############################################################################## # # # 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/ddldic.c95 # # # # Copyright 2004 International Union of Crystallography # ############################################################################## data_on_this_dictionary _dictionary_name cif_core.dic _dictionary_version 2.3.1 _dictionary_update 2005-06-27 _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 ; ############### ## 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