_face_index_' _enumeration_range 0.0: _units mm _units_detail 'millimetres' _definition ; The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. ; ########## ## GEOM ## ########## data_geom_[] _name '_geom_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; ; ; Example 1 - based on data set bagan of Yamane & DiSalvo [Acta Cryst. (1996), C52, 760-761]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular and crystal geometry as calculated from the ATOM, CELL and SYMMETRY data. Geometry data are usually redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they serve the dual purposes of providing a check on the correctness of both sets of data and of enabling the most important geometric data to be identified for publication by setting the appropriate publication flag. ; data_geom_special_details _name '_geom_special_details' _category geom _type char _definition ; The description of geometrical information not covered by the existing data names in the geometry categories, such as least-squares planes. ; ################ ## GEOM_ANGLE ## ################ data_geom_angle_[] _name '_geom_angle_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_2 _geom_angle_site_symmetry_3 _geom_angle_publ_flag C2 O1 C5 111.6(2) 1_555 1_555 1_555 yes O1 C2 C3 110.9(2) 1_555 1_555 1_555 yes O1 C2 O21 122.2(3) 1_555 1_555 1_555 yes C3 C2 O21 127.0(3) 1_555 1_555 1_555 yes C2 C3 N4 101.3(2) 1_555 1_555 1_555 yes C2 C3 C31 111.3(2) 1_555 1_555 1_555 yes C2 C3 H3 107(1) 1_555 1_555 1_555 no N4 C3 C31 116.7(2) 1_555 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the ATOM, CELL and SYMMETRY data. ; data_geom_angle _name '_geom_angle' _category geom_angle _type numb _type_conditions esd _list yes _list_reference '_geom_angle_atom_site_label_' _units deg _units_detail 'degrees' _definition ; Angle in degrees defined by the three sites _geom_angle_atom_site_label_1, *_2 and *_3. The site at *_2 is at the apex of the angle. ; data_geom_angle_atom_site_label_ loop_ _name '_geom_angle_atom_site_label_1' '_geom_angle_atom_site_label_2' '_geom_angle_atom_site_label_3' _category geom_angle _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of the three atom sites which define the angle given by _geom_angle. These must match labels specified as _atom_site_label in the atom list. Label 2 identifies the site at the apex of the angle. ; data_geom_angle_publ_flag _name '_geom_angle_publ_flag' _category geom_angle _type char _list yes _list_reference '_geom_angle_atom_site_label_' loop_ _enumeration _enumeration_detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' _enumeration_default no _definition ; This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. ; data_geom_angle_site_symmetry_ loop_ _name '_geom_angle_site_symmetry_1' '_geom_angle_site_symmetry_2' '_geom_angle_site_symmetry_3' _category geom_angle _type char _list yes _list_reference '_geom_angle_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ############### ## GEOM_BOND ## ############### data_geom_bond_[] _name '_geom_bond_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2 _geom_bond_publ_flag O1 C2 1.342(4) 1_555 1_555 yes O1 C5 1.439(3) 1_555 1_555 yes C2 C3 1.512(4) 1_555 1_555 yes C2 O21 1.199(4) 1_555 1_555 yes C3 N4 1.465(3) 1_555 1_555 yes C3 C31 1.537(4) 1_555 1_555 yes C3 H3 1.00(3) 1_555 1_555 no N4 C5 1.472(3) 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM_BOND category record details about bonds as calculated from the ATOM, CELL and SYMMETRY data. ; data_geom_bond_atom_site_label_ loop_ _name '_geom_bond_atom_site_label_1' '_geom_bond_atom_site_label_2' _category geom_bond _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of two atom sites that form a bond. These must match labels specified as _atom_site_label in the atom list. ; data_geom_bond_distance _name '_geom_bond_distance' _category geom_bond _type numb _type_conditions esd _list yes _list_reference '_geom_bond_atom_site_label_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The intramolecular bond distance in angstroms. ; data_geom_bond_publ_flag _name '_geom_bond_publ_flag' _category geom_bond _type char _list yes _list_reference '_geom_bond_atom_site_label_' loop_ _enumeration _enumeration_detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' _enumeration_default no _definition ; This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. ; data_geom_bond_site_symmetry_ loop_ _name '_geom_bond_site_symmetry_1' '_geom_bond_site_symmetry_2' _category geom_bond _type char _list yes _list_reference '_geom_bond_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_geom_bond_valence _name '_geom_bond_valence' _category geom_bond _type numb _list yes _list_reference '_geom_bond_atom_site_label_' _definition ; The bond valence calculated from _geom_bond_distance. ; ################## ## GEOM_CONTACT ## ################## data_geom_contact_[] _name '_geom_contact_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _geom_contact_atom_site_label_1 _geom_contact_atom_site_label_2 _geom_contact_distance _geom_contact_site_symmetry_1 _geom_contact_site_symmetry_2 _geom_contact_publ_flag O(1) O(2) 2.735(3) . . yes H(O1) O(2) 1.82 . . no ; ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the ATOM, CELL and SYMMETRY data. ; data_geom_contact_atom_site_label_ loop_ _name '_geom_contact_atom_site_label_1' '_geom_contact_atom_site_label_2' _category geom_contact _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of two atom sites that are within contact distance. The labels must match _atom_site_label codes in the atom list. ; data_geom_contact_distance _name '_geom_contact_distance' _category geom_contact _type numb _type_conditions esd _list yes _list_reference '_geom_contact_atom_site_label_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The interatomic contact distance in angstroms. ; data_geom_contact_publ_flag _name '_geom_contact_publ_flag' _category geom_contact _type char _list yes _list_reference '_geom_contact_atom_site_label_' loop_ _enumeration _enumeration_detail no 'do not include distance in special list' n 'abbreviation for "no"' yes 'do include distance in special list' y 'abbreviation for "yes"' _enumeration_default no _definition ; This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. ; data_geom_contact_site_symmetry_ loop_ _name '_geom_contact_site_symmetry_1' '_geom_contact_site_symmetry_2' _category geom_contact _type char _list yes _list_reference '_geom_contact_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the contact. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ################ ## GEOM_HBOND ## ################ data_geom_hbond_[] _name '_geom_hbond_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_publ_flag N6 HN6 OW 0.888(8) 1.921(12) 2.801(8) 169.6(8) yes OW HO2 O7 0.917(6) 1.923(12) 2.793(8) 153.5(8) yes OW HO1 N10 0.894(8) 1.886(11) 2.842(8) 179.7(9) yes ; ; Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the ATOM, CELL and SYMMETRY data. ; data_geom_hbond_angle_DHA _name '_geom_hbond_angle_DHA' _category geom_hbond _type numb _type_conditions esd _list yes _list_reference '_geom_hbond_atom_site_label_' _units deg _units_detail 'degrees' _definition ; Angle in degrees defined by the three sites _geom_hbond_atom_site_label_D, *_H and *_A. The site at *_H (the hydrogen atom participating in the interaction) is at the apex of the angle. ; data_geom_hbond_atom_site_label_ loop_ _name '_geom_hbond_atom_site_label_D' '_geom_hbond_atom_site_label_H' '_geom_hbond_atom_site_label_A' _category geom_hbond _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of three atom sites (respectively, the donor atom, hydrogen atom and acceptor atom) participating in a hydrogen bond. These must match labels specified as _atom_site_label in the atom list. ; data_geom_hbond_distance_ loop_ _name '_geom_hbond_distance_DH' '_geom_hbond_distance_HA' '_geom_hbond_distance_DA' _category geom_hbond _type numb _type_conditions esd _list yes _list_reference '_geom_hbond_atom_site_label_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Distances in angstroms between the donor and hydrogen (*_DH), hydrogen and acceptor (*_HA) and donor and acceptor (*_DA) sites in a hydrogen bond. ; data_geom_hbond_publ_flag _name '_geom_hbond_publ_flag' _category geom_hbond _type char _list yes _list_reference '_geom_hbond_atom_site_label_' loop_ _enumeration _enumeration_detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' _enumeration_default no _definition ; This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. ; data_geom_hbond_site_symmetry_ loop_ _name '_geom_hbond_site_symmetry_D' '_geom_hbond_site_symmetry_H' '_geom_hbond_site_symmetry_A' _category geom_hbond _type char _list yes _list_reference '_geom_hbond_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the hydrogen bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ################## ## GEOM_TORSION ## ################## data_geom_torsion_[] _name '_geom_torsion_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 _geom_torsion_publ_flag C(9) O(2) C(7) C(2) 71.8(2) . . . . yes C(7) O(2) C(9) C(10) -168.0(3) . . . 2_666 yes C(10) O(3) C(8) C(6) -167.7(3) . . . . yes C(8) O(3) C(10) C(9) -69.7(2) . . . 2_666 yes O(1) C(1) C(2) C(3) -179.5(4) . . . . no O(1) C(1) C(2) C(7) -0.6(1) . . . . no ; ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the GEOM_TORSION category record details about interatomic torsion angles as calculated from the ATOM, CELL and SYMMETRY data. ; data_geom_torsion _name '_geom_torsion' _category geom_torsion _type numb _type_conditions esd _list yes _list_reference '_geom_torsion_atom_site_label_' _units deg _units_detail 'degrees' _definition ; The torsion angle in degrees bounded by the four atom sites identified by the _geom_torsion_atom_site_label_ codes. These must match labels specified as _atom_site_label in the atom list. The torsion-angle definition should be that of Klyne and Prelog. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. ; data_geom_torsion_atom_site_label_ loop_ _name '_geom_torsion_atom_site_label_1' '_geom_torsion_atom_site_label_2' '_geom_torsion_atom_site_label_3' '_geom_torsion_atom_site_label_4' _category geom_torsion _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of the four atom sites which define the torsion angle specified by _geom_torsion. These must match codes specified as _atom_site_label in the atom list. The torsion-angle definition should be that of Klyne and Prelog. The vector direction *_label_2 to *_label_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. ; data_geom_torsion_publ_flag _name '_geom_torsion_publ_flag' _category geom_torsion _type char _list yes _list_reference '_geom_torsion_atom_site_label_' loop_ _enumeration _enumeration_detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' _enumeration_default no _definition ; This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. ; data_geom_torsion_site_symmetry_ loop_ _name '_geom_torsion_site_symmetry_1' '_geom_torsion_site_symmetry_2' '_geom_torsion_site_symmetry_3' '_geom_torsion_site_symmetry_4' _category geom_torsion _type char _list yes _list_reference '_geom_torsion_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ############# ## JOURNAL ## ############# data_journal_[] _name '_journal_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _journal_date_recd_electronic 91-04-15 _journal_date_from_coeditor 91-04-18 _journal_date_accepted 91-04-18 _journal_date_printers_first 91-08-07 _journal_date_proofs_out 91-08-07 _journal_coeditor_code HL0007 _journal_techeditor_code C910963 _journal_coden_ASTM ACSCEE _journal_name_full 'Acta Crystallographica Section C' _journal_year 1991 _journal_volume 47 _journal_issue NOV91 _journal_page_first 2276 _journal_page_last 2277 ; ; Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a CIF submitted for publication. The creator of a CIF will not normally specify these data items. The data names are not defined in the dictionary because they are for journal use only. ; data_journal_ loop_ _name '_journal_coden_ASTM' '_journal_coden_Cambridge' '_journal_coeditor_address' '_journal_coeditor_code' '_journal_coeditor_email' '_journal_coeditor_fax' '_journal_coeditor_name' '_journal_coeditor_notes' '_journal_coeditor_phone' '_journal_data_validation_number' '_journal_date_accepted' '_journal_date_from_coeditor' '_journal_date_to_coeditor' '_journal_date_printers_final' '_journal_date_printers_first' '_journal_date_proofs_in' '_journal_date_proofs_out' '_journal_date_recd_copyright' '_journal_date_recd_electronic' '_journal_date_recd_hard_copy' '_journal_issue' '_journal_language' '_journal_name_full' '_journal_page_first' '_journal_page_last' '_journal_paper_category' '_journal_suppl_publ_number' '_journal_suppl_publ_pages' '_journal_techeditor_address' '_journal_techeditor_code' '_journal_techeditor_email' '_journal_techeditor_fax' '_journal_techeditor_name' '_journal_techeditor_notes' '_journal_techeditor_phone' '_journal_volume' '_journal_year' _category journal _type char _definition ; Data items specified by the journal staff. ; ################### ## JOURNAL_INDEX ## ################### data_journal_index_[] _name '_journal_index_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _journal_index_type _journal_index_term _journal_index_subterm O C16H19NO4 . S alkaloids (-)-norcocaine S (-)-norcocaine . S ; [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate ; . ; ; Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a CIF will not normally specify these data items. ; data_journal_index_ loop_ _name '_journal_index_subterm' '_journal_index_term' '_journal_index_type' _category journal_index _type char _definition ; Indexing terms supplied by the journal staff. ; ########## ## PUBL ## ########## data_publ_[] _name '_publ_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _publ_section_title ; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)- 1,3-oxazolidin-5-one ; _publ_section_abstract ; The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\%, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\%A]. ; ; ; Example 1 - based on Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _publ_section_title ; Hemiasterlin methyl ester ; _publ_section_title_footnote ; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl- 2-methylamino-3-(N-methylbenzo[b]pyrrol- 3-yl)butanamido]-3,3-dimethyl-N-methyl- butanamido}-2-hexenoate. ; ; ; Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the PUBL category are used when submitting a manuscript for publication. They refer either to the paper as a whole, or to specific named elements within a paper (such as the title and abstract, or the Comment and Experimental sections of Acta Crystallographica Section C). The data items in the PUBL_BODY category should be used for the text of other submissions. Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. ; data_publ_contact_author _name '_publ_contact_author' _category publ _type char loop_ _example ; Professor George Ferguson Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; _definition ; The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ_contact_author_name and _publ_contact_author_address. ; data_publ_contact_author_address _name '_publ_contact_author_address' _category publ _type char _example ; Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; _definition ; The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; data_publ_contact_author_email _name '_publ_contact_author_email' _category publ _type char loop_ _example name@host.domain.country bm@iucr.org _definition ; E-mail address in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; data_publ_contact_author_fax _name '_publ_contact_author_fax' _category publ _type char loop_ _example '12(34)9477334' '12()349477334' _definition ; Facsimile telephone number of the author submitting the manuscript and data block. The recommended style is the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; data_publ_contact_author_id_iucr _name '_publ_contact_author_id_iucr' _category publ _type char _example 2985 _definition ; Identifier in the IUCr contact database of the author submitting the manuscript and data block. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org). ; data_publ_contact_author_name _name '_publ_contact_author_name' _category publ _type char _example 'Professor George Ferguson' _definition ; The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; data_publ_contact_author_phone _name '_publ_contact_author_phone' _category publ _type char loop_ _example '12(34)9477330' '12()349477330' '12(34)9477330x5543' _definition ; Telephone number of the author submitting the manuscript and data block. The recommended style is the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; data_publ_contact_letter _name '_publ_contact_letter' _category publ _type char _definition ; A letter submitted to the journal editor by the contact author. ; data_publ_manuscript_creation _name '_publ_manuscript_creation' _category publ _type char _example 'Tex file created by FrameMaker on a Sun 3/280' _definition ; A description of the word-processor package and computer used to create the word-processed manuscript stored as _publ_manuscript_processed. ; data_publ_manuscript_processed _name '_publ_manuscript_processed' _category publ _type char _definition ; The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item _publ_manuscript_creation. ; data_publ_manuscript_text _name '_publ_manuscript_text' _category publ _type char _definition ; The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. ; data_publ_requested_category _name '_publ_requested_category' _category publ _type char loop_ _enumeration _enumeration_detail FA 'Full article' FI 'Full submission - inorganic (Acta C)' FO 'Full submission - organic (Acta C)' FM 'Full submission - metal-organic (Acta C)' CI 'CIF-access paper - inorganic (Acta C) (no longer in use)' CO 'CIF-access paper - organic (Acta C) (no longer in use)' CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)' EI 'Electronic submission - inorganic (Acta E)' EO 'Electronic submission - organic (Acta E)' EM 'Electronic submission - metal-organic (Acta E)' QI 'Inorganic compounds (Acta E)' QO 'Organic compounds (Acta E)' QM 'Metal-organic compounds (Acta E)' AD 'Addenda and Errata (Acta C, Acta E)' SC 'Short communication' _enumeration_default FA _definition ; The category of paper submitted. For submission to Acta Crystallographica Section C or Acta Crystallographica Section E, ONLY those codes indicated for use with those journals should be used. ; data_publ_requested_coeditor_name _name '_publ_requested_coeditor_name' _category publ _type char _definition ; The name of the co-editor whom the authors would like to handle the submitted manuscript. ; data_publ_requested_journal _name '_publ_requested_journal' _category publ _type char _definition ; The name of the journal to which the manuscript is being submitted. ; data_publ_section_ loop_ _name '_publ_section_title' '_publ_section_title_footnote' '_publ_section_synopsis' '_publ_section_abstract' '_publ_section_comment' '_publ_section_introduction' '_publ_section_experimental' '_publ_section_exptl_prep' '_publ_section_exptl_refinement' '_publ_section_exptl_solution' '_publ_section_discussion' '_publ_section_acknowledgements' '_publ_section_references' '_publ_section_related_literature' '_publ_section_figure_captions' '_publ_section_table_legends' _category publ _type char _definition ; The sections of a manuscript if submitted in parts. As an alternative, see _publ_manuscript_text and _publ_manuscript_processed. The _publ_section_exptl_prep, _publ_section_exptl_refinement and _publ_section_exptl_solution items are preferred for separating the chemical preparation, refinement and structure solution aspects of the experimental description. ; ################# ## PUBL_AUTHOR ## ################# data_publ_author_[] _name '_publ_author_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publ_author_name _publ_author_address 'Willis, Anthony C.' ; Research School of Chemistry Australian National University GPO Box 4 Canberra, ACT Australia 2601 ; ; ; Example 1 - based on Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. ; data_publ_author_address _name '_publ_author_address' _category publ_author _type char _list both _list_reference '_publ_author_name' _example ; Department Institute Street City and postcode COUNTRY ; _definition ; The address of a publication author. If there is more than one author, this will be looped with _publ_author_name. ; data_publ_author_footnote _name '_publ_author_footnote' _category publ_author _type char _list both _list_reference '_publ_author_name' loop_ _example 'On leave from U. Western Australia' 'Also at Department of Biophysics' _definition ; A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease. ; data_publ_author_email _name '_publ_author_email' _category publ_author _type char _list both _list_reference '_publ_author_name' loop_ _example name@host.domain.country bm@iucr.org _definition ; The e-mail address of a publication author. If there is more than one author, this will be looped with _publ_author_name. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; data_publ_author_id_iucr _name '_publ_author_id_iucr' _category publ_author _type char _list both _example 2985 _definition ; Identifier in the IUCr contact database of a publication author. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org). ; data_publ_author_name _name '_publ_author_name' _category publ_author _type char _list both _list_mandatory yes loop_ _example 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' 'M\"uller, H.A.' 'Ross II, C.R.' _definition ; The name of a publication author. If there are multiple authors, this will be looped with _publ_author_address. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials. ; ############### ## PUBL_BODY ## ############### data_publ_body_[] _name '_publ_body_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publ_body_element _publ_body_label _publ_body_title _publ_body_format _publ_body_contents section 1 Introduction cif ; X-ray diffraction from a crystalline material provides information on the thermally and spatially averaged electron density in the crystal... ; section 2 Theory tex ; In the rigid-atom approximation, the dynamic electron density of an atom is described by the convolution product of the static atomic density and a probability density function, $\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$ ; ; ; Example 1 - based on a paper by R. Restori & D. Schwarzenbach [Acta Cryst. (1996), A52, 369-378]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publ_body_element _publ_body_label _publ_body_title _publ_body_contents section 3 ; The two-channel method for retrieval of the deformation electron density ; . subsection 3.1 'The two-channel entropy S[\D\r(r)]' ; As the wide dynamic range involved in the total electron density... ; subsection 3.2 'Uniform vs informative prior model densities' . subsubsection 3.2.1 'Use of uniform models' ; Straightforward algebra leads to expressions analogous to... ; ; ; Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens [Acta Cryst. (1996), A52, 397-407]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. ; data_publ_body_contents _name '_publ_body_contents' _category publ_body _type char _list yes _list_reference '_publ_body_label' _definition ; A text section of a paper. ; data_publ_body_element _name '_publ_body_element' _category publ_body _type char _list yes _list_reference '_publ_body_label' loop_ _enumeration section subsection subsubsection appendix footnote _definition ; The functional role of the associated text section. ; data_publ_body_format _name '_publ_body_format' _category publ_body _type char _list yes _list_reference '_publ_body_label' loop_ _enumeration _enumeration_detail ascii 'no coding for special symbols' cif 'CIF convention' latex 'LaTeX' rtf 'Rich Text Format' sgml 'SGML (ISO 8879)' tex 'TeX' troff 'troff or nroff' _enumeration_default cif _definition ; Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section. ; data_publ_body_label _name '_publ_body_label' _category publ_body _type char _list yes _list_mandatory yes _list_uniqueness '_publ_body_element' loop_ _example 1 1.1 2.1.3 _definition ; Code identifying the section of text. The combination of this with _publ_body_element must be unique. ; data_publ_body_title _name '_publ_body_title' _category publ_body _type char _list yes _list_reference '_publ_body_label' _definition ; Title of the associated section of text. ; ########################## ## PUBL_MANUSCRIPT_INCL ## ########################## data_publ_manuscript_incl_[] _name '_publ_manuscript_incl_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publ_manuscript_incl_extra_item _publ_manuscript_incl_extra_info _publ_manuscript_incl_extra_defn # # Include Hydrogen Bonding Geometry Description # ============================================= # Name explanation standard? # ---- ----------- --------- '_geom_hbond_atom_site_label_D' 'H-bond donor' yes '_geom_hbond_atom_site_label_H' 'H-bond hydrogen' yes '_geom_hbond_atom_site_label_A' 'H-bond acceptor' yes '_geom_hbond_distance_DH' 'H-bond D-H' yes '_geom_hbond_distance_HA' 'H-bond H...A' yes '_geom_hbond_distance_DA' 'H-bond D...A' yes '_geom_hbond_angle_DHA' 'H-bond D-H...A' yes ; ; Example 1 - directive to include a hydrogen-bonding table, including cosmetic headings in comments. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publ_manuscript_incl_extra_item _publ_manuscript_incl_extra_info _publ_manuscript_incl_extra_defn '_atom_site_symmetry_multiplicity' 'to emphasise special sites' yes '_chemical_compound_source' 'rare material, unusual source' yes '_reflns_d_resolution_high' 'limited data is a problem here' yes '_crystal_magnetic_permeability' 'unusual value for this material' no ; ; Example 2 - hypothetical example including both standard CIF data items and a non-CIF quantity which the author wishes to list. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software. Although these fields are primarily intended to identify CIF data items that the author wishes to include in a published paper, they can also be used to identify data names created so that non-CIF items can be included in the publication. Note that *_item names MUST be enclosed in single quotes. ; data_publ_manuscript_incl_extra_defn _name '_publ_manuscript_incl_extra_defn' _category publ_manuscript_incl _type char _list yes _list_reference '_publ_manuscript_incl_extra_item' loop_ _enumeration _enumeration_detail no 'not a standard CIF data name' n 'abbreviation for "no"' yes 'a standard CIF data name' y 'abbreviation for "yes"' _enumeration_default yes _definition ; Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not. ; data_publ_manuscript_incl_extra_info _name '_publ_manuscript_incl_extra_info' _category publ_manuscript_incl _type char _list yes _list_reference '_publ_manuscript_incl_extra_item' _definition ; A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published. ; data_publ_manuscript_incl_extra_item _name '_publ_manuscript_incl_extra_item' _category publ_manuscript_incl _type char _list yes _list_mandatory yes _definition ; Specifies the inclusion of specific data into a manuscript which are not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list. ; ############ ## REFINE ## ############ data_refine_[] _name '_refine_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _refine_special_details sfls:_F_calc_weight_full_matrix _refine_ls_structure_factor_coef F _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'w=1/(u^2^(F)+0.0004F^2^)' _refine_ls_hydrogen_treatment refxyz _refine_ls_extinction_method Zachariasen _refine_ls_extinction_coef 3514(42) _refine_ls_extinction_expression ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard. ; _refine_ls_abs_structure_details ; The absolute configuration was assigned to agree with that of its precursor l-leucine at the chiral centre C3. ; _refine_ls_number_reflns 1408 _refine_ls_number_parameters 272 _refine_ls_number_restraints 0 _refine_ls_number_constraints 0 _refine_ls_R_factor_all .038 _refine_ls_R_factor_gt .034 _refine_ls_wR_factor_all .044 _refine_ls_wR_factor_gt .042 _refine_ls_goodness_of_fit_all 1.462 _refine_ls_goodness_of_fit_gt 1.515 _refine_ls_shift/su_max .535 _refine_ls_shift/su_mean .044 _refine_diff_density_min -.108 _refine_diff_density_max .131 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFINE category record details about the structure-refinement parameters. ; data_refine_diff_density_ loop_ _name '_refine_diff_density_max' '_refine_diff_density_min' '_refine_diff_density_rms' _category refine _type numb _type_conditions esd _units e_A^-3^ _units_detail 'electrons per cubic angstrom' _definition ; The largest and smallest values and the root-mean-square deviation, in electrons per angstrom cubed, of the final difference electron density. The *_rms value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of *_min and *_max values, and also for defining suitable contour levels. ; data_refine_ls_abs_structure_details _name '_refine_ls_abs_structure_details' _category refine _type char _definition ; The nature of the absolute structure and how it was determined. ; data_refine_ls_abs_structure_Flack _name '_refine_ls_abs_structure_Flack' _category refine _type numb _type_conditions esd _enumeration_range 0.0:1.0 _definition ; The measure of absolute structure as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures, the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (e.s.d.) u must be supplied. The _enumeration_range of 0.0:1.0 is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. ; data_refine_ls_abs_structure_Rogers _name '_refine_ls_abs_structure_Rogers' _category refine _type numb _type_conditions esd _enumeration_range -1.0:1.0 _definition ; The measure of absolute structure as defined by Rogers (1981). The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must be supplied. The _enumeration_range of -1.0:1.0 is correctly interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. ; data_refine_ls_d_res_high _name '_refine_ls_d_res_high' _category refine _type numb _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The smallest value in angstroms of the interplanar spacings of the reflections used in the refinement. This is called the highest resolution. ; data_refine_ls_d_res_low _name '_refine_ls_d_res_low' _category refine _type numb _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The largest value in angstroms of the interplanar spacings of the reflections used in the refinement. This is called the lowest resolution. ; data_refine_ls_extinction_coef _name '_refine_ls_extinction_coef' _category refine _type numb _type_conditions esd _example 3472(52) _example_detail 'Zachariasen coefficient r* = 0.347(5) E04' _definition ; The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine_ls_extinction_expression and _refine_ls_extinction_method. For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; data_refine_ls_extinction_expression _name '_refine_ls_extinction_expression' _category refine _type char _example ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22), p. 292. Copenhagen: Munksgaard. ; _definition ; A description of or reference to the extinction-correction equation used to apply the data item _refine_ls_extinction_coef. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors. ; data_refine_ls_extinction_method _name '_refine_ls_extinction_method' _category refine _type char _enumeration_default 'Zachariasen' loop_ _example 'B-C type 2 Gaussian isotropic' 'none' _definition ; A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine_special_details. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; data_refine_ls_goodness_of_fit_all _name '_refine_ls_goodness_of_fit_all' _category refine _type numb _type_conditions esd _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for all reflections after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = the standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_goodness_of_fit_gt _name '_refine_ls_goodness_of_fit_gt' _category refine _type numb _type_conditions esd _related_item '_refine_ls_goodness_of_fit_obs' _related_function alternate _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns_threshold_expression) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_goodness_of_fit_obs _name '_refine_ls_goodness_of_fit_obs' _category refine _type numb _type_conditions esd _related_item '_refine_ls_goodness_of_fit_gt' _related_function replace _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for observed reflections (see _reflns_observed_criterion) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty (e.s.d.) Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_goodness_of_fit_ref _name '_refine_ls_goodness_of_fit_ref' _category refine _type numb _type_conditions esd _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; data_refine_ls_hydrogen_treatment _name '_refine_ls_hydrogen_treatment' _category refine _type char loop_ _enumeration _enumeration_detail refall 'refined all H-atom parameters' refxyz 'refined H-atom coordinates only' refU 'refined H-atom U's only' noref 'no refinement of H-atom parameters' constr 'H-atom parameters constrained' mixed 'some constrained, some independent' undef 'H-atom parameters not defined' _enumeration_default undef _definition ; Treatment of hydrogen atoms in the least-squares refinement. ; data_refine_ls_matrix_type _name '_refine_ls_matrix_type' _category refine _type char loop_ _enumeration _enumeration_detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only' _enumeration_default full _definition ; Type of matrix used to accumulate the least-squares derivatives. ; data_refine_ls_number_constraints _name '_refine_ls_number_constraints' _category refine _type numb _enumeration_range 0: _enumeration_default 0 _definition ; The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site_constraints and _atom_site_refinement_flags. A general description of constraints may appear in _refine_special_details. ; data_refine_ls_number_parameters _name '_refine_ls_number_parameters' _category refine _type numb _enumeration_range 0: _definition ; The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. ; data_refine_ls_number_reflns _name '_refine_ls_number_reflns' _category refine _type numb _enumeration_range 0: _definition ; The number of unique reflections contributing to the least-squares refinement calculation. ; data_refine_ls_number_restraints _name '_refine_ls_number_restraints' _category refine _type numb _enumeration_range 0: _definition ; The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site_constraints and _atom_site_refinement_flags. A general description of refinement constraints may appear in _refine_special_details. ; data_refine_ls_R_factor_all _name '_refine_ls_R_factor_all' _category refine _type numb _enumeration_range 0.0: _definition ; Residual factor for all reflections satisfying the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. This is the conventional R factor. See also _refine_ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; data_refine_ls_R_factor_gt _name '_refine_ls_R_factor_gt' _category refine _type numb _related_item '_refine_ls_R_factor_obs' _related_function alternate _enumeration_range 0.0: _definition ; Residual factor for the reflections (with number given by _reflns_number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. This is the conventional R factor. See also _refine_ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; data_refine_ls_R_factor_obs _name '_refine_ls_R_factor_obs' _category refine _type numb _related_item '_refine_ls_R_factor_gt' _related_function replace _enumeration_range 0.0: _definition ; Residual factor for the reflections classified as 'observed' (see _reflns_observed_criterion) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. This is the conventional R factor. See also _refine_ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; data_refine_ls_R_Fsqd_factor _name '_refine_ls_R_Fsqd_factor' _category refine _type numb _enumeration_range 0.0: _definition ; Residual factor R(Fsqd), calculated on the squared amplitudes of the observed and calculated structure factors, for significantly intense reflections (satisfying _reflns_threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; data_refine_ls_R_I_factor _name '_refine_ls_R_I_factor' _category refine _type numb _enumeration_range 0.0: _definition ; Residual factor R(I) for significantly intense reflections (satisfying _reflns_threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the specified reflections ; data_refine_ls_restrained_S_all _name '_refine_ls_restrained_S_all' _category refine _type numb _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also _refine_ls_goodness_of_fit_ definitions. {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/square of standard uncertainty (e.s.d.)] P(calc) = the calculated restraint values P(targ) = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine_ls_number_reflns) N~restr~ = the number of restraints (see _refine_ls_number_restraints) N~param~ = the number of refined parameters (see _refine_ls_number_parameters) sum is taken over the specified reflections sum~r~ is taken over the restraints ; data_refine_ls_restrained_S_gt _name '_refine_ls_restrained_S_gt' _category refine _type numb _related_item '_refine_ls_restrained_S_obs' _related_function alternate _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S' for significantly intense reflections (satisfying _reflns_threshold_expression) after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also _refine_ls_goodness_of_fit_ definitions. {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/square of standard uncertainty (e.s.d.)] P(calc) = the calculated restraint values P(targ) = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine_ls_number_reflns) N~restr~ = the number of restraints (see _refine_ls_number_restraints) N~param~ = the number of refined parameters (see _refine_ls_number_parameters) sum is taken over the specified reflections sum~r~ is taken over the restraints ; data_refine_ls_restrained_S_obs _name '_refine_ls_restrained_S_obs' _category refine _type numb _related_item '_refine_ls_restrained_S_gt' _related_function replace _enumeration_range 0.0: _definition ; The least-squares goodness-of-fit parameter S' for observed reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also _refine_ls_goodness_of_fit_ definitions. {sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ { + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } } S' = { -------------------------------------------------- } { N~ref~ + N~restr~ - N~param~ } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/square of standard uncertainty (e.s.d.)] P(calc) = the calculated restraint values P(targ) = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine_ls_number_reflns) N~restr~ = the number of restraints (see _refine_ls_number_restraints) N~param~ = the number of refined parameters (see _refine_ls_number_parameters) sum is taken over the specified reflections sum~r~ is taken over the restraints ; data_refine_ls_shift/esd_max _name '_refine_ls_shift/esd_max' _category refine _type numb _related_item '_refine_ls_shift/su_max' _related_function replace _enumeration_range 0.0: _definition ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty (s.u., formerly described as estimated standard deviation, e.s.d.). ; data_refine_ls_shift/esd_mean _name '_refine_ls_shift/esd_mean' _category refine _type numb _related_item '_refine_ls_shift/su_mean' _related_function replace _enumeration_range 0.0: _definition ; The average ratio of the final least-squares parameter shift to the final standard uncertainty (s.u., formerly described as estimated standard deviation, e.s.d.). ; data_refine_ls_shift/su_max _name '_refine_ls_shift/su_max' _category refine _type numb _related_item '_refine_ls_shift/esd_max' _related_function alternate _enumeration_range 0.0: _definition ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty. ; data_refine_ls_shift/su_max_lt _name '_refine_ls_shift/su_max_lt' _category refine _type numb _related_item '_refine_ls_shift/su_max' _related_function alternate _enumeration_range 0.0: _definition ; An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure. ; data_refine_ls_shift/su_mean _name '_refine_ls_shift/su_mean' _category refine _type numb _related_item '_refine_ls_shift/esd_mean' _related_function alternate _enumeration_range 0.0: _definition ; The average ratio of the final least-squares parameter shift to the final standard uncertainty. ; data_refine_ls_shift/su_mean_lt _name '_refine_ls_shift/su_mean_lt' _category refine _type numb _related_item '_refine_ls_shift/su_mean' _related_function alternate _enumeration_range 0.0: _definition ; An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure. ; data_refine_ls_structure_factor_coef _name '_refine_ls_structure_factor_coef' _category refine _type char loop_ _enumeration _enumeration_detail F 'structure-factor magnitude' Fsqd 'structure factor squared' Inet 'net intensity' _enumeration_default F _definition ; Structure-factor coefficient |F|, F^2^ or I used in the least-squares refinement process. ; data_refine_ls_weighting_details _name '_refine_ls_weighting_details' _category refine _type char _example ; Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. ; _definition ; A description of special aspects of the weighting scheme used in the least-squares refinement. Used to describe the weighting when the value of _refine_ls_weighting_scheme is specified as 'calc'. ; data_refine_ls_weighting_scheme _name '_refine_ls_weighting_scheme' _category refine _type char loop_ _enumeration _enumeration_detail sigma "based on measured s.u.'s" unit 'unit or no weights applied' calc 'calculated weights applied' _enumeration_default sigma _definition ; The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine_ls_weighting_details for a preferred approach). ; data_refine_ls_wR_factor_all _name '_refine_ls_wR_factor_all' _category refine _type numb _enumeration_range 0.0: _definition ; Weighted residual factors for all reflections. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refine_ls_wR_factor_gt _name '_refine_ls_wR_factor_gt' _category refine _type numb _related_item '_refine_ls_wR_factor_obs' _related_function alternate _enumeration_range 0.0: _definition ; Weighted residual factors for significantly intense reflections (satisfying _reflns_threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refine_ls_wR_factor_obs _name '_refine_ls_wR_factor_obs' _category refine _type numb _related_item '_refine_ls_wR_factor_gt' _related_function replace _enumeration_range 0.0: _definition ; Weighted residual factors for the reflections classified as 'observed' (see _reflns_observed_criterion) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refine_ls_wR_factor_ref _name '_refine_ls_wR_factor_ref' _category refine _type numb _enumeration_range 0.0: _definition ; Weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. See also the _refine_ls_R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine_ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine_ls_structure_factor_coef w = the least-squares weight and the sum is taken over the specified reflections ; data_refine_special_details _name '_refine_special_details' _category refine _type char _definition ; Description of special aspects of the refinement process. ; ##################### ## REFINE_LS_CLASS ## ##################### data_refine_ls_class_[] _name '_refine_ls_class_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _refine_ls_class_R_factor_gt _refine_ls_class_code 0.057 'Main' 0.074 'Com' 0.064 'NbRefls' 0.046 'LaRefls' 0.112 'Sat1' 0.177 'Sat2' ; ; Example 1 - example for a modulated structure extracted from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263.] ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFINE_LS_CLASS category record details (for each reflection class separately) about the reflections used for the structure refinement. ; data_refine_ls_class_code _name '_refine_ls_class_code' _category refine_ls_class _type char _list yes _list_link_parent '_reflns_class_code' loop_ _example '1' 'm1' 's2' _definition ; The code identifying a certain reflection class. This code must match a _reflns_class_code. ; data_refine_ls_class_d_res_high _name '_refine_ls_class_d_res_high' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; For each reflection class, the highest resolution in angstroms for the reflections used in the refinement. This is the lowest d value in a reflection class. ; data_refine_ls_class_d_res_low _name '_refine_ls_class_d_res_low' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; For each reflection class, the lowest resolution in angstroms for the reflections used in the refinement. This is the highest d value in a reflection class. ; data_refine_ls_class_R_factor_ loop_ _name '_refine_ls_class_R_factor_all' '_refine_ls_class_R_factor_gt' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factors for all reflections, and for significantly intense reflections (see _reflns_threshold_expression), included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low. This is the conventional R factor. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. See also _refine_ls_class_wR_factor_all definitions. ; data_refine_ls_class_R_Fsqd_factor _name '_refine_ls_class_R_Fsqd_factor' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; data_refine_ls_class_R_I_factor _name '_refine_ls_class_R_I_factor' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; data_refine_ls_class_wR_factor_all _name '_refine_ls_class_wR_factor_all' _category refine_ls_class _type numb _list yes _list_reference '_refine_ls_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed 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. See also _refine_ls_class_R_factor_ definitions. ; ########### ## REFLN ## ########### data_refln_[] _name '_refln_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_calc _refln_F_squared_meas _refln_F_squared_sigma _refln_include_status 2 0 0 85.57 58.90 1.45 o 3 0 0 15718.18 15631.06 30.40 o 4 0 0 55613.11 49840.09 61.86 o 5 0 0 246.85 241.86 10.02 o 6 0 0 82.16 69.97 1.93 o 7 0 0 1133.62 947.79 11.78 o 8 0 0 2558.04 2453.33 20.44 o 9 0 0 283.88 393.66 7.79 o 10 0 0 283.70 171.98 4.26 o ; ; Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_meas _refln_F_calc _refln_F_sigma _refln_include_status _refln_scale_group_code 0 0 6 34.935 36.034 3.143 o 1 0 0 12 42.599 40.855 2.131 o 1 0 1 0 42.500 42.507 4.719 o 1 0 1 1 59.172 57.976 4.719 o 1 0 1 2 89.694 94.741 4.325 o 1 0 1 3 51.743 52.241 3.850 o 1 0 1 4 9.294 10.318 2.346 o 1 0 1 5 41.160 39.951 3.313 o 1 0 1 6 6.755 7.102 .895 < 1 0 1 7 30.693 31.171 2.668 o 1 0 1 8 12.324 12.085 2.391 o 1 0 1 9 15.348 15.122 2.239 o 1 0 1 10 17.622 19.605 1.997 o 1 ; ; Example 2 - based on standard test data set p6122 of the Xtal distribution [Hall, King & Stewart (1995). Xtal3.4 User's Manual. University of Western Australia]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFLN category record details about the reflections used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; data_refln_A_ loop_ _name '_refln_A_calc' '_refln_A_meas' _category refln _type numb _list yes _list_reference '_refln_index_' _definition ; The calculated and measured structure-factor component A (in electrons for X-ray diffraction). A =|F|cos(phase) ; data_refln_B_ loop_ _name '_refln_B_calc' '_refln_B_meas' _category refln _type numb _list yes _list_reference '_refln_index_' _definition ; The calculated and measured structure-factor component B (in electrons for X-ray diffraction). B =|F|sin(phase) ; data_refln_class_code _name '_refln_class_code' _category refln _type char _list yes _list_reference '_refln_index_' _list_link_parent '_reflns_class_code' _definition ; The 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. ; data_refln_d_spacing _name '_refln_d_spacing' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression _refln_d_spacing = 2/(_refln_sint/lambda) ; data_refln_crystal_id _name '_refln_crystal_id' _category refln _type char _list yes _list_link_parent '_exptl_crystal_id' _list_reference '_refln_index_' _definition ; Code identifying each crystal if multiple crystals are used. Is used to link with _exptl_crystal_id in the _exptl_crystal_ list. ; data_refln_F_ loop_ _name '_refln_F_calc' '_refln_F_meas' '_refln_F_sigma' _category refln _type numb _list yes _list_reference '_refln_index_' _definition ; The calculated, measured and standard uncertainty (derived from measurement) of the structure factors (in electrons for X-ray diffraction). ; data_refln_F_squared_ loop_ _name '_refln_F_squared_calc' '_refln_F_squared_meas' '_refln_F_squared_sigma' _category refln _type numb _list yes _list_reference '_refln_index_' _definition ; Calculated, measured and estimated standard uncertainty (derived from measurement) of the squared structure factors (in electrons squared for X-ray diffraction). ; data_refln_include_status _name '_refln_include_status' _category refln _type char _related_item '_refln_observed_status' _related_function alternate _list yes _list_reference '_refln_index_' loop_ _enumeration _enumeration_detail o ; (lower-case letter o for 'observed') satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low exceeds _reflns_threshold_expression ; < ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low does not exceed _reflns_threshold_expression ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine_ls_d_res_high' l 'does not satisfy _refine_ls_d_res_low' _enumeration_default o _definition ; Classification of a reflection indicating its status with respect to inclusion in the refinement and the calculation of R factors. ; data_refln_index_ loop_ _name '_refln_index_h' '_refln_index_k' '_refln_index_l' _category refln _type numb _list yes _list_mandatory yes _definition ; Miller indices of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by the cell lengths and cell angles in the CELL category. ; data_refln_intensity_ loop_ _name '_refln_intensity_calc' '_refln_intensity_meas' '_refln_intensity_sigma' _category refln _type numb _list yes _list_reference '_refln_index_' _definition ; The calculated, measured and standard uncertainty (derived from measurement) of the intensity, all in the same arbitrary units as _refln_intensity_meas. ; data_refln_mean_path_length_tbar _name '_refln_mean_path_length_tbar' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 0.0: _units mm _units_detail 'millimetres' _definition ; Mean path length in millimetres through the crystal for this reflection. ; data_refln_observed_status _name '_refln_observed_status' _category refln _type char _related_item '_refln_include_status' _related_function replace _list yes _list_reference '_refln_index_' loop_ _enumeration _enumeration_detail o ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low observed by _reflns_observed_criterion ; < ; satisfies _refine_ls_d_res_high satisfies _refine_ls_d_res_low unobserved by _reflns_observed_criterion ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine_ls_d_res_high' l 'does not satisfy _refine_ls_d_res_low' _enumeration_default o _definition ; Classification of a reflection indicating its status with respect to inclusion in the refinement and the calculation of R factors. ; data_refln_phase_calc _name '_refln_phase_calc' _category refln _type numb _list yes _list_reference '_refln_index_' _units deg _units_detail 'degrees' _definition ; The calculated structure-factor phase in degrees. ; data_refln_phase_meas _name '_refln_phase_meas' _category refln _type numb _type_conditions esd _list yes _list_reference '_refln_index_' _units deg _units_detail 'degrees' _definition ; The measured structure-factor phase in degrees. ; data_refln_refinement_status _name '_refln_refinement_status' _category refln _type char _list yes _list_reference '_refln_index_' loop_ _enumeration _enumeration_detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction' _enumeration_default incl _definition ; Status of a reflection in the structure-refinement process. ; data_refln_scale_group_code _name '_refln_scale_group_code' _category refln _type char _list yes _list_link_parent '_reflns_scale_group_code' _list_reference '_refln_index_' loop_ _example 1 2 3 s1 A B c1 c2 c3 _definition ; Code identifying the structure-factor scale. This code must correspond to one of the _reflns_scale_group_code values. ; data_refln_sint/lambda _name '_refln_sint/lambda' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 0.0: _units A^-1^ _units_detail 'reciprocal angstroms' _definition ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; data_refln_symmetry_epsilon _name '_refln_symmetry_epsilon' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 1:48 _definition ; The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. ; data_refln_symmetry_multiplicity _name '_refln_symmetry_multiplicity' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 1:48 _definition ; 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 (2002), Chapter 10.1. ; data_refln_wavelength _name '_refln_wavelength' _category refln _type numb _list yes _list_reference '_refln_index_' _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The mean wavelength in angstroms of the radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. ; data_refln_wavelength_id _name '_refln_wavelength_id' _category refln _type char _list yes _list_link_parent '_diffrn_radiation_wavelength_id' _list_reference '_refln_index_' _definition ; Code identifying the wavelength in the _diffrn_radiation_ list. See _diffrn_radiation_wavelength_id. ; ############ ## REFLNS ## ############ data_reflns_[] _name '_reflns_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _reflns_limit_h_min 0 _reflns_limit_h_max 6 _reflns_limit_k_min 0 _reflns_limit_k_max 17 _reflns_limit_l_min 0 _reflns_limit_l_max 22 _reflns_number_total 1592 _reflns_number_gt 1408 _reflns_threshold_expression 'F > 6.0u(F)' _reflns_d_resolution_high 0.8733 _reflns_d_resolution_low 11.9202 ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFLNS category record details about the reflections used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; data_reflns_d_resolution_ loop_ _name '_reflns_d_resolution_high' '_reflns_d_resolution_low' _category reflns _type numb _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The highest and lowest resolution in angstroms for the reflections. These are the smallest and largest d values. ; data_reflns_Friedel_coverage _name '_reflns_Friedel_coverage' _category reflns _type numb _enumeration_range 0.0:1.0 _definition ; The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item _reflns_number_total. This proportion is calculated as the ratio: [N(crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the _diffrn_refln_ list, N(crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, _reflns_Friedel_coverage 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, _reflns_Friedel_coverage will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in the space 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 value of zero for _reflns_Friedel_coverage. ; data_reflns_limit_ loop_ _name '_reflns_limit_h_max' '_reflns_limit_h_min' '_reflns_limit_k_max' '_reflns_limit_k_min' '_reflns_limit_l_max' '_reflns_limit_l_min' _category reflns _type numb _definition ; Miller indices limits for the reported reflections. These need not be the same as the _diffrn_reflns_limit_ values. ; data_reflns_number_gt _name '_reflns_number_gt' _category reflns _type numb _related_item '_reflns_number_observed' _related_function alternate _enumeration_range 0: _definition ; The number of reflections in the _refln_ list (not the _diffrn_refln_ list) that are significantly intense, satisfying the criterion specified by _reflns_threshold_expression. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Special characteristics of the reflections included in the _refln_ list should be given in the item _reflns_special_details. ; data_reflns_number_observed _name '_reflns_number_observed' _category reflns _type numb _related_item '_reflns_number_gt' _related_function replace _enumeration_range 0: _definition ; The number of 'observed' reflections in the _refln_ list (not the _diffrn_refln_ list). The observed reflections satisfy the threshold criterion specified by _reflns_threshold_expression (or the deprecated item _reflns_observed_criterion). They may include Friedel-equivalent reflections according to the nature of the structure and the procedures used. Special characteristics of the reflections included in the _refln_ list should be given in the item _reflns_special_details. ; data_reflns_number_total _name '_reflns_number_total' _category reflns _type numb _enumeration_range 0: _definition ; The total number of reflections in the _refln_ list (not the _diffrn_refln_ list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Special characteristics of the reflections included in the _refln_ list should be given in the item _reflns_special_details. ; data_reflns_observed_criterion _name '_reflns_observed_criterion' _category reflns _type char _related_item '_reflns_threshold_expression' _related_function replace _example 'I>2u(I)' _definition ; The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. ; data_reflns_special_details _name '_reflns_special_details' _category reflns _type char _definition ; Description of the properties of the reported reflection list that are not given in other data items. In particular, this should include information about the averaging (or not) of symmetry-equivalent reflections including Friedel pairs. ; data_reflns_threshold_expression _name '_reflns_threshold_expression' _category reflns _type char _related_item '_reflns_observed_criterion' _related_function alternate _example 'I>2u(I)' _definition ; The threshold, usually based on multiples of u(I), u(F^2^) or u(F), that serves to identify significantly intense reflections, the number of which is given by _reflns_number_gt. These reflections are used in the calculation of _refine_ls_R_factor_gt. ; ################## ## REFLNS_CLASS ## ################## data_reflns_class_[] _name '_reflns_class_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _reflns_class_number_gt _reflns_class_code 584 'Main' 226 'Sat1' 50 'Sat2' ; ; Example 1 - corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFLNS_CLASS category record details, for each reflection class, about the reflections used to determine the structural parameters. ; data_reflns_class_code _name '_reflns_class_code' _category reflns_class _type char _list yes loop_ _list_link_child '_refln_class_code' '_refine_ls_class_code' loop_ _example '1' 'm1' 's2' _definition ; The code identifying a certain reflection class. ; data_reflns_class_description _name '_reflns_class_description' _category reflns_class _type char _list yes _list_reference '_reflns_class_code' loop_ _example 'm=1 first order satellites' 'H0L0 common projection reflections' _definition ; Description of each reflection class. ; data_reflns_class_d_res_high _name '_reflns_class_d_res_high' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; For each reflection class, the highest resolution in angstroms for the reflections used in the refinement. This is the smallest d value. ; data_reflns_class_d_res_low _name '_reflns_class_d_res_low' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _units A _units_detail 'Angstroms' _definition ; For each reflection class, the lowest resolution in angstroms for the reflections used in the refinement. This is the largest d value. ; data_reflns_class_number_gt _name '_reflns_class_number_gt' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the number of significantly intense reflections (see _reflns_threshold_expression) in the _refln_ list (not the _diffrn_refln_ list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Special characteristics of the reflections included in the _refln_ list should be given in the item _reflns_special_details. ; data_reflns_class_number_total _name '_reflns_class_number_total' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the total number of reflections in the _refln_ list (not the _diffrn_refln_ list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Special characteristics of the reflections included in the _refln_ list should be given in the item _reflns_special_details. ; data_reflns_class_R_factor_ loop_ _name '_reflns_class_R_factor_all' '_reflns_class_R_factor_gt' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factors for all reflections, and for significantly intense reflections (see _reflns_threshold_expression), included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class_d_res_high and _reflns_class_d_res_low. This is the conventional R factor. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. See also _reflns_class_wR_factor_all definitions. ; data_reflns_class_R_Fsqd_factor _name '_reflns_class_R_Fsqd_factor' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and 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 | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; data_reflns_class_R_I_factor _name '_reflns_class_R_I_factor' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; data_reflns_class_wR_factor_all _name '_reflns_class_wR_factor_all' _category reflns_class _type numb _list yes _list_reference '_reflns_class_code' _enumeration_range 0.0: _definition ; 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(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed 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. See also _reflns_class_R_factor_ definitions. ; ################## ## REFLNS_SCALE ## ################## data_reflns_scale_[] _name '_reflns_scale_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _reflns_scale_group_code _reflns_scale_meas_F 1 .895447 2 .912743 ; ; Example 1 - based on standard test data set p6122 of the Xtal distribution [Hall, King & Stewart (1995). Xtal3.4 User's Manual. University of Western Australia]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln_scale_group_code. ; data_reflns_scale_group_code _name '_reflns_scale_group_code' _category reflns_scale _type char _list yes _list_mandatory yes _list_link_child '_refln_scale_group_code' _definition ; The code identifying a scale _reflns_scale_meas_. These are linked to the _refln_ list by the _refln_scale_group_code. These codes need not correspond to those in the _diffrn_scale_ list. ; data_reflns_scale_meas_ loop_ _name '_reflns_scale_meas_F' '_reflns_scale_meas_F_squared' '_reflns_scale_meas_intensity' _category reflns_scale _type numb _type_conditions esd _enumeration_range 0.0: _list yes _list_reference '_reflns_scale_group_code' _definition ; Scales associated with _reflns_scale_group_code. ; ################## ## REFLNS_SHELL ## ################## data_reflns_shell_[] _name '_reflns_shell_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _reflns_shell_d_res_high _reflns_shell_d_res_low _reflns_shell_meanI_over_uI_gt _reflns_shell_number_measured_gt _reflns_shell_number_unique_gt _reflns_shell_percent_possible_gt _reflns_shell_Rmerge_F_gt 31.38 3.82 69.8 9024 2540 96.8 1.98 3.82 3.03 26.1 7413 2364 95.1 3.85 3.03 2.65 10.5 5640 2123 86.2 6.37 2.65 2.41 6.4 4322 1882 76.8 8.01 2.41 2.23 4.3 3247 1714 70.4 9.86 2.23 2.10 3.1 1140 812 33.3 13.99 ; ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the REFLNS_SHELL category record details about the reflections used to determine the ATOM_SITE data items, as broken down by shells of resolution. ; data_reflns_shell_d_res_high _name '_reflns_shell_d_res_high' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The highest resolution in angstroms for the reflections in this shell. This is the smallest d value. ; data_reflns_shell_d_res_low _name '_reflns_shell_d_res_low' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; The lowest resolution in angstroms for the reflections in this shell. This is the largest d value. ; data_reflns_shell_meanI_over_sigI_all _name '_reflns_shell_meanI_over_sigI_all' _category reflns_shell _type numb _related_item '_reflns_shell_meanI_over_uI_all' _related_function replace _list yes _definition ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in the resolution shell. ; data_reflns_shell_meanI_over_sigI_gt _name '_reflns_shell_meanI_over_sigI_gt' _category reflns_shell _type numb _related_item '_reflns_shell_meanI_over_uI_gt' _related_function replace _list yes _definition ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns_threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in the resolution shell. ; data_reflns_shell_meanI_over_sigI_obs _name '_reflns_shell_meanI_over_sigI_obs' _category reflns_shell _type numb _related_item '_reflns_shell_meanI_over_sigI_gt' _related_function replace _list yes _definition ; The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns_observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in the resolution shell. ; data_reflns_shell_meanI_over_uI_all _name '_reflns_shell_meanI_over_uI_all' _category reflns_shell _type numb _related_item '_reflns_shell_meanI_over_sigI_all' _related_function alternate _list yes _definition ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in the resolution shell. ; data_reflns_shell_meanI_over_uI_gt _name '_reflns_shell_meanI_over_uI_gt' _category reflns_shell _type numb loop_ _related_item _related_function '_reflns_shell_meanI_over_sigI_gt' alternate '_reflns_shell_meanI_over_sigI_obs' alternate _list yes _definition ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns_threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in the resolution shell. ; data_reflns_shell_number_measured_all _name '_reflns_shell_number_measured_all' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The total number of reflections measured for this resolution shell. ; data_reflns_shell_number_measured_gt _name '_reflns_shell_number_measured_gt' _category reflns_shell _type numb _related_item '_reflns_shell_number_measured_obs' _related_function alternate _list yes _enumeration_range 0.0: _definition ; The number of significantly intense reflections (see _reflns_threshold_expression) measured for this resolution shell. ; data_reflns_shell_number_measured_obs _name '_reflns_shell_number_measured_obs' _category reflns_shell _type numb _related_item '_reflns_shell_number_measured_gt' _related_function replace _list yes _enumeration_range 0.0: _definition ; The number of reflections classified as 'observed' (see _reflns_observed_criterion) measured for this resolution shell. ; data_reflns_shell_number_possible _name '_reflns_shell_number_possible' _category reflns_shell _type numb _list yes _enumeration_range 0: _definition ; The number of unique reflections it is possible to measure in this reflection shell. ; data_reflns_shell_number_unique_all _name '_reflns_shell_number_unique_all' _category reflns_shell _type numb _list yes _enumeration_range 0: _definition ; The total number of measured reflections resulting from merging measured symmetry-equivalent reflections for this resolution shell. ; data_reflns_shell_number_unique_gt _name '_reflns_shell_number_unique_gt' _category reflns_shell _type numb _related_item '_reflns_shell_number_unique_obs' _related_function alternate _list yes _enumeration_range 0: _definition ; The total number of significantly intense reflections (see _reflns_threshold_expression) resulting from merging measured symmetry-equivalent reflections for this resolution shell. ; data_reflns_shell_number_unique_obs _name '_reflns_shell_number_unique_obs' _category reflns_shell _type numb _related_item '_reflns_shell_number_unique_gt' _related_function replace _list yes _enumeration_range 0: _definition ; The total number of reflections classified as 'observed' (see _reflns_observed_criterion) resulting from merging measured symmetry-equivalent reflections for this resolution shell. ; data_reflns_shell_percent_possible_all _name '_reflns_shell_percent_possible_all' _category reflns_shell _type numb _list yes _enumeration_range 0.0:100.0 _definition ; The percentage of geometrically possible reflections represented by all reflections measured for this resolution shell. ; data_reflns_shell_percent_possible_gt _name '_reflns_shell_percent_possible_gt' _category reflns_shell _type numb _related_item '_reflns_shell_percent_possible_obs' _related_function alternate _list yes _enumeration_range 0.0:100.0 _definition ; The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns_threshold_expression) measured for this resolution shell. ; data_reflns_shell_percent_possible_obs _name '_reflns_shell_percent_possible_obs' _category reflns_shell _type numb _related_item '_reflns_shell_percent_possible_gt' _related_function replace _list yes _enumeration_range 0.0:100.0 _definition ; The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns_observed_criterion) measured for this resolution shell. ; data_reflns_shell_Rmerge_F_all _name '_reflns_shell_Rmerge_F_all' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The value of 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. ; data_reflns_shell_Rmerge_F_gt _name '_reflns_shell_Rmerge_F_gt' _category reflns_shell _type numb _related_item '_reflns_shell_Rmerge_F_obs' _related_function alternate _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(F) for significantly intense reflections (see _reflns_threshold_expression) 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. ; data_reflns_shell_Rmerge_F_obs _name '_reflns_shell_Rmerge_F_obs' _category reflns_shell _type numb _related_item '_reflns_shell_Rmerge_F_gt' _related_function replace _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(F) for reflections classified as 'observed' (see _reflns_observed_criterion) 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. ; data_reflns_shell_Rmerge_I_all _name '_reflns_shell_Rmerge_I_all' _category reflns_shell _type numb _list yes _enumeration_range 0.0: _definition ; The value of 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. ; data_reflns_shell_Rmerge_I_gt _name '_reflns_shell_Rmerge_I_gt' _category reflns_shell _type numb _related_item '_reflns_shell_Rmerge_I_obs' _related_function alternate _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(I) for significantly intense reflections (see _reflns_threshold_expression) 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. ; data_reflns_shell_Rmerge_I_obs _name '_reflns_shell_Rmerge_I_obs' _category reflns_shell _type numb _related_item '_reflns_shell_Rmerge_I_gt' _related_function replace _list yes _enumeration_range 0.0: _definition ; The value of Rmerge(I) for reflections classified as 'observed' (see _reflns_observed_criterion) 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. ; ################# ## SPACE_GROUP ## ################# data_space_group_[] _name '_space_group_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _space_group_id 1 _space_group_name_H-M_alt 'C 2/c' _space_group_IT_number 15 _space_group_name_Hall '-C 2yc' _space_group_crystal_system monoclinic ; ; Example 1 - the monoclinic space group No. 15 with unique axis b. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in the core dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary. ; data_space_group_crystal_system _name '_space_group_crystal_system' _category space_group _type char _list both _list_reference '_space_group_id' _related_item '_symmetry_cell_setting' _related_function alternate loop_ _enumeration triclinic monoclinic orthorhombic tetragonal trigonal hexagonal cubic _definition ; The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system. ; data_space_group_id _name '_space_group_id' _category space_group _type char _list yes _list_mandatory yes _list_link_child '_space_group_symop_sg_id' _definition ; This is an identifier needed if _space_group_ items are looped. ; data_space_group_IT_number _name '_space_group_IT_number' _category space_group _type numb _list both _list_reference '_space_group_id' _related_item '_symmetry_Int_Tables_number' _related_function alternate _enumeration_range 1:230 _definition ; The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed. ; data_space_group_name_Hall _name '_space_group_name_Hall' _category space_group _type char _list both _list_reference '_space_group_id' _related_item '_symmetry_space_group_name_Hall' _related_function alternate loop_ _example _example_detail 'P 2c -2ac' 'equivalent to Pca21' '-I 4bd 2ab 3' 'equivalent to Ia-3d' _definition ; Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in older files. It should not be used in new CIFs. _space_group_name_Hall uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2] ; data_space_group_name_H-M_alt _name '_space_group_name_H-M_alt' _category space_group _type char _list both _list_reference '_space_group_id' _related_item '_symmetry_space_group_name_H-M' _related_function alternate loop_ _example _example_detail ; loop_ _space_group_id _space_group_name_H-M_alt 1 'C m c m' 2 'C 2/c 2/m 21/m' 3 'A m a m' ; 'three examples for space group No. 63' _definition ; _space_group_name_H-M_alt allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in older files. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using _space_group_IT_number. The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use _space_group_name_Hall or list the symmetry operations. ; ####################### ## SPACE_GROUP_SYMOP ## ####################### data_space_group_symop_[] _name '_space_group_symop_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 x,y,z 2 -x,-y,-z 3 -x,1/2+y,1/2-z 4 x,1/2-y,1/2+z ; ; Example 1 - the symmetry operations for the space group P21/c. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Contains information about the symmetry operations of the space group. ; data_space_group_symop_id _name '_space_group_symop_id' _type char _category space_group_symop _list yes _list_mandatory yes _related_item '_symmetry_equiv_pos_site_id' _related_function alternate _definition ; An arbitrary identifier that uniquely labels each symmetry operation in the list. ; data_space_group_symop_operation_xyz _name '_space_group_symop_operation_xyz' _category space_group_symop _type char _list both _list_reference '_space_group_symop_id' _enumeration_default 'x,y,z' _related_item '_symmetry_equiv_pos_as_xyz' _related_function alternate loop_ _example _example_detail 'x,1/2-y,1/2+z' ; glide reflection through the plane (x,1/4,z), with glide vector (1/2)c ; _definition ; A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicitly all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used. ; data_space_group_symop_sg_id _name '_space_group_symop_sg_id' _category space_group_symop _type numb _list both _list_mandatory no _list_reference '_space_group_symop_id' _list_link_parent '_space_group_id' _definition ; This must match a particular value of _space_group_id, allowing the symmetry operation to be identified with a particular space group. ; ############## ## SYMMETRY ## ############## data_symmetry_[] _name '_symmetry_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _symmetry_cell_setting orthorhombic _symmetry_space_group_name_H-M 'P 21 21 21' _symmetry_space_group_name_Hall 'P 2ac 2ab' ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the SYMMETRY category record details about the space-group symmetry. ; data_symmetry_cell_setting _name '_symmetry_cell_setting' _category symmetry _type char loop_ _enumeration triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic _related_item '_space_group_crystal_system' _related_function replace _definition ; The cell settings for this space-group symmetry. ; data_symmetry_Int_Tables_number _name '_symmetry_Int_Tables_number' _category symmetry _type numb _enumeration_range 1:230 _related_item '_space_group_IT_number' _related_function replace _definition ; Space-group number from International Tables for Crystallography Vol. A (2002). ; data_symmetry_space_group_name_Hall _name '_symmetry_space_group_name_Hall' _category symmetry _type char _related_item '_space_group_name_Hall' _related_function replace loop_ _example '-P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' _definition ; Space-group symbol as described by Hall. This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. ; data_symmetry_space_group_name_H-M _name '_symmetry_space_group_name_H-M' _category symmetry _type char _related_item '_space_group_name_H-M_alt' _related_function replace loop_ _example 'P 1 21/m 1' 'P 2/n 2/n 2/n (origin at -1)' 'R -3 2/m' _definition ; Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv_pos_as_xyz or *_Hall data items as well. Leave spaces between symbols referring to different axes. ; #################### ## SYMMETRY_EQUIV ## #################### data_symmetry_equiv_[] _name '_symmetry_equiv_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _symmetry_equiv_pos_as_xyz +x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z ; ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 1/2-x,-y,1/2+z 3 1/2+x,1/2-y,-z 4 -x,1/2+y,1/2-z ; ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. Formally, the value of _symmetry_equiv_pos_site_id can be any unique character string; it is recommended that it be assigned the sequence number of the list of equivalent positions for compatibility with older files in which it did not appear. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group. ; data_symmetry_equiv_pos_as_xyz _name '_symmetry_equiv_pos_as_xyz' _category symmetry_equiv _type char _list both _example -y+x,-y,1/3+z _related_item '_space_group_symop_operation_xyz' _related_function replace _definition ; Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A. (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. ; data_symmetry_equiv_pos_site_id _name '_symmetry_equiv_pos_site_id' _category symmetry_equiv _type numb _list yes _list_reference '_symmetry_equiv_pos_as_xyz' _related_item '_space_group_symop_id' _related_function replace _definition ; A code identifying each entry in the _symmetry_equiv_pos_as_xyz list. It is normally the sequence number of the entry in that list, and should be identified with the code 'n' in _geom_*_symmetry_ codes of the form 'n_klm'. ; ################### ## VALENCE_PARAM ## ################### data_valence_param_[] _name '_valence_param_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _valence_param_id _valence_param_atom_1 _valence_param_atom_1_valence _valence_param_atom_2 _valence_param_atom_2_valence _valence_param_Ro _valence_param_B _valence_param_ref_id _valence_param_details 1 Cu 2 O -2 1.679 0.37 a . 2 Cu 2 O -2 1.649 0.37 j . 3 Cu 2 N -3 1.64 0.37 m '2-coordinate N' 4 Cu 2 N -3 1.76 0.37 m '3-coordinate N' loop_ _valence_ref_id _valence_ref_reference a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247' j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205' m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375' ; ; Example 1 - a bond-valence parameter list with accompanying references. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken. ; data_valence_param_atom_1 _name '_valence_param_atom_1' _category valence_param _type char _list yes _list_reference '_valence_param_id' _definition ; The element symbol of the first atom forming the bond whose bond-valence parameters are given in this category. ; data_valence_param_atom_1_valence _name '_valence_param_atom_1_valence' _category valence_param _type numb _list yes _list_reference '_valence_param_id' _definition ; The valence (formal charge) of the first atom whose bond-valence parameters are given in this category. ; data_valence_param_atom_2 _name '_valence_param_atom_2' _category valence_param _type char _list yes _list_reference '_valence_param_id' _definition ; The element symbol of the second atom forming the bond whose bond-valence parameters are given in this category. ; data_valence_param_atom_2_valence _name '_valence_param_atom_2_valence' _category valence_param _type numb _list yes _list_reference '_valence_param_id' _definition ; The valence (formal charge) of the second atom whose bond-valence parameters are given in this category. ; data_valence_param_B _name '_valence_param_B' _category valence_param _type numb _list yes _list_reference '_valence_param_id' _units A _units_detail Angstrom _definition ; The bond-valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; data_valence_param_details _name '_valence_param_details' _category valence_param _type char _list yes _list_reference '_valence_param_id' _definition ; Details of or comments on the bond-valence parameters. ; data_valence_param_id _name '_valence_param_id' _category valence_param _type char _list yes _definition ; An identifier for the valence parameters of a bond between the given atoms. ; data_valence_param_ref_id _name '_valence_param_ref_id' _category valence_param _type char _list yes _list_reference '_valence_param_id' _list_link_parent '_valence_ref_id' _definition ; An identifier which links to the reference to the source from which the bond-valence parameters are taken. A child of _valence_ref_id, which it must match. ; data_valence_param_Ro _name '_valence_param_Ro' _category valence_param _type numb _list yes _list_reference '_valence_param_id' _units A _units_detail Angstrom _definition ; The bond-valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; ################# ## VALENCE_REF ## ################# data_valence_ref_[] _name '_valence_ref_[]' _category category_overview _type null _definition ; Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken. ; data_valence_ref_id _name '_valence_ref_id' _category valence_ref _type char _list yes _list_reference '_valence_ref_id' _list_link_child '_valence_param_ref_id' _definition ; An identifier for items in this category. Parent of _valence_param_ref_id, which must have the same value. ; data_valence_ref_reference _name '_valence_ref_reference' _type char _category valence_ref _list yes _list_reference '_valence_ref_id' _definition ; Literature reference from which the valence parameters identified by _valence_param_id were taken. ; #-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof