Dictionary Index mmcif_std.dic
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General 
- Dictionary title
- mmCIF Dictionary
- Dictionary description
- Original IUCr mmCIF Dictionary
- Original developers
- IUCr working group: Paula M. Fitzgerald, Helen Berman,Phil Bourne, Brian McMahon, Keith Watenpaugh, and John Westbrook
- Dictionary maintainers
- wwPDB for the IUCr
- Dictionary name
- mmcif_std.dic
- Dictionary version
- 2.0.11
- Last update
- 2007-05-30
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 2.0.11 | 2007-05-30 | Changes (jdw): + Make all key items mandatory. |
mmcif_std.dic |
| 2.0.10 | 2006-02-24 | Changes (jdw): + Added category groups to audit_link, diffrn_reflns_class, refine_ls_class, reflns_class, space_group, space_group_symop, valence_param, valence_ref. |
mmcif_std.dic |
| 2.0.09 | 2005-06-27 | Internal dates used for housekeeping prior to release 2005-04-13 Changes (NJA) 2005-04-13 + Minor corrections to spelling and punctuation. + pdb_group definition: Brookhaven Protein Data Bank changed to Protein Data Bank. 2005-04-14 Changes (NJA) 2005-04-14 + Minor corrections to spelling and punctuation. + _atom_sites.solution_* descriptions edited so each appropriate to the particular data name. +_chem_comp.formula description edited to match that in core dictionary +_chem_comp.three_letter_code: several typing errors in amino-acid and base names corrected. +_chem_comp_atom.model_Cartn_z: 'The x component ...' changed to 'The z component...' +_chemical.melting_point_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_decomposition_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_sublimation_* descriptions edited so each appropriate to the particular data name. 2005-04-15 Changes (NJA) 2005-04-15 + Minor corrections to spelling and punctuation. +_citation.journal_id_CSD description, Brookhaven Protein Data Bank changed to Protein Data Bank. +_database.code_* entries edited so each is relevant to the particular data name +_database_PDB_matrix.scale[3][3]: description changed from 'The [1][1] element of the PDB SCALE matrix.' to 'The [3][3] element of the PDB SCALE matrix.' +_diffrn.ambient_pressure_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn.ambient_temp_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn_attenuator.scale description changed to match that in the core dictionary. +_diffrn_radiation_wavelength.id: _diffrn_radiation_wavelength in description changed to _diffrn_radiation_wavelength.wavelength +_diffrn_reflns_class.av_sgI/I description [sum|u(net I)|/sum|net I|] changed to [sum|sigma(net I)|/sum|net I|] +_diffrn_reflns_class.d_res_high and _low descriptions changed to match those in the core dictionary +diffrn_source Example 1 _diffrn_source.power '50 kw, 180 mA' changed to _diffrn_source.power 50 and _diffrn_source.current 180 +_exptl_crystal.density_Matthews year of reference corrected from 1960 to 1968 +_exptl_crystal.density_meas_gt and _lt descriptions edited so each is relevant to the particular data name. +_exptl_crystal.density_meas_temp_gt and _lt descriptions edited so each is relevant to the particular data name. +geom_contact and geom_bond Example 1 year for reference corrected from 1991 to 1992 +_phasing_MAD_ratio.d_res_high and low ; _phasing_MAD_set.d_res_high and _low; _phasing_MIR.d_res_high and low; _phasing_MIR_der.d_res_high and low; _phasing_MIR_der_shell.d_res_high and low; _phasing_MIR_shell.d_res_high and low and _refine.ls_d_res_high and low rephrased to correspond to similar terms in the core dictionary. +Spelling of Lattman corrected in references to Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. +Temperature factor replaced by displacement parameter throughout. +refine Example 2 _refine.ls_weighting_scheme 'calc w=1/(\s^2^(F)+0.0004F^2^)' split into _refine.ls_weighting_scheme and _refine.ls_weighting_details +_refine.ls_extinction_coef and _refine.ls_extinction_method reference to Becker and Coppens corrected to 129-147, 148-153 (is two articles). +_refine.ls_restrained_S_all and _obs: Y~calc~ = the observed coefficients changed toY~calc~ = the calculated coefficients 2005-04-18 Changes (NJA) 2005-04-18 + Minor corrections to spelling and punctuation. + temperature factor changed to displacement parameter throughout + _refine_ls_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression) ' removed from description. + _refine_ls_class.R_factor_gt 'for all reflections' removed from description. + _refine_ls_class.d_res_high and _low, _refine_analyze.RG_d_res_high and _low, _refine_ls_shell.d_res_high and _low, _reflns.d_resolution_high and low, _reflns_class.d_res_high and _low, _reflns_shell.d_res_high and _low definitions edited to match related definitions in the core dictionary + _refln.intensity_calc _meas, _sigma edited to match corresponding entries in the core dictionary + _reflns.Friedel_coverage in description _reflns_number_total changed to _reflns.number_all. + _reflns_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression)' removed from description. + _reflns_class.R_factor_gt 'all reflections, and for' removed from description + _reflns_class.number_total in description: _reflns_special_details changed to _reflns.details 2005-04-19 Changes (NJA) 2005-04-19 + Minor corrections to spelling and punctuation. + _valence_param.ref_id description: _valence_ref_id changed to _valence_ref.id + References to International Tables updated. 2005-04-22 Changes (NJA) 2005-04-22 + _cell.reciprocal_angle_alpha, beta and gamma: descriptions edited so each appropriate to the particular data name. + _cell.reciprocal_length_a, b and c: descriptions edited so each appropriate to the particular data name. + _struct_mon_nucl.chi1 and _chi2; descriptions edited from `... sugar-base torsion angle chi...' to '... sugar-base torsion angle chi1' and '... sugar-base torsion angle chi2' 2005-05-03 Changes (NJA) 2005-05-03 + several data items *_esd edited so that the description reads 'the standard uncertainly of *', not 'the standard uncertainty of *_esd' + several DDL1 datanames in descriptions changed to DDL2 datanames 2005-05-10 Changes (NJA) 2005-05-10 + _citation.journal_id_CSD example changed from 070 to 0070 + Mursudov and Dodson (1997) references corrected + References to Cruickshank DPI updated + References to Luzzati (1952) corrected 2005-06-23 Changes (NJA) 2005-06-23 _publ_author.email added. Corrections for IT G Chapter 4.5 included. 2005-06-25 (BM) ITEM_UNITS_LIST: cosmetic changes to definitions of some units ITEM_UNITS_CONVERSION: multipliers in electrons per <unit> cubed terms fixed 2005-06-27 (BM) Some minor editorial changes to ensure consistency with latest pdbx dictionary version. Only significant change: + in _citation.id the listing for _software.citation_id has _item.mandatory_code changed to "no" to match the value in save__software.citation_id and to match pdbx |
mmcif_std.dic |
| 2.0.08 | 2005-04-06 | Changes (JDW) 2005-04-06 + Added mandatory code _cell.reciprocal_angle_beta |
mmcif_std.dic |
| 2.0.07 | 2005-03-03 | Changes (JDW) 2005-03-08 + Changed related references to _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed related references to _refln.observed_status to _refln.status + Restore original case to FOM - although case is not an issue for mmCIF it is an issue for XML translations. |
mmcif_std.dic |
| 2.0.06 | 2005-03-03 | Changes (JDW): + The following data items added to maintain data item correspondence with the CIF CORE dictionary V 2.3. All aliases in section 1 updated to version 2.3. _atom_site.adp_type _atom_site.refinement_flags _atom_site.refinement_flags_adp _atom_site.refinement_flags_occupancy _atom_site.refinement_flags_posn _atom_sites.special_details _atom_type.scat_dispersion_source _audit_link.block_code _audit_link.block_description _cell.reciprocal_angle_alpha _cell.reciprocal_angle_beta _cell.reciprocal_angle_gamma _cell.reciprocal_angle_alpha_esd _cell.reciprocal_angle_beta_esd _cell.reciprocal_angle_gamma_esd _cell.reciprocal_length_a _cell.reciprocal_length_b _cell.reciprocal_length_c _cell.reciprocal_length_a_esd _cell.reciprocal_length_b_esd _cell.reciprocal_length_c_esd _cell.special_details _chemical.absolute_configuration _chemical.melting_point_gt _chemical.melting_point_lt _chemical.optical_rotation _chemical.properties_biological _chemical.properties_physical _chemical.temperature_decomposition _chemical.temperature_decomposition_esd _chemical.temperature_decomposition_gt _chemical.temperature_decomposition_lt _chemical.temperature_sublimation _chemical.temperature_sublimation_esd _chemical.temperature_sublimation_gt _chemical.temperature_sublimation_lt _citation.database_id_CSD _database.CSD_history _database.code_CAS _database.code_CSD _database.code_ICSD _database.code_MDF _database.code_NBS _database.code_PDB _database.code_PDF _database.code_depnum_ccdc_fiz _database.code_depnum_ccdc_journal _database.code_depnum_ccdc_archive _diffrn.ambient_pressure _diffrn.ambient_pressure_esd _diffrn.ambient_pressure_gt _diffrn.ambient_pressure_lt _diffrn.ambient_temperature _diffrn.ambient_temperature_esd _diffrn.ambient_temperature_gt _diffrn.ambient_temperature_lt _diffrn_attenuator.material _diffrn_detector.area_resol_mean _diffrn_detector.dtime _diffrn_refln.class_code _diffrn_refln.intensity_u _diffrn_reflns.av_unetI/netI _diffrn_reflns_class.av_R_eq _diffrn_reflns_class.av_sgI/I _diffrn_reflns_class.av_uI/I _diffrn_reflns_class.code _diffrn_reflns_class.description _diffrn_reflns_class.d_res_high _diffrn_reflns_class.d_res_low _diffrn_reflns_class.number _diffrn_source.take-off_angle _diffrn_standards.scale_u _exptl_crystal.colour_lustre _exptl_crystal.colour_modifier _exptl_crystal.colour_primary _exptl_crystal.density_meas _exptl_crystal.density_meas_esd _exptl_crystal.density_meas_gt _exptl_crystal.density_meas_lt _exptl_crystal.density_meas_temp _exptl_crystal.density_meas_temp_esd _exptl_crystal.density_meas_temp_gt _exptl_crystal.density_meas_temp_lt _geom_bond.valence _publ_author.id_iucr _refine.ls_R_factor_gt _refine.ls_goodness_of_fit_gt _refine.ls_goodness_of_fit_ref _refine.ls_shift/esd_max _refine.ls_shift/esd_mean _refine.ls_shift/su_max _refine.ls_shift/su_max_lt _refine.ls_shift/su_mean _refine.ls_shift/su_mean_lt _refine_ls_class.code _refine_ls_class.d_res_high _refine_ls_class.d_res_low _refine_ls_class.R_factor_gt _refine_ls_class.R_factor_all _refine_ls_class.R_Fsqd_factor _refine_ls_class.R_I_factor _refine_ls_class.wR_factor_all _refln.class_code _refln.d_spacing _refln.include_status _refln.mean_path_length_tbar _refln.observed_status _refln.sint/lambda _reflns.Friedel_coverage _reflns.number_gt _reflns_class.code _reflns_class.description _reflns_class.d_res_high _reflns_class.d_res_low _reflns_class.number_gt _reflns_class.number_total _reflns_class.R_factor_all _reflns_class.R_factor_gt _reflns_class.R_Fsqd_factor _reflns_class.R_I_factor _reflns_class.wR_factor_all _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _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 _reflns_shell.Rmerge_I_gt _space_group.crystal_system _space_group.id _space_group.IT_number _space_group.name_Hall _space_group.name_H-M_alt _space_group_symop.id _space_group_symop.operation_xyz _space_group_symop.sg_id _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence _valence_param.B _valence_param.details _valence_param.id _valence_param.ref_id _valence_param.Ro _valence_ref.id _valence_ref.reference Changes (BM): 2005-03-03 Editorial changes to accompany International Tables Volume G publication (B. McMahon): + Fixed broken example loop for _phasing_MAD_ratio.* + Expanded the definitions for _phasing_MIR_der_refln.HL_A_iso (and B, C and D terms) and provided literature reference + Abbreviation .FOM (for figure-of-merit) consistently rendered lowercase + Expanded the definitions for _refine.solvent_model_param_bsol (and *_ksol) and provided literature reference + Rearranged the order of entries in the REFINE_ANALYZE category to preserve strict alphabetisation + Removed _refine_ls_restr_type.U_sigma_weights from example in REFINE_LS_RESTR_TYPE category + Commented out the incorrect example for the CHEM_COMP_LINK category + For the example in the ENTITY_NAME_SYS category supplied the EC number and the systematic name "water"; also trimmed the irrelevant last line of the definition. + Changed the vague 'x,x-pyranoside' example of _entity_name_sys.name to 'hydroquinone-beta-D-pyranoside' and matched this with 'arbutin' for _entity_name_com.name + Removed the CAVEAT and REMARK terms (and PDB code trailers) from the contents pf the _database_PDB_caveat.* and *_remark.* examples in accordance with current PDB practice + Updated reference to Tickle et al. in _refine_analyze.RG_free_work_ratio + Fixed few minor typos + Cosmetic reflowing of textual examples to aid typesetting + Added Engh & Huber and Priestle references to example details + Changed upper enumeration limit of _atom_site_attached_hydrogens to 8 in line with current Core dictionary + Added URL of PDB format description to _database_PDB_rev.mod_type + Extended enumeration list of _publ.requested_category for Acta E papers + Updated definition of _refine.ls_abs_structure_Flack and *_Rogers to reflect the more correct wording of the current Core dictionary. + Added _item_range.maximum and *minimum to _refine.ls_abs_structure_Rogers in line with new wording of definition. Changes (NJA): 2005-03-03 + Commented out duplicate save frames for following items with _item_aliases.version 2.0.1: _atom_site.refinement flags, _database.code_CAS, _database.code_CSD _database.code_ICSD, _database.code_MDF, _database.code_NBS _database.code_PDF, _diffrn.ambient_pressure, _diffrn.ambient_pressure.esd _diffrn_detector.dtime, _exptl_crystal.density.meas _exptl_crystal.density_meas_temp, _refln.mean_path_length_tbar Changes (BM): 2005-03-03 + Fixed erroneous _item.name in save__diffrn.ambient_pressure_esd + Removed erroneous aliases to *_esd quantities in coreCIF 2.3: _cell_reciprocal_angle_alpha_esd, _cell_reciprocal_angle_beta_esd _cell_reciprocal_angle_gamma_esd, _cell_reciprocal_length_a_esd _cell_reciprocal_length_b_esd, _cell_reciprocal_length_c_esd _chemical_temperature_decomposition_esd _chemical_temperature_sublimation_esd _diffrn.ambient_pressure_esd, _diffrn_ambient_temperature_esd _exptl_crystal_density_meas_esd, _exptl_crystal_density_meas_temp_esd + Removed redundant aliases: _cell.special_details ( = _cell.details) _diffrn.ambient_temperature ( = _diffrn.ambient_temp) _refine.ls_shift/esd_max ( = _refine.ls_shift_over_esd_max) _refine.ls_shift/esd_mean ( = _refine.ls_shift_over_esd_mean) _refln.observed_status ( = _refln.status) _refln.sint/lambda ( = _refln.sint_over_lambda) + Changed _refine.ls_shift/su_max to _refine.ls_shift_over_su_max and likewise for *_lt, *_mean and *_max_lt Changes (NJA): 2005-03-07 + Changed _reflns.class_d_res_low to _reflns_class.d_res_low in description of _reflns_class.wR_factor_all + Added [][] to _atom_sites.Cartn_transf_matrix, _diffrn_reflns.transf_matrix and _diffrn_orient_matrix.UB for consistency throughout. + Changed _chem_comp_link.type_1 and _2 to _chem_comp_link.type_comp_1 and 2 in _chem_link_angle.atom_id_1 and _2 + Changed all occurences of _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed _diffrn_reflns.class_code to _diffrn_reflns_class.code in _diffrn_refln.class_code + Changed _geom_bond.distance to _geom_bond.dist in description of _geom_bond.valence. + Changed _refln.observed_status to _refln.status in refln.include_status + Changed _reflns.special_details to _reflns.details in _reflns.number_gt and _reflns_class.number_gt + Created new entry for _reflns.threshold_expression, as no entry existed and many item descriptions referred to _reflns_threshold_expression (these were then changed to _reflns.threshold_expression). + Changed _struct_mon_prot.alt_id, _struct_mon_prot.asym_id, _struct_mon_prot.comp_id and _struct_mon_prot.seq_id to _struct_mon_prot.label_alt_id, _struct_mon_prot.label_asym_id, _struct_mon_prot.label_comp_id and _struct_mon_prot.label_seq_id in Example 1 of _struct_mon_prot. + Changed _struct_site_view.view_id to _struct_site_view.id in Example 1 of _struct_site_view. |
mmcif_std.dic |
| 2.0.05 | 2004-08-04 | Changes (JDW): + Changed data type of _refine.ls_redundancy_reflns_all, _refine.ls_redundancy_reflns_obs, _refine_ls_shell.redundancy_reflns_all, _refine_ls_shell.redundancy_reflns_obs from int to float. |
mmcif_std.dic |
| 2.0.04 | 2004-04-21 | Changes (JDW): + Changed working name and packaging of dictionary. + _reflns_shell_number_possible range data type error fixed + Fix syntax errors in category examples. + Remove nonsense zero value default values + Remove all default values from *_esd items + Make _atom_site.label_* mandatory + Make _atom_site.auth_asym_id mandatory + Make _software.citation_id optional |
mmcif_std.dic |
| 2.0.03 | 2000-11-09 | Changes (JDW): + Relax regular expression for atom names to accept blanks in atom names in order to support nomenclature used in many existing macromolecular data files. Data type "atcode" has been assigned to _chem_comp_atom.atom_id, _atom_site.auth_atom_id and all related items. |
mmcif_std.dic |
| 2.0.02 | 2000-10-24 | Changes (JDW): + Updated enumerations for _database_PDB_rev.mod_type. + Updated enumerations for _struct_conn_type.id + Corrected data type of _refine_ls_shell.percent_reflns_obs from int to float + Updated preliminary description of _database_PDB_rev.status. + Changed regular expression for float to accept trailing decimal (ie. dd.) + Add () to regular expressions for code and ucode. + Added L-saccharide, D-saccharide, saccharide to enumerants for _chem_comp.type to handle monosaccarided components where linking cannot be inferred. |
mmcif_std.dic |
| 2.0.01 | 2000-10-17 | Changes (JDW): + Integrated new definitions and extensions to existing categories. Additional data definitions submitted by Kim Henrick. Content of phasing definitions reviewed by Paula Fitgerald. Content of refinement definitions reviewed by Dale Tronrud. Editorial review by Helen Berman, John Westbrook, and Paula Fitzgerald. New Items included in this version: _phasing_MIR.d_res_high, _phasing_MIR.d_res_low, _phasing_MIR.FOM, _phasing_MIR.FOM_acentric, _phasing_MIR.FOM_centric, _phasing_MIR.reflns, _phasing_MIR.reflns_acentric, _phasing_MIR.reflns_centric, _phasing_MIR.reflns_criterion, _phasing_MIR_der.power_acentric, _phasing_MIR_der.power_centric, _phasing_MIR_der.R_cullis_acentric, _phasing_MIR_der.R_cullis_anomalous, _phasing_MIR_der.R_cullis_centric, _phasing_MIR_der.reflns_acentric, _phasing_MIR_der.reflns_anomalous, _phasing_MIR_der.reflns_centric, _phasing_MIR_der_site.occupancy_anom, _phasing_MIR_der_site.occupancy_anom_su, _phasing_MIR_der_site.occupancy_iso, _phasing_MIR_der_site.occupancy_iso_su, _phasing_MIR_shell.FOM_acentric, _phasing_MIR_shell.FOM_centric, _phasing_MIR_shell.reflns_acentric, _phasing_MIR_shell.reflns_anomalous, _phasing_MIR_shell.reflns_centric, _refine.correlation_coeff_Fo_to_Fc, _refine.correlation_coeff_Fo_to_Fc_free, _refine.overall_SU_B, _refine.overall_SU_ML, _refine.overall_SU_R_Cruickshank_DPI, _refine.overall_SU_R_free, _refine.overall_FOM_free_R_set, _refine.overall_FOM_work_R_set, _refine_analyze.RG_d_res_high, _refine_analyze.RG_d_res_low, _refine_analyze.RG_free, _refine_analyze.RG_work, and _refine_analyze.RG_free_work_ratio. + New categories included in this version: REFINE_FUNCT_MINIMIZED,REFINE_LS_RESTR_TYPE, REFLN_SYS_ABS. + Modification of examples for _refine_ls_restr.type + Contributed editorial and typographical corrections. + Corrected incomplete keys in categories PHASING_MAD_SET and DATABASE_PDB_REV_RECORD. + _exptl.method enumerations moved to examples. + Added database codes for RCSB and EBI. + Fixed item examples in _publ_body.label. |
mmcif_std.dic |
| 1.0.00 | 1997-10-14 | Changes (PMDF): + Editorial changes in light of proof-reading by B. McMahon and I.D. Brown + No data names or enumeration values have changed, with the exception of the addition of the enumeration value 'other' to exptl.method + The bulk of the changes, which are too numerous to list there, were fixing spelling and grammar errors, and providing missing definitions + In a few cases, data definitions were reworded for clarity + Replaced erroneous occurances of Y~calc~ with Y~obs~ in the defintions of weighted R factors (Ian Tickle) |
mmcif_std.dic |
| 0.9.01 | 1997-01-31 | Changes (PMDF): + Removed occurrance of two or more blank lines + Enforced rule of no apostrophes around values for _item_sub_category.id + Enforced rule of no apostrophes around values for_item_default.value + Enforced rule of no apostrophes around values for_item.mandatory_code and fixed one alignment problem + Enforced rule of no apostrophes around values for _item_related.function_code and fixed a few alignment problems + Added _item.mandatory_code for _diffrn_refln.wavelength_id + Changed cifdic.c94 to cif_core.dic in _item_aliases.dictionary everywhere + Changed 2.0 to 2.0.1 in _item_aliases.version everywhere + Changed to consistent usage of kelvins instead of kelvin, got rid of capitalized versions + Removed capitalized usages of angstroms + Enforced rule of no apostrophes around values for _item_units.code + Fixed alignment problems with a few _category_key.name values |
mmcif_std.dic |
| 0.9.0 | 1997-01-30 | Changes (PMDF): + Corrected _reflns_observed_criterion to _reflns.observed_criterion in a number of places + Aligned enumeration lists in this dictionary with those in version 2.0 of the core dictionary. This involved changes in: _citation.coordinate_linkage _diffrn_radiation.xray_symbol _diffrn_refln.scan_mode _diffrn_refln.scan_mode_backgd _exptl.absorpt_correction_type _publ_manuscript_incl.extra_defn _refine.ls_hydrogen_treatment _refine.ls_structure_factor_coef + A number of corrections to errors pointed out by H. Bernstein Added category.id to _database_PDB_tvect.id Fixed spelling of _publ.section_exptl_soltuion Corrected _refine.ls_R_factor_work to _refine.ls_R_factor_R_work in description Corrected spelling of _refine_analyze.Luzaatti_d_res_low_obs in example Corrected spelling of _refine_analyze.Luzzatti_coordinate_error_obs in example Corrected _geom_hbond.atom_site_label_id_D to _geom_hbond.atom_site_id_D in example Corrected _geom_hbond.atom_site_label_id_H to _geom_hbond.atom_site_id_H in example Corrected _geom_hbond.atom_site_label_id_A to _geom_hbond.atom_site_id_A in example Corrected _entry_link.description to _entry_link.details Corrected _DIFFRN_SCALE_GROUP to DIFFRN_SCALE_GROUP in description Corrected _refine_ls_restr_ncs.model_details to _refine_ls_restr_ncs.ncs_model_details in example Corrected _refln.observed_criterion to _reflns.observed_criterion in description Corrected _struct_biol_view.view_id to _struct_biol_view.id in example Corrected _chem_comp_link.id to _chem_comp_link.link_id in example Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _entry_link.link_id to _entry_link.entry_id in description Changes (JDW): Corrections to REFINE_HIST category example and removal of a few misplaced colons. |
mmcif_std.dic |
| 0.8.12 | 1997-01-28 | Changes (JDW): Replaced all tabs with spaces. Fixed instances of lines > 80 characters. Added 'GLX' to the enumeration list for _chem_comp.three_letter_code. Added 'B' and 'Z' to the enumeration list for _chem_comp.one_letter_code. Corrected definition for _cell_measurement.wavelength. Corrected definitions for _atom_type.scat_dispersion_imag and _atom_type.scat_dispersion_real. Corrected examples for categories: CITATION, DIFFRN_DETECTOR, DIFFRN_MEASUREMENT, DIFFRN_SOURCE, GEOM_HBOND, REFINE_ANALYZE, REFINE_LS_RESTR, Corrected definition for _reflns_shell.Rmerge_F_obs. Corrected definition for _reflns_scale.group_code. Changed _refine_ls_restr_ncs.weight_iso_B to _refine_ls_restr_ncs.weight_B_iso. Corrected definitions in: _diffrn_refln.angle_[chi-theta]. Using experimental data kindly provided by Tom Emge, Shri Jain, Rachel Kramer, Jinsong Liu, and Gary Parkinson examples were added for the following categories: DIFFRN_ORIENT_MATRIX, DIFFRN_ORIENT_REFLN, DIFFRN_REFLN, DIFFRN_SCALE_GROUP, EXPTL, EXPTL_CRYSTAL, EXPTL_CRYSTAL_FACE, STRUCT_REF_SEQ, STRUCT_REF_SEQ_DIF, STRUCT_NCS_OPER, STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, REFINE_LS_RESTR_NCS, PHASING_MIR_DER_REFLN, PHASING_SET, PHASING_SET_REFLN, STRUCT_MON_NUCL, STRUCT_MON_PROT, REFINE_HIST, ATOM_SITE_ANISOTROP, CHEM_COMP_LINK, JOURNAL, PUBL, CELL_MEASUREMENT_REFLN, CHEMICAL, CHEMICAL_CONN_ATOM, CHEMICAL_CONN_BOND, STRUCT_BIOL_VIEW, STRUCT_SITE_VIEW, STRUCT_MON_PROT_CIS. Added _exptl_crystal_face.crystal_id. Added items: _reflns.observed_criterion_I_min _reflns.observed_criterion_I_max _reflns.observed_criterion_F_max _reflns.observed_criterion_F_min. Changed dictionary tile and data block name to the conforming name recommended by SRH/BMcM, cif_mm.dic. Restore consistency to the 'arbitrary units' suffix: Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _phasing_mir_der_refln.F_meas_au_sigma to _phasing_mir_der_refln.F_meas_sigma_au Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _refln.F_meas_au_sigma to _refln.F_meas_sigma_au Although data item names and category names are not case sensitive, as a matter of style certain abbreviations are consistently expressed in upper case (e.g. B, MIR, MAD, PDB). Corrected definition for category DATABASE. Added category ENTRY_LINK and corresponding aliases to CIF core category audit_link. Corrected alias name _refine_ls_R_I_factor. Added core CIF alias _diffrn_refln_crystal_id to data item _diffrn.crystal_id. |
mmcif_std.dic |
| 0.8.11 | 1997-01-22 | Changes (PMDF): Enforced style of only one space at the end of a sentence and after a ; Enforced stye in the categories section Enforced style of Need example 1 + More changes to provide compatibility for PDB Remark 3 Added _refine.B_iso_mean Added _refine.ls_percent_reflns_obs Added _refine.ls_R_factor_R_free_error Added _refine.ls_R_factor_R_free_error_details Added _refine_ls_shell.percent_reflns_obs Added _refine_ls_shell.R_factor_R_free_error Added _refine_ls_shell.redundancy_reflns_all Added _refine_ls_shell.redundancy_reflns_obs Added _refine.ls_redundancy_reflns_all Added _refine.ls_redundancy_reflns_obs Added _reflns.observed_criterion_sigma_F Added _reflns.observed_criterion_sigma_I Added REFINE_LS_RESTR_NCS category Added _refine.solvent_model_details Added _refine.solvent_model_param_bsol Added _refine.solvent_model_param_ksol |
mmcif_std.dic |
| 0.8.10 | 1997-01-22 | Changes (PMDF): + Still more changes to align with new core: Added _refine.ls_R_Fsqd_factor_obs Added _refine.ls_R_I_factor_obs Added _atom_site.disorder_assembly Added new definition of _atom_site.disorder_group Many more style and wording changes Changes to provide compatibility with PDB Remark 3 Added _chem_comp_chir_atom.comp_id Added _diffrn.ambient_temp_details Added _exptl_crystal_grow.temp_details Enlarged enumeration list of _phasing.method Added _reflns.Rmerge_F_all Added _reflns.Rmerge_F_obs Added _reflns.B_iso_Wilson_estimate Added _reflns.percent_possible_obs Added _refine_ls_restr.weight Added _refine.aniso_B data items Added _exptl_crystal.density_matthews Added _refine.ls_percent_reflns_R_free Added _refine_ls_shell.percent_reflns_R_free Added _refine.Luzzati_coordinate_error_obs Added _refine.Luzzati_d_res_low_obs Added _refine.Luzzati_sigma_a_obs Added _refine.Luzzati_sigma_a_obs_details Added _refine.Luzzati_coordinate_error_free Added _refine.Luzzati_d_res_low_free Added _refine.Luzzati_sigma_a_free Added _refine.Luzzati_sigma_a_free_details Added _refine.number_disordered_residues Added _refine.occupancy_sum_hydrogen Added _refine.occupancy_sum_non_hydrogen |
mmcif_std.dic |
| 0.8.09 | 1997-01-07 | Changes (PMDF): + More changes to align with new core: Changed _citation.book_coden_ISBN to _citation.book_id_ISBN Changed _citation.journal_coden_ASTM to _citation.journal_id_ASTM Changed _citation.journal_coden_CAS to _citation.abstract_id_ASTM Changed _citation.journal_coden_CSD to _citation.journal_id_CSD Changed _citation.journal_coden_ISSN to _citation.journal_id_ISSN Changed _citation.medline_AN to _citation.database_id_Medline Added _publ.requested_category Corrected alias for _atom_type.scat_length_neutron Added _journal.data_validation_number Changed _diffrn_detector.detector_specific to _diffrn_detector.type Deleted _diffrn_detector.detector_type Added _diffrn_radiation.probe Adjusted definition of _diffrn_radiation.type Changed _diffrn_source.source_specific to _diffrn_source.type Deleted old _diffrn_source.type Changed _diffrn_radiation_wavelength.wavelength_wt to _diffrn_radiation_wavelength.wt Added _diffrn_radiation.xray_symbol Aliased both versions 1.0 and 2.0 of the core for _diffrn_detector.detector _diffrn_detector.dtime _diffrn_source.source |
mmcif_std.dic |
| 0.8.08 | 1997-01-06 | Changes (PMDF): + Added R_work data items to the various REFINE categories + Rewrote definitions for existing R-factor definitions to distinguish between R_work, R_free and conventional R Changes (JDW) (retrieved from earlier, misplaced version): + Added data item _chem_comp.mon_nstd_parent_comp_id to provide explicit reference between a nonstandard component and the parent component. + Changed _item_type.code for _chem_comp.id and all of its children to 'ucode'. + Changed char3 and char1 to uchar3 and uchar1 to be consistent with other case insensitive data type codes. Corrected the regular expressions and primitive codes for these data types. + Added _chem_comp_atom.partial_charge. + Corrected the descriptions for _chem_comp_tor.comp_id, _chem_comp_bond.comp_id and _chem_comp_angle.comp_id. + Added _chem_comp_tor_value.comp_id as a key for category CHEM_COMP_TOR_VALUE. + Added _chem_comp_plane_atom.comp_id as a key in category CHEM_COMP_PLANE_ATOM. + Miscellaneous corrections in item descriptions in CHEM_COMP_GROUP categories. + Added item _chem_comp_plane_atom.dist_esd |
mmcif_std.dic |
| 0.8.07 | 1996-12-18 | Changes (PMDF): + Removed single quote from value of DDL items where they were not needed + Cleaned up style of range minimum/maximum data value + Cleaned up alignment of various DDL items + Deleted _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd |
mmcif_std.dic |
| 0.8.06 | 1996-11-13 | Changes (JDW): + Reorganized categories in the DIFFRN group to formally support multiple diffraction data sets. |
mmcif_std.dic |
| 0.8.05 | 1996-11-11 | Changes (PMDF): + More changes to bring this dictionary into alignement with the extended core + Added _chemical_forumula.iupac + Added _atom_site.B_equiv_geom_mean (and its esd) + Added _atom_site.U_equiv_geom_mean (and its esd) + Added _atom_type.scat_length_neutron |
mmcif_std.dic |
| 0.8.04 | 1996-11-04 | Changes (PMDF): + Changed format of references in data item definitions to match style of extended core. + Changed format of matrices in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Changed format of equivations in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Added aliases to data items where they were missing to establish correspondence with extended core. + Changed frac to fract in _atom_site.frac... data items. + Added _citation_editor_ordinal. + Added JOURNAL_INDEX data items, as well as _journal.language and _journal.paper_category. + Added _diffrn_measurement_specimen_support _diffrn_orient_refln_angle_omega _diffrn_orient_refln_angle_theta + Added PUBL_BODY category and data items. + Added _publ.contact_author_address _publ.contact_author_name + Added _publ.section_exptl_solution _publ.section_synopsis _publ.section_title_footnote + Added AUDIT_CONFORM category and data items. + Added GEOM_HBOND category and data items. |
mmcif_std.dic |
| 0.8.03 | 1996-04-03 | Changes (PMDF): + Began implementing changes to bring this dictionary into alignment with the current version of the CIF core dictionary. These differences were provided by Brian McMahon and I. David Brown. As most of these changes are matters of style and not substance, they will not be noted individually here. Anything that does involve substance will be. + Changed specification of the format of names to included that provision for a dynanastic modifier. |
mmcif_std.dic |
| 0.8.02 | 1996-03-18 | Changes (PMDF): + Changed category from chem_comp to chem_comp_link for data items _chem_comp_link.type_comp_1 and _chem_comp_link.type_comp_1 in the parent/child tree for the chem_comp.type data item. + Added _struct_ref_seq.seq_align_beg and _struct_ref_seq.seq_aling_end to the mandatory code table for _entity_poly_seq.num. + Added _struct_ref_seq_dif.seq_num to both the parent/child and mandatory code tables for _entity_poly_seq.num. + Added data item _struct_ncs_oper.code. + Changed units type to 8pi2_angstroms_squares for _atom_site.B_iso_or_equiv and _atom_site.B_iso_or_equiv_esd. + Moved TVECT vector from DATABASE_PDB_MATRIX to a new category DATABASE_PDB_TVECT and added a identifier and details item to this new category. The matrix component of TVECT has been removed. |
mmcif_std.dic |
| 0.8.01 | 1996-03-12 | Changes (PMDF): + Added missing circumflex to definition of _exptl_crystal.density_percent_sol. + Fixed erroneous reference to _atom_site.entity_seq_num in definition of _atom_site.auth_seq_id. + Changed _chem_comp_link.id to _chem_link.id in definition of _chem_comp_link.link_id. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD in citation category example + Changed _entity_link.id to _chem_link.id in definition of _entity_link.link_id. + Changed _chem_link.type_comp_1 to _chem_comp_link.type_comp_1 in _item_name and parent/child tables for _chem_comp.type. The same change was made for component 2. |
mmcif_std.dic |
| 0.8.0 | 1996-03-06 | Changes (PMDF, HB, JDW): + Added unit type 8pi2_angstroms_squared B anisotropic temperature factors, and added conversion factor for this new unit type in the ITEM_UNITS_CONVERSION category. + Changed _item_type.code for _symmetry_equiv.id to 'code' + Added default value 'no' to _chem_comp.mon_nstd_flag. |
mmcif_std.dic |
| 0.7.34 | 1996-02-20 | Changes (JDW): + Integrated STRUCT_REF, STRUCT_REF_SEQ and STRUCT_REF_SEQ_DIF from PMDF. + Removed ENTITY_REFERENCE and ENTITY_POLY_SEQ_DIF. + Integrated modified categories STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, and STRUCT_NCS_OPER from PMDF. + changed _item_type.code's 'char' and 'uchar' to 'line' and 'uline'. |
mmcif_std.dic |
| 0.7.33 | 1996-02-19 | Changes (JDW): + Replaced category COMP_PROG with category SOFTWARE supplied by P. Bourne. + Fine tuned some values of _item_type.code. Fixed regular expression for code and ucode. |
mmcif_std.dic |
| 0.7.32 | 1996-02-17 | Changes (JDW): + atom_site.entity_id renamed atom_site.label_entity_id. + atom_site.entity_seq_num deleted. + added items _atom_site.auth_asym_id, _atom_site.auth_atom_id, _atom_site.auth_comp_id, and _atom_site.auth_seq_id. These items provide placeholders for alternative nomenclature that may be used by the author. + Set the parentage for _atom_site.label_seq_id to _entity_poly_seq.num. All components of the atom site label (_atom_site.label_*) are now linked to the mmCIF hierarchical description of structure. The data items in _atom_site.auth_* may be used by authors to provide alternative identifiers in the atom site which conform with the scheme that is used in the publication of the structure. + added category group mm_atom_site_auth_label + added auth_asym_id, auth_atom_id, auth_comp_id, and auth_seq_id child data items to the categories: GEOM_ANGLE,GEOM_BOND, GEOM_CONTACT, STRUCT_CONF, STRUCT_CONN, STRUCT_MON_NUCL, STRUCT_PROT, STRUCT_PROT_CIS, STRUCT_NCS_DOM_GEN, STRUCT_SHEET_HBOND, STRUCT_SHEET_RANGE, and STRUCT_SITE_GEN. |
mmcif_std.dic |
| 0.7.31 | 1996-02-12 | Changes (JDW): + Added data items for _database_pdb_matrix.tvect_matrix[][] and _database_pdb_matrix.tvect_vector[]. + Generalized category CHEM_LINK to handle descriptions of a any type of linkage. Created CHEM_COMP_LINK to describe linkages between components, and ENTITY_LINK to describe linkages between entities (and within entities between nonsequential components). Both CHEM_COMP_LINK and ENTITY_LINK reference the linkage description in the CHEM_LINK_* categories. |
mmcif_std.dic |
| 0.7.30 | 1996-01-29 | Changes (PMDF, HB, JDW): + Added data items for pseudorotation in STRUCT_MON_NUCL. + Globally changed future tense usage to present tense (eg. will be -> is) + Added _citation.book_publisher_city. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD. + Added _citation.journal_coden_CAS. + Generalized the defintion of _atom_site.calc_flag. + Corrections to definitions defining beginning and ends of ranges in category STRUCT_SHEET_HBOND. + Added data items _diffrn_refln.scan_rate and _diffrn_refln.scan_time_backgd + Added HELX_LH_27_P and HELX_RH_27_P helix enumeration types. + Added figure of merit data item _refln.fom. |
mmcif_std.dic |
| 0.7.29 | 1995-12-11 | Changes (PMDF): + Changes to my title and Brian's in header information. + Enhanced description of the 'Hill system' of element ordering in the definition of _chem_comp.formula. + Added _item.mandatory_code to _phasing_mir_der.native_set_id + Added DATABASE_PDB_CAVEAT category. + Changed supercedes to superseded in DATABASE category description. + Changed DATABASE_NEW to DATABASE_2 in category description. + Changed SRUCT_SHEET_TOPOLOGY to STRUCT_SHEET_TOPOLOGY in category description. + Changed examples for STRUCT_SHEET_RANGE to contain only _struct_sheet_range.symmetry, not _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry + Added cell.Z_PDB data item + Changed _atoms_sites.Cartn_tran_matrix to atom_sites.Cartn_transf_matrix in definition of _atom_sites.Cartn_transform_axes + Changed _chem_comp.nstd_class to _chem_comp.mon_nstd_class in definition of _chem_comp.mon_nstd_flag + Added data items for _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd + Changed reference to _chemical_formula.appendix to CHEMICAL_FORMULA category description in definition of _chemical_formula.moiety + Changed _comp.prog.version to _comp_prog.version and _comp.prog.citation_id to _comp_prog.citation_id in COMP_PROG example + Changed reference to _computing.phasing_mir in _phasing_mir.method to a reference to the COMP_PROG category. Similarly with _computing.phasing_averaging in _phasing_averaging.method and _computing.phasing_mad in _phasing_mad.method and _computing.save_reduction in _reflns.data_reduction_method + Changed _entity.name_com.name to _entity_name_com.name in ENTITY_NAME_COM example + Changed reference to _exptl_crystal.face_ to data items in the EXPTL_CRYSTAL_FACE category in the definition of _exptl_crystal.description. + Changed _diffrn.attenuator_code to _diffrn_attenuator.code in the definition of _diffrn_refln.attenuator_code + Changed _exptl.crystal_preparation to _exptl_crystal.preparation in the definition of _exptl.details + Changed _geom_bond.distance to _geom_bond.dist in the definition of _geom_bond.dist_esd + Added data items for _refine.ls_d_res_high and _refine.ls_d_res_low + Changed _refine.d_res_high to _refine.ls_d_res_high and _refine.d_res_low to _refine.ls_d_res_low in the definition of _refln.status + Changed _reflns_scale_group.code to _reflns_scale.group_code in the definition of _refln.scale_group_code + Changed _struct_site_view_details to _struct_biol_view.details in the rotation matrix element definitions in the STRUCT_BIOL_VIEW category (even though I realize that this isn't really correct in terms of the definition of _struct_biol_view.details) + Changed _symmetry.equiv_pos_as_xyz to _symmetry_equiv.pos_as_xyz in the definition of _symmetry.space_group_name_H-M + Changed _struct_mon.details_RSSR to _struct_mon_details.RSSR and _struct_mon.details_RSR to _struct_mon_details.RSR in a number of definitions in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories + Changed _reflns_shell.possible_%_obs to _reflns_shell.percent_possible_obs in the REFLNS_SHELL example + Corrected alphabetical order of data items in the REFLNS_SHELL category + Changed _struct_sheet.number_details to _struct_sheet.details in the STRUCT_SHEET examples + Replaced _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry with _struct_sheet_range.symmetry in the STRUCT_SHEET_RANGE category and fixed example itself + Changed _refine.ls_number_reflns to _refine.ls_number_reflns_obs in the definitions of _refine.ls_restrained_S_all and _refine.ls_restrained_S_obs + Changed _refine_ls_shell.reflns to _refine_ls_shell.number_reflns_obs in the REFINE_LS_SHELL example + Removed example from DATABASE category as it was not longer valid |
mmcif_std.dic |
| 0.7.28 | 1995-10-06 | Changes (PMDF): + Removed loop from category example for DATABASE_2 + Fixed data names in category example for STRUCT_KEYWORDS + Rewrote enumeration list for _struct_conf_type.id + Removed references to chemical_formula.appendix and replaced them with reference to the CHEMICAL_FORMULA category description + Added data items _chem_comp.formula and _chem_comp.formula_weight + Changed _chem_link_angle.atom_1_atom_id to _chem_link_angle.atom_id_1 + Changed _chem_link_angle.atom_2_atom_id to _chem_link_angle.atom_id_2 + Changed _chem_link_angle.atom_3_atom_id to _chem_link_angle.atom_id_3 + Changed _chem_link_bond.atom_1_atom_id to _chem_link_bond.atom_id_1 + Changed _chem_link_bond.atom_2_atom_id to _chem_link_bond.atom_id_2 + Realphabetized to accomodation the above changes + Added CHEM_LINK_CHIR category + Added CHEM_LINK_CHIR_ATOM category + Added CHEM_LINK_PLANE category + Added CHEM_LINK_PLANE_ATOM category + Added CHEM_LINK_TOR category + Added CHEM_LINK_TOR_VALUE category + Added entries to parent/child table for _chem_link.id for reflect the addition of the new categories. + Added Engh and Huber/Priestle examples to CHEM_LINK_BOND and CHEM_LINK_ANGLE + Realphabetized categories in PHASING_MAD section Changes (JDW): + Added _item_type.code's for _chem_link_chir*.atom_id and _chem_link_tor.atom_id_*. |
mmcif_std.dic |
| 0.7.27 | 1995-09-27 | Changes (JDW & SH): + Added _item_aliases.dictionary and _item_aliases.version to all alias items. + Added several missing aliases from cifdic.C94. + Added a few missing data type codes in chem_link_* + Modified all _item_range items to reflect the correction in DDL 2.1.1. Checked all of the boundary conditions on ranges. + Made corrections in virtually all of the regular expressions. + Added data types 'ucode' and 'uchar'. These are case insensitive character types for words and single line strings, respectively. The regular expressions for these items will match characters of upper and lower case but the primitive type is uchar so all comparisons are performed in upper case. This avoids problems with case, where case is really not important. + Reviewed all items with character data types and made the following changes (hopefully uniformly): - Data items with single word enumerates were set to type 'ucode'. - Data items with multi word enumerates were set to type 'uchar'. - Any item which could potentially exceed 80 characters was set to type text. - Items which are restricted to single words were set to type 'code'. - Items which are short strings which may not span lines were set to type 'char'. + Moved aliases for anisotropic temperature factors from category ATOM_SITE to ATOM_SITE_ANISOTROP + Added category DATABASE_PDB_MATRIX to hold the SCALE and ORIGX matrices/vectors. + Modified the defintions of data types 'char1' and 'char3' to permit leading '+' to indicate a modification. + Checked dictionary with SIFLIB and returned to Paula ... |
mmcif_std.dic |
| 0.7.26 | 1995-09-25 | Changes (PMDF): + Put single quotes around 5HVP in those examples where they were missing. + Fixed registration of '5VHP' in examples. + Fixed typos in definition of _diffrn_measurement.device_specific. + Added _item.name loop and parent-child tree to _chem_comp.type + Fixed _item.name for _phasing_mir_der.der_set_id + Fixed _item.name for _phasing_mir_der.native_set_id + Added _phasing_mir_der_refln.set_id to _item.name loops and parent-child tree of _phasing_set.id + Fixed two misspellings of reference (refence). |
mmcif_std.dic |
| 0.7.25 | 1995-08-31 | Changes (PMDF): + Eliminated duplicate line in _entry_id parent/child table + Changed the three occurrences of _item_type.code text to char _atom_sites_alt.details _atom_sites_alt_ens.details _database_PDB_remark.text + Fixed Klyne and Prelog reference in GEOM_TORSION category description + Added data item _chem_comp_chir.atom_config + Added hyphen in non-crystallographic in definition sof _struct_ncs_ens.point_group + Changed Data Base to Database when referring to the CSD + Fixed four occurrances of 'the the' in definitions + Added _item_range.maximum and _item_range.minimum DDL items to _refine.ls_abs_structure_Flack and removed discussion of limits from the definition. + Changed two occurances of 'will be' to 'are' in the definition of _entity.type. + Changed ENTITY_NPOL to CHEM_COMP in definition of _entity.type. + Changes ATOM to HETATM for APS coordinates in Example 1 for the ATOM_SITE category + Corrected _item.category_id for _struct_mon_details.prot_cis. + Corrected _item.category_id for _refine_hist.details. + Rewrote header comments to emphasize use of the mmCIF listserver as the forum for the dictionary review process. |
mmcif_std.dic |
| 0.7.24 | 1995-08-21 | Changes (PMDF): + Corrected category.id for data items in the DIFFRN_STANDARDS category + Corrected category.id for data items in the PHASING_MAD_EXPT category + Corrected category.id for selected data items in the PHASING_SET category + Corrected alias for _atom_site.thermal_displace_type + Introduced alias of _atom_site_aniso_label for _atom_site_anistrop.id + Introduced alias of _atom_site_aniso_type_symbol for _atom_site_anisotrop.type_symbol |
mmcif_std.dic |
| 0.7.23 | 1995-08-10 | Changes (PMDF): + Changed _struct_sheet_gen.label_seq_id to _struct_site_gen.label_seq_id in _atom_site.label_seq_id tree + Removed duplicate entry of _phasing_MIR.entry_id in _entry.id tree + Removed alias in definitionof _refln.A_meas_au + Removed _item.category_id from _chem_link.type_comp_1 _chem_link.type_comp_2 _phasing_mad_clust.expt_id _phasing_mad_set.clust_id _phasing_mad_set.expt_id _phasing_mad_set.set_id _phasing_mad_ratio.expt_id _phasing_mad_ratio.clust_id _phasing_mad_ratio.wavelength_1 _phasing_mad_ratio.wavelength_2 + Removed _item_type.code from most of the above (it wasn't there in all of them). + Added _item.mandatory_code to _phasing_mir_der.der_set_id + Corrected _item.name for _phasing_mad_ratio.wavelength_2 |
mmcif_std.dic |
| 0.7.22 | 1995-08-09 | Changes (PMDF): + Added definitions for _chem_link_angle.link_id and _chem_link_bond.link_id + Straighted out spacing inconsistencies with _item.mandatory_code + Another quick pass at spell checking |
mmcif_std.dic |
| 0.7.21 | 1995-08-08 | Changes (PMDF): + Added _citation_author.ordinal and updated examples to reflect this addition. + Changed _item.mandatory_code for _citation_author.name to 'yes'. + First pass at checking the dictionary for spelling - lots of little changes in lots of places. + Removed many occurrences of 'with with' in definitions. |
mmcif_std.dic |
| 0.7.20 | 1995-08-02 | Changes (PMDF): + Enforced 80 character per line limit throughout. + Realphabetized _geom_angle.value and _geom_angle.value_esd. + Realphabetized _geom_torsion.value and _geom_torsion.value_esd. + Removed trailing blanks. + Fixed a couple of problems with missing terminal '. |
mmcif_std.dic |
| 0.7.19 | 1995-07-23 | Changes (JDW & PMDF): + Minor corrections in sheet example and version update. + Removed illegal characters from data item names. Changed any "/" in data item names to "_over_". |
mmcif_std.dic |
| 0.7.18 | 1995-07-20 | Changes (JDW): + Added '_struct_biol_gen.symmetry' to the key on struct_biol_gen. + Changed category block to entry. + Added _dictionary.datablock_id + Replace publ_group and journal_group with category group named iucr_group + Added category group named pdb_group + Removed all the _atom_site.label references and repointed any references to this item to _atom_site.id. + Added optional atom identifiers to all of the GEOM categories. + Added translation vector to transformations in ATOM_SITES + Created subcategories for matrices and vectors + Moved _struct.keywords to a new category STRUCT_KEYWORDS + Added pointer to exptl_crystal.id as part of key in category EXPTL_CRYSTAL_GROW_COMP. + Restructured DATABASE_PDB_REMARK category + Changed alternate_exclusive to replaces and replacedby in DATABASE and DATABASE_2 + Restructured examples in _chem_comp.one_letter_code ... + Added data item _chem_comp.three_letter_code + Made atom_site.label_alt_id and its children an optional item + Changed item names _atom_sites.frac_tran_* _atom_site.frac_transf_* and _atom_sites.Cartn_tran_* _atom_site.Cartn_transf_* + Changed the key of ATOM_SITE_ANISOTROP to _atom_site_anisotrop.id + Added all of the GEOM category atom label items to their appropriate parent data items. + 'arbitrary' added to list of item_units_list.code's + Fixed conflicting mandatory codes... |
mmcif_std.dic |
| 0.7.17 | 1995-05-22 | Changes (PMDF): + Added _phasing_MIR_refln.F_meas_au and _phasing_MIR_refln.F_meas_au_sigma and adjusted appropriate _item.related DDL Added _refln.F_meas_au and _refln.F_meas_au_sigma and adjusted as above Added _phasing_MIR_refln.F_calc_au and adjusted as above Added _refln.F_calc_au and adjusted as above Added _refln.A_calc_au and adjusted as above Added _refln.B_calc_au and adjusted as above Added _refln.A_meas_au and adjusted as above Added _refln.B_meas_au and adjusted as above Changed _item_related.function_code from 'replace' to 'alternate_exclusive' in database_2 data items Added _item_related DDL to appropriate _database data items |
mmcif_std.dic |
| 0.7.16 | 1995-05-18 | Changes (PMDF): + Added _item.name DDL to those data items that didn't have it Wrote program to check that the added names were all correct Fixed problems that turned up (including one missing . in _diffrn_radiation_detector_details |
mmcif_std.dic |
| 0.7.15 | 1995-05-18 | Changes (PMDF): + Added DDL linking data names that are value to the data names that are esds of those values Changed _geom_bond.distance to _geom_bond.dist and _geom_bond.distance_esd to _geom_bond.dist_esd Changed _geom_contact.distance to _geom_contact.dist and _geom_contact.distance_esd to _geom_contact.dist_esd Changed _cell_measurement.temperature to _cell_measurement.temp and _cell_measurement.temperature_esd to _cell_measurement.temp_esd Changed _diffrn.ambient_temperature to _diffrn.ambient_temp and _diffrn.ambient_temperature_esd to _diffrn.ambient_temp_esd |
mmcif_std.dic |
| 0.7.14 | 1995-05-03 | Changes (PMDF): + Fixed definitions of _phasing_MIR_refln.index_k and _phasing_MIR_refln.index_l |
mmcif_std.dic |
| 0.7.13 | 1995-04-20 | Changes (PMDF): + Changed all matrices back to element by element representation. + Reworded definitions of B and U matrices to clarify alternate exclusive relationship + Changed 'miller' to 'Miller' in some definitions, but left it 'miller' in data values. + Changed 'CIF' to 'data bock' where appropriate. + Made changes according to notes from last Rutgers meeting. Mostly this is clearer wording of definitions. Made formal Ref: for scattering factors. Changed atom_site.description to atom_site.details Expanded definitions for the components of the atom site label. Added disclaimer to some records in ATOM_SITE and ATOM_SITES categories. Changed _atom_type.analytical_mass_% to _atom_type.analytical_mass_percent Expanded definition of AUDIT category Added separate esd data items to examples in CELL category Added real formula in definition of _cell.volume Moved disclaimer to the top in CHEMICAL categories Changed enumeration to example in _chem_comp.one_letter_code Changed _phasing_MIR_refln.F_sigma to _phasing_MIR_refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _phasing_MIR_refln.F_meas Changed refln.observed_status to refln.status in example Changed _refln.F_sigma to _refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _refln.F_meas |
mmcif_std.dic |
| 0.7.12 | 1995-02-09 | Changes (JDW): + Changed _atom_site.label_res_id to _atom_site.label_comp_id which is a child of _chem_comp.id. + Changed all children items named label_res_id to label_comp_id + Changed descriptions of many label_comp_id to reference correct parent item. (_atom_site.label_comp_id rather than comp_comp.id). + Changed ENTITY_MON to CHEM_COMP and removed polymer component specific terminology. + Changed ENTITY_LINK to CHEM_LINK and removed polymer component specific terminology. + Added data type for yyyy-mm-dd and applied this where appropriate. + Added chem_comp_group and chem_link_group to the category group list. + Added '_' prefix to all data item save frame names. |
mmcif_std.dic |
| 0.7.11 | 1995-02-07 | Changes (PMDF): + Finished standardizing style of equations in definitions Moved ITEM_TYPE_LIST to bottom of dictionary Moved ITEM_UNITS_LIST to bottom of dictionary Moved ITEM_STRUCTURE_LIST to bottom of dictionary Moved DICTIONARY_HISTORY to bottom of dictionary (it will come back up to the top with version 1.0.0) Rewrote dictionary header comments to reflect this dictionary |
mmcif_std.dic |
| 0.7.10 | 1995-02-03 | Changes (PMDF): + Removed loop_ construction from loop_ or order one, except not for category examples and not for parent/child loops Standardized style of yes/no enumeration lists Made style of all enumeration lists more standard (still not happy here) Standardized style of examples Standardized style of references in definitions Began standardizing style of equations in definitions |
mmcif_std.dic |
| 0.7.9 | 1995-01-30 | Changes (PMDF): + Fixed syntax errors unearthed by checking of JW and PDB |
mmcif_std.dic |
| 0.7.8 | 1995-01-25 | Changes (PMDF): + Added _entity_mon.type, _entity_mon.number_atoms_all, _entity_mon.number_atoms_nh, _entity_mon.one_letter_code Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd, _entity_mon_bond.value_dist_esd Added _entity_mon_atom.type_energy, but since this is intended to be a pointer to a category (_atom_type_energy) that doesn't exist yet, have left it commented out Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and _entity_mon_chir.volume_flag Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh Added _entity_mon_chir_atom.dev Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd Added ENTITY_LINK category Added ENTITY_LINK_ANGLE category Added ENTITY_LINK_BOND category Changes (HB et al.): + Added STRUCT_MON_NUCL category Changes (PMDF): + Added label links from STRUCT_MON_NUCL to rest of dictionary Added label links from STRUCT_MON_PROT as well (forget them initially) |
mmcif_std.dic |
| 0.7.7 | 1995-01-18 | Changes (PMDF): + Added PHASING_MIR_REFLN category |
mmcif_std.dic |
| 0.7.6 | 1995-01-17 | Changes (PMDF): + Added ENTITY_SRC_NAT category Added ENTITY_SRC_GEN category Added ENTITY_NAM_COM category Added ENTITY_NAM_SYS category Added _entity.src_method data item Moved other entity data items to new categories as appropriate |
mmcif_std.dic |
| 0.7.5 | 1995-01-13 | Changes (PMDF): + Provided for sequence microheterogeneity by making _entity_poly_seq.mon_id part of the category key and by adding the data item _entity_poly_seq.hetero as a flag Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer in referenced data items. Added _entity_mon_atom.alt_atom_id. Added COMP_PROG category Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR) |
mmcif_std.dic |
| 0.7.4 | 1995-01-12 | Changes (PMDF): + Finished working on STRUCT_MON_PROT category Added STRUCT_MON_DETAILS category Added STRUCT_MON_PROT_CIS category Added STRUCT_NCS_ENS category Added STRUCT_NCS_ENS_OPER category Added STRUCT_NCS_DOM category Added STRUCT_NCS_DOM_GEN category Added equations to definitions of _phasing_MIR_der_shell.fom and _phasing_MIR_shell.fom Added REFINE_HIST category |
mmcif_std.dic |
| 0.7.3 | 1994-12-22 | Changes (PMDF): + Fixed things turned up by JDW checking of 0.7.2 Couple of small typos Added angstroms_cubed to units list and conversion tables Added _phasing_MIR_site.atom_type_symbol and added this reference to the table until _atom_type.symbol Added _entity_mon_atom.substruct_code Began adding STRUCT_MON_PROT, but this is not yet complete |
mmcif_std.dic |
| 0.7.2 | 1994-12-20 | Changes (PMDF): + Merged JDW changes with version 0.6.12 Changed _item_type.code of numb to either int or float Changed _item_description.description to category.description where appropriate Fixed a bunch of pure syntax errors Removed 'refln_scale_group' from list of category groups. Changed _refln_scale_group_code to _refln.scale_group_code somewhere Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere Reformatted CATEGORY_GROUP_LIST items to match style of other header categories Ensures that all _category data items obey they rule of first alphabetic character is column 34 (most didn't before this check) Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the rest) data items, and added wording to description that these items are only there for compliance via the alias (but left in the one _item_related thing that made the matrix element data item alternate exclusive to the full matrix data item Added language about compliance to _atom_sites.Cartn_tran_matrix Added language about compliance to _diffrn_orient_matrix.UB Added language about compliance to _diffrn_reflns.transf_matrix Removed matrix element data items for _atom_sites.fract_tran_matrix - this wasn't in c91 and so doesn't need aliasing |
mmcif_std.dic |
| 0.7.1 | 1994-12-19 | Changes (JDW): + First pass through SIFLIB checking tools. Corrected syntax errors and missing parent references. |
mmcif_std.dic |
| 0.6.14 | 1994-12-19 | Changes (PMDF): + Changed refine.ls_number_reflns to refine.ls_number_reflns_obs Added refine.ls_number_reflns_all Added refine.ls_number_reflns_R_free Changed _refln.observed_status to refln.status Expanded enumeration list to include resolution limits and R-free flag Rewrote definition Eliminated refln.R_free_status Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs Changed _refine_ls_shell.number_R_free to _refine_ls_shell.number_reflns_R_free Added PHASING category Filled in and reformatted units conversion table |
mmcif_std.dic |
| 0.6.13 | 1994-12-16 | Changes (PMDF): + Added data item _refln.R_free_status Added data item _reflns.R_free_details Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs Added _refine_ls_shell.number_R_free Added _refine_ls_shell.number_all Added _refine_ls_shell.R_factor_R_free Added _refine_ls_shell.wR_factor_R_free Tidied up the count and R-factor descriptions in REFINE_LS_SHELL Added appropriate item_related names to the R-factors in REFINE_LS_SHELL Changed 'count' to 'number' in several data names Changed _reflns.number_total to _reflns.number_all Changed _reflns.number_observed to _reflns.number.obs Added _refine.ls_R_factor_R_free Added _refine.ls_wR_factor_R_free Edited descriptions of the other R-factor data items in the REFINE category to conform to the style in REFINE_LS_SHELL Re-alphabetized the things I changed yesterday from special_details to details - I had forgotten to do that yesterday |
mmcif_std.dic |
| 0.6.12 | 1994-12-15 | Changes (PMDF): + Changed _enumeration_default.code to _item_default.value Changed _enumeration_default.value to _item_default.value Changed _enumeration.code to _item_enumeration.value Changed _enumeration.detail to _item_enumeration.detail Changed _enumeration.case to _item_enumeration.value Changed _enumeration_limit.maximum to _item_range.maximum Changed _enumeration_limit.minimum to _item_range.minimum Checked that matrix were properly labeled as either rw_rowwise or just plan rowwise. Reworded matrix descriptions for consistency. Got rid of the last of the a.b_* constructions in descriptions Added cell_length, cell_length_esd, cell_angle and cell_angle_esd subcategories Changed special_details to details for core items - original names retained in aliases Added atom_site.id Added mm_atom_site_label subcategory Commented out _atom_site.label_component until it can be dealt with properly Changed 'SIF' to 'data block' in a number of descriptions. |
mmcif_std.dic |
| 0.6.11 | 1994-12-14 | Changes (PMDF): + Fixed R-Kraut reference Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol Included full formula for this calculation in description Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target Improved wording of all definitions in REFINE_LS_RESTR Explained sums in _reflns_shell.Rmerge_I_obs and related data items |
mmcif_std.dic |
| 0.6.10 | 1994-12-13 | Changes (PMDF): + Established check-list for unfinished tasks and began dealing with them Added enumeration limits of 0 and 1 and enumeration default of 1.0 to occupancy data items Left heavy-atom maximum with an enumeration of ? Added enumeration default of 1_555 to all _symmetry data items where it was missing Changed 'connect type' to 'interaction' in _struct_conn_type data items. Filled out sub_category ddl items for cartesian coordinates, fractional coordinates, cartesian coordinates esds, and Miller indices. |
mmcif_std.dic |
| 0.6.9 | 1994-12-09 | Changes (PMDF): + Added _esd data items where needed Rationalized descriptions for all of the coordinate data items |
mmcif_std.dic |
| 0.6.8 | 1994-12-08 | Changes (PMDF): + Created ATOM_SITE_ANISOTROP category to provide for ability to have anisotropic data is a separate loop, if desired. Checked and fixed a bunch of style things Added item_units.code of degrees in data items with degrees in the description but not in the ddl Added item_units.code of kelvin in data items with kelvin in the description but not in the ddl (and added 'in degrees kelvin' to the description of those with item_units.code of kelvin but no corresponding phrase in the description) Added item_units.code of microseconds to _diffrn_radiation.detector_dtime (added to units list at same time) Added 'in minutes' to description of _diffrn_refln.elapsed_time Added 'in kilopascals' to to the description of those with item_units.code of kilopascals but no corresponding phrase in the description Added BLOCK category Added appropriate pointers (in category key, and with a data item pointing to _data_block.id) in all categories that needed them |
mmcif_std.dic |
| 0.6.7 | 1994-12-07 | Changes (PMDF): + Created DATABASE_NEW category to solve logical problems with old DATABASE category. Need to think some more about how old data items are handled. Added aliases for remaining c91 data items Changed geom_angle to geom_angle.value (aliased to original name) Changed geom_torsion to geom_torsion.value (aliased to original name) Returned ATOM_SITE items taken out during ATOM_SITE_MM transition |
mmcif_std.dic |
| 0.6.6 | 1994-12-06 | Changes (PMDF): + Finished conversion of _list_link_parent items to appropriate new DDL relationships Filled out category_key.id items in each category Had to add diffrn_refln.id item, as cannot use h k l in that category (perfectly valid to measure same reflection more than once). Used _diffrn_standard_refln.code in that category - this may cause a problem with old files, as example file did not give this data item Moved _entity_poly items back to _entity category Moved _entity_poly.formula_weight to entity.formula_weight Used _exptl_crystal.id in that category - this may cause a problem with old files, as example file did not give this data item Added _exptl_crystal_grow.crystal_id in that category Added _symmetry_equiv.id in that category - this may cause a problem with old files, as this is a new data item |
mmcif_std.dic |
| 0.6.5 | 1994-12-02 | Changes (PMDF): + Began implementation of new scheme for relationships in the entity category All entities will be treated as polymers - non-polymers will have a number of monomers of 1 All data items in ENTITY_NPOL categories are eliminated All data items in ENTITY_POLY category are moved to ENTITY |
mmcif_std.dic |
| 0.6.4 | 1994-12-01 | Changes (PMDF): + Began conversion of _list_link_parent items to appropriate new DDL relationships |
mmcif_std.dic |
| 0.6.3 | 1994-11-30 | Changes (PMDF): + Finished conversion of units data items Added a number of unit types to the table Conversation table still need to be fleshed out Removed _list_mandatory and changed _item_mandatory.code to yes for those data items |
mmcif_std.dic |
| 0.6.2 | 1994-11-28 | Changes (PMDF): + Made loop_ _item.name data items into separate data items This involved rewriting the definitions of most of them. In doing so I continued to eliminate the a.b_* construction. Added unit type of degrees. Added unit type of minutes. Added unit type of electrons. |
mmcif_std.dic |
| 0.6.1 | 1994-11-21 | Changes (JDW): + Converted dictionary and dictionary_history categories. Incorporated core dictionary history list into the new history list in the revision 0.5.1 where the dictionary merger is firsted discussed. |
mmcif_std.dic |
| 0.5.5 | 1994-11-15 | Implementation of DDL 2.0.7 dictionary wide - PMDF Finished putting .'s in itme names Changed _diffrn_measure_ to _diffrn_measurement. Changed _diffrn_rad_ to _diffrn_radiation. <saved newddl_all_4 at this point> Implemented category and ID pointers for entity category. Found all sorts of errors while doing this, and attempted to fix them consistently. Did not remove child data Items, even though they don't have to be specified - they should help keep all of this straight during the transition. Some silly reformatting to ensure that data values always have the first alphabetic character in column 33. More silly reformatting to put each example in an example loop on a separate line. <saved newddl_all_4 at this point and sent copy to JW> |
mmcif_std.dic |
| 0.5.4 | 1994-11-14 | Implementation of DDL 2.0.7 dictionary wide - PMDF Changed _enumeration to _enumeration.code Changed _enumeration_detail to _enumeration.code_detail Changed _enumeration_default to _enumeration_default.code Put .'s in item names (incomplete) Moved _PDB back to appropriate place in item names in the _database_remark_PDB_ and _database_rev_PDB_ and _database_rev_record_PDB_ categories Changed database_rev_PDB to database_PDB_rev Changed database_remark_PDB to database_PDB_remark Changed database_rev_record_PDB to database_PDB_rev_record Changed category items from item to category Began getting rid of *_whatever construction in category and item descriptions <saved newddl_all_3 at this point> |
mmcif_std.dic |
| 0.5.3 | 1994-11-13 | Implementation of DDL 2.0.7 dictionary wide - PMDF Finished merging [] and [mm] sections <Saved newddl_all_1 at this point> Changed data_ to save_ everywhere Changed _name to _item.name everywhere Added _item.mandatory_code everywhere Added save_ everywhere Moved _description to top of _save frame everywhere Changed _example to _item_examples.case everywhere Changed _example_detail to _item_examples.detail everywhere Changed _description to _item.description.description everywhere Removed _list yes everywhere Removed _list_reference everywhere Changed _enumeration_range to enumeration_limit.minimum and enumeration_limit.maximum everywhere <saved newddl_all_2 at this point> |
mmcif_std.dic |
| 0.5.2 | 1994-11-09 | Implementation of DDL 2.0.7 in CITATION category - PMDF & JW |
mmcif_std.dic |
| 0.5.1 | 1994-10-10 | Implementation of Treaty of Brussels - PMDF Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary dated 1994-05-20. The history records for the core dictionary are included here to identify the version of the core that was merged: _dictionary_name cifdic.c94 _dictionary_version 2.0 _dictionary_update 1994-03-01 _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 fine tuning 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 -------------- Removed all mm sections that enumeration items present in core but not present in mm dictionary. Fixed errors with missing trailing _'s in some category headers Also unbalanced ##'s in same place Removed "End of Example" statement everywhere Standardized syntax for missing examples Standardized syntax and style for category _definition data items. Added a bunch of ending dashed lines where they were missing. <Saved Brussels_airplane_1 at this point and began new file.> Merged [] and [mm] category explanation sections. Made HIV example always example 1, moved examples from core (where they were different from the HIV example) to higher numbers. <Saved Bussels_airplane_2 at this point - [] and [mm] sections not yet completely merged.. |
mmcif_std.dic |
| 0.4.3 | 1994-03-28 | Various changes following suggestions by IDB - PMDF Changed _entity_mon_angle_value to _entity_mon_angle_value_angle in example Changed _entity_npol_bond_value to _entity_npol_bond_value_dist Changed nonp to npol in _entity_npol_tor_value category Reworded angle _enumeration_details in _refine_ls_restr_type Reworded definitions in _struct_asym_[mm] and _struct_biol_[mm] Reworded definitions of _struct_conn_symmetry_* _struct_site_gen_symmetry _struct_biol_gen_symmetry Split _struct_conn_symmetry_* into _struct_conn_ptnr1_symmetry and _struct_conn_ptnr2_symmetry Split _struct_conn_role_* into _struct_conn_ptnr1_role and _struct_conn_ptnr2_role Removed _list_link_child from _struct_conn_conn_type_id Added _list_link_child to _struct_conn_type_id |
mmcif_std.dic |
| 0.4.2 | 1994-02-25 | Corrected spelling errors found by BMcM - PMDF |
mmcif_std.dic |
| 0.4.1 | 1994-02-04 | Major modifications of _entity_ subcategories - PMDF Added angles, planes, torsion angles and chiral centers to _entity_mon_ and _entity_npol_ Added many missing definitions Added many missing examples |
mmcif_std.dic |
| 0.3.14 | 1994-01-26 | Lots more re-alphabetization - PMDF Changed non_s to nstd throughout - PMDF Changed nonp to npol throughout - PMDF Removed all multiple spaces - PMDF Fixed a couple of alignment problems - PMDF |
mmcif_std.dic |
| 0.3.13 | 1994-01-13 | Rationalization of categories between mm and core dicts - BMcM Deleted _diffrn_crystal_environment (same as core _diffrn_ambient_environment) and moved other _diffrn_crystal items to core - BMcM Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM Some re-alphabetization - BMcM |
mmcif_std.dic |
| 0.3.12 | 1993-12-23 | Broke out examples from intro sections to loop_ _item_examples.case _example_detail construction - BMcM |
mmcif_std.dic |
| 0.3.11 | 1993-12-22 | Made a number of fixes relayed by PEB from MS AND RH _type of _atom_site_footnote_id (numb->char) - PMDF _type of _database_rev_record_rev_num_PDB (char->numb) - PMDF _type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF _atom_sites_fract_tran_matrx to _matrix - PMDF _type of _phasing_MIR_site_details (numb->char) - PMDF _example of _struct_conf_type_reference - PMDF |
mmcif_std.dic |
| 0.3.10 | 1993-12-15 | Various changes following suggestions from BMcM Refined definition of _atoms_site_label_atom_id - PMDF Removed _atom_sites_fract_tran (moved to core) - PMDF Changed _diffrn_crystal_physical_device to _diffrn_crystal_support - PMDF Changed _diffrn_measure_device_part to _diffrn_measure_device_specific - PMDF Changed _diffrn_rad_detector_part to _diffrn_rad_detector_specific - PMDF Changed _diffrn_rad_source_part to _diffrn_rad_source_specific - PMDF Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF Fixed several occurrences of \&A instead of \%A - PMDF |
mmcif_std.dic |
| 0.3.9 | 1993-12-02 | Deleted section summarizing categories - PMDF Returned definitions for most *_[mm] sections - PMDF Added _list and _list_level to global - PMDF Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF Checked lists of data items in core, fixing some problems with missing names and alphabetization - PMDF Resorted some categories to correct alphabetization - PMDF Changed form and definitions of _database_remark_num_PDB and _database_remark_text_PDB - PMDF Added data item _database_rev_replaced_by_PDB - PMDF Reordered data items in _citation example - PMDF Added data item _exptl_crystal_density_%_sol - PMDF |
mmcif_std.dic |
| 0.3.8 | 1993-11-30 | Moved _audit_author_, _citation_ categories to CIF core Definitions and small-molecule examples removed from *_[mm] sections that don't extend core categories - BMcM |
mmcif_std.dic |
| 0.3.7 | 1993-11-16 | Changed form of dates in _update_history to CIF style Changed ? to . in examples, where appropriate Added _example_detail to _refine_ls_restr_type Expanded definition of _refine_ls_restr_type |
mmcif_std.dic |
| 0.3.6 | 1993-10-10 | Changed *_appendix to *_[mm] throughout Removed 'Need example here' from _chemical_[mm] Removed 'Need example here' from _chemical_conn_atom_[mm] Removed 'Need example here' from _chemical_conn_bond_[mm] Moved _PDB to end of all relevant data names (except _[mm]) Added _database_rev_record_details_PDB data name Changed _refine_occupancy_limit_high to _refine_occupancy_max Changed _refine_occupancy_limit_low to _refine_occupancy_min Changed _refine_B_iso_limit_high to _refine_B_iso_max Changed _refine_B_iso_limit_low to _refine_B_iso_min Changed all definitions and examples in _refine_iso_B_ category to _refine_B_iso_ equivalents |
mmcif_std.dic |
| 0.3.5 | 1993-09-08 | Added missing _diffrn_orient_matrix_UB_33 (in appendix) Added missing _phasing_MIR_der_shell_der_id to appropriate example |
mmcif_std.dic |
| 0.3.4 | 1993-09-01 | Added _struct_conn_ptnr1_label_alt_id and _struct_conn_ptnr2_label_alt_id Corrected definitions for _struct_conn_ptnr2_ items Added _struct_site_gen_label_alt_id Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis Change _database_PDB_rev_ example to _loop construction Added _PDB_remark category (data items _PDB_remark_num and _PDB_remark_text) Added 'obsolete' to enumeration list for _database_PDB_rev_status Added _database_PDB_rev_replaces data item |
mmcif_std.dic |
| 0.3.3 | 1993-08-12 | Syntax and consistency checks - SRH Added _type of null for appendix items. |
mmcif_std.dic |
| 0.3.2 | 1993-08-11 | Cleaning up of stray notes |
mmcif_std.dic |
| 0.3.1 | 1993-08-08 | Began implementing DDL v0.7 |
mmcif_std.dic |
| 0.2.8 | 1993-08-03 | More work on phasing_MIR Created phasing_MIR_der and phasing_MIR_der_shell categories |
mmcif_std.dic |
| 0.2.7 | 1993-08-01 | Redesigned phasing_MIR definitions |
mmcif_std.dic |
| 0.2.6 | 1993-06-02 | Fixed _atom_site_ example (_entity_poly_seq_num) Removed _list_link_parent from _entity_mon_atom_atom_id a _entity_nonp_atom_atom_id Added real APS coordinates to _atom_site_ example Rewrote _atom_sites_footnote_ example |
mmcif_std.dic |
| 0.2.5 | 1993-05-20 | A general merging of updates from PMR, BMcM and SRH Fixed typographical and stylistic problems a la BMcM |
mmcif_std.dic |
| 0.2.4 | 1993-05-20 | DDL adjustment from down under ):-(> |
mmcif_std.dic |
| 0.2.3 | 1993-05-19 | Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon |
mmcif_std.dic |
| 0.2.2 | 1993-05-18 | Style consistency and proof reading changes throughout Make page numbers general to articles and chapters in citation Added *_method to all phasing categories Looped out keywords from _struct_site_ list Added _atom_site_label_ definitions as per H. Berman Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne Added _atom_sites_alt_ data items to formally handle alternative conformations Verified with Cyclops and RGB tools |
mmcif_std.dic |
| 0.2.1 | 1993-05-13 | Major rethinking of _entity_ data based following discussions of 1993-05-10 meeting |
mmcif_std.dic |
| 1.1.18 | 1993-05-12 | Looped out authors and editors in citation list Verified with RGB tools Some style consistency imposed Fleshed out category definitions and imposed style Updated "sets of data item" at beginning of document Checked alphabetical order of data names - moved id's |
mmcif_std.dic |
| 0.1.17 | 1993-05-11 | Changed _atom_site_label_component_? to new nomenclature Introduced category DDL throughout Introduced refers_to DDL throughout Introduced part_of_key DDL throughout Mandated that _list must be in each data definition Standardized 'need not be unique' statements Standardized example headers |
mmcif_std.dic |
| 0.1.16 | 1993-05-10 | Made corrections based on written comments from K. Watenpaugh Made corrections/additions based on discussions at Rutgers |
mmcif_std.dic |
| 0.1.15 | 1993-05-09 | Reconciled nonconcurrent versions Removed trailing blanks Made corrections based on email suggestions from P. Bourne |
mmcif_std.dic |
| 0.1.14 | 1993-04-07 | Experiment with refers_to, category and part_of_key in entity_conn_atom_ and entity_conn_bond_ sections. Discovered horror show with nonconcurrent versions on different computers - not yet resolved. |
mmcif_std.dic |
| 0.1.13 | 1993-04-07 | Introduced _exptl_crystal_grow_ data names |
mmcif_std.dic |
| 0.1.12 | 1993-04-06 | More syntax problems fixed a la Peter Murray-Rust |
mmcif_std.dic |
| 0.1.11 | 1993-04-03 | Syntax checked using tools of Peter Murray-Rust - many problems fixed |
mmcif_std.dic |
| 0.1.10 | 1993-03-28 | Filled in examples for several data categories |
mmcif_std.dic |
| 0.1.9 | 1993-03-26 | Removed _struct_topol_ section until it gets straightened out |
mmcif_std.dic |
| 0.1.8 | 1993-03-25 | Still testing for Cyclops compliance - reveal many additional syntax problems Also verified with new tool by RG Ball - still more errors fixed Dealt with issue raised by PE Bourne - amongst changes Rewrote _database_ section completely Changed _audit_contact_author_ to _audit_contact_author_name _audit_contact_author_address |
mmcif_std.dic |
| 0.1.7 | 1993-03-24 | Tested for Cyclops compliance - most problems are names that are too long. Changed crystal_preparation to crystal_prep Changed d_resolution to d_res Many other such changes |
mmcif_std.dic |
| 0.1.6 | 1993-03-24 | Dealt with many issues raised by SR Hall. Some were merely typographical. Changed temp to B_iso Changed occ to occupancy Changed special_details to details. Changed asl to label everywhere. Shuffled data names in _struct_conf_ and _struct_conn_ |
mmcif_std.dic |
| 0.1.5 | 1993-03-24 | Finished moving examples to *_appendix data items |
mmcif_std.dic |
| 0.1.4 | 1993-02-11 | Added example for _symmetry_ |
mmcif_std.dic |
| 0.1.3 | 1993-02-11 | Started moving core data names to the *_appendix data items |
mmcif_std.dic |
| 0.1.2 | 1993-02-11 | Started moving examples to *_appendix data items. |
mmcif_std.dic |
| 0.1.1 | 1993-02-11 | Highlighted all notes with # %%%%% surrounds. |
mmcif_std.dic |
| 2.0.11 | 2007-05-30 | Changes (jdw): + Make all key items mandatory. |
mmcif_std.dic |
| 2.0.10 | 2006-02-24 | Changes (jdw): + Added category groups to audit_link, diffrn_reflns_class, refine_ls_class, reflns_class, space_group, space_group_symop, valence_param, valence_ref. |
mmcif_std.dic |
| 2.0.09 | 2005-06-27 | Internal dates used for housekeeping prior to release 2005-04-13 Changes (NJA) 2005-04-13 + Minor corrections to spelling and punctuation. + pdb_group definition: Brookhaven Protein Data Bank changed to Protein Data Bank. 2005-04-14 Changes (NJA) 2005-04-14 + Minor corrections to spelling and punctuation. + _atom_sites.solution_* descriptions edited so each appropriate to the particular data name. +_chem_comp.formula description edited to match that in core dictionary +_chem_comp.three_letter_code: several typing errors in amino-acid and base names corrected. +_chem_comp_atom.model_Cartn_z: 'The x component ...' changed to 'The z component...' +_chemical.melting_point_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_decomposition_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_sublimation_* descriptions edited so each appropriate to the particular data name. 2005-04-15 Changes (NJA) 2005-04-15 + Minor corrections to spelling and punctuation. +_citation.journal_id_CSD description, Brookhaven Protein Data Bank changed to Protein Data Bank. +_database.code_* entries edited so each is relevant to the particular data name +_database_PDB_matrix.scale[3][3]: description changed from 'The [1][1] element of the PDB SCALE matrix.' to 'The [3][3] element of the PDB SCALE matrix.' +_diffrn.ambient_pressure_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn.ambient_temp_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn_attenuator.scale description changed to match that in the core dictionary. +_diffrn_radiation_wavelength.id: _diffrn_radiation_wavelength in description changed to _diffrn_radiation_wavelength.wavelength +_diffrn_reflns_class.av_sgI/I description [sum|u(net I)|/sum|net I|] changed to [sum|sigma(net I)|/sum|net I|] +_diffrn_reflns_class.d_res_high and _low descriptions changed to match those in the core dictionary +diffrn_source Example 1 _diffrn_source.power '50 kw, 180 mA' changed to _diffrn_source.power 50 and _diffrn_source.current 180 +_exptl_crystal.density_Matthews year of reference corrected from 1960 to 1968 +_exptl_crystal.density_meas_gt and _lt descriptions edited so each is relevant to the particular data name. +_exptl_crystal.density_meas_temp_gt and _lt descriptions edited so each is relevant to the particular data name. +geom_contact and geom_bond Example 1 year for reference corrected from 1991 to 1992 +_phasing_MAD_ratio.d_res_high and low ; _phasing_MAD_set.d_res_high and _low; _phasing_MIR.d_res_high and low; _phasing_MIR_der.d_res_high and low; _phasing_MIR_der_shell.d_res_high and low; _phasing_MIR_shell.d_res_high and low and _refine.ls_d_res_high and low rephrased to correspond to similar terms in the core dictionary. +Spelling of Lattman corrected in references to Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. +Temperature factor replaced by displacement parameter throughout. +refine Example 2 _refine.ls_weighting_scheme 'calc w=1/(\s^2^(F)+0.0004F^2^)' split into _refine.ls_weighting_scheme and _refine.ls_weighting_details +_refine.ls_extinction_coef and _refine.ls_extinction_method reference to Becker and Coppens corrected to 129-147, 148-153 (is two articles). +_refine.ls_restrained_S_all and _obs: Y~calc~ = the observed coefficients changed toY~calc~ = the calculated coefficients 2005-04-18 Changes (NJA) 2005-04-18 + Minor corrections to spelling and punctuation. + temperature factor changed to displacement parameter throughout + _refine_ls_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression) ' removed from description. + _refine_ls_class.R_factor_gt 'for all reflections' removed from description. + _refine_ls_class.d_res_high and _low, _refine_analyze.RG_d_res_high and _low, _refine_ls_shell.d_res_high and _low, _reflns.d_resolution_high and low, _reflns_class.d_res_high and _low, _reflns_shell.d_res_high and _low definitions edited to match related definitions in the core dictionary + _refln.intensity_calc _meas, _sigma edited to match corresponding entries in the core dictionary + _reflns.Friedel_coverage in description _reflns_number_total changed to _reflns.number_all. + _reflns_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression)' removed from description. + _reflns_class.R_factor_gt 'all reflections, and for' removed from description + _reflns_class.number_total in description: _reflns_special_details changed to _reflns.details 2005-04-19 Changes (NJA) 2005-04-19 + Minor corrections to spelling and punctuation. + _valence_param.ref_id description: _valence_ref_id changed to _valence_ref.id + References to International Tables updated. 2005-04-22 Changes (NJA) 2005-04-22 + _cell.reciprocal_angle_alpha, beta and gamma: descriptions edited so each appropriate to the particular data name. + _cell.reciprocal_length_a, b and c: descriptions edited so each appropriate to the particular data name. + _struct_mon_nucl.chi1 and _chi2; descriptions edited from `... sugar-base torsion angle chi...' to '... sugar-base torsion angle chi1' and '... sugar-base torsion angle chi2' 2005-05-03 Changes (NJA) 2005-05-03 + several data items *_esd edited so that the description reads 'the standard uncertainly of *', not 'the standard uncertainty of *_esd' + several DDL1 datanames in descriptions changed to DDL2 datanames 2005-05-10 Changes (NJA) 2005-05-10 + _citation.journal_id_CSD example changed from 070 to 0070 + Mursudov and Dodson (1997) references corrected + References to Cruickshank DPI updated + References to Luzzati (1952) corrected 2005-06-23 Changes (NJA) 2005-06-23 _publ_author.email added. Corrections for IT G Chapter 4.5 included. 2005-06-25 (BM) ITEM_UNITS_LIST: cosmetic changes to definitions of some units ITEM_UNITS_CONVERSION: multipliers in electrons per <unit> cubed terms fixed 2005-06-27 (BM) Some minor editorial changes to ensure consistency with latest pdbx dictionary version. Only significant change: + in _citation.id the listing for _software.citation_id has _item.mandatory_code changed to "no" to match the value in save__software.citation_id and to match pdbx |
mmcif_std.dic |
| 2.0.08 | 2005-04-06 | Changes (JDW) 2005-04-06 + Added mandatory code _cell.reciprocal_angle_beta |
mmcif_std.dic |
| 2.0.07 | 2005-03-03 | Changes (JDW) 2005-03-08 + Changed related references to _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed related references to _refln.observed_status to _refln.status + Restore original case to FOM - although case is not an issue for mmCIF it is an issue for XML translations. |
mmcif_std.dic |
| 2.0.06 | 2005-03-03 | Changes (JDW): + The following data items added to maintain data item correspondence with the CIF CORE dictionary V 2.3. All aliases in section 1 updated to version 2.3. _atom_site.adp_type _atom_site.refinement_flags _atom_site.refinement_flags_adp _atom_site.refinement_flags_occupancy _atom_site.refinement_flags_posn _atom_sites.special_details _atom_type.scat_dispersion_source _audit_link.block_code _audit_link.block_description _cell.reciprocal_angle_alpha _cell.reciprocal_angle_beta _cell.reciprocal_angle_gamma _cell.reciprocal_angle_alpha_esd _cell.reciprocal_angle_beta_esd _cell.reciprocal_angle_gamma_esd _cell.reciprocal_length_a _cell.reciprocal_length_b _cell.reciprocal_length_c _cell.reciprocal_length_a_esd _cell.reciprocal_length_b_esd _cell.reciprocal_length_c_esd _cell.special_details _chemical.absolute_configuration _chemical.melting_point_gt _chemical.melting_point_lt _chemical.optical_rotation _chemical.properties_biological _chemical.properties_physical _chemical.temperature_decomposition _chemical.temperature_decomposition_esd _chemical.temperature_decomposition_gt _chemical.temperature_decomposition_lt _chemical.temperature_sublimation _chemical.temperature_sublimation_esd _chemical.temperature_sublimation_gt _chemical.temperature_sublimation_lt _citation.database_id_CSD _database.CSD_history _database.code_CAS _database.code_CSD _database.code_ICSD _database.code_MDF _database.code_NBS _database.code_PDB _database.code_PDF _database.code_depnum_ccdc_fiz _database.code_depnum_ccdc_journal _database.code_depnum_ccdc_archive _diffrn.ambient_pressure _diffrn.ambient_pressure_esd _diffrn.ambient_pressure_gt _diffrn.ambient_pressure_lt _diffrn.ambient_temperature _diffrn.ambient_temperature_esd _diffrn.ambient_temperature_gt _diffrn.ambient_temperature_lt _diffrn_attenuator.material _diffrn_detector.area_resol_mean _diffrn_detector.dtime _diffrn_refln.class_code _diffrn_refln.intensity_u _diffrn_reflns.av_unetI/netI _diffrn_reflns_class.av_R_eq _diffrn_reflns_class.av_sgI/I _diffrn_reflns_class.av_uI/I _diffrn_reflns_class.code _diffrn_reflns_class.description _diffrn_reflns_class.d_res_high _diffrn_reflns_class.d_res_low _diffrn_reflns_class.number _diffrn_source.take-off_angle _diffrn_standards.scale_u _exptl_crystal.colour_lustre _exptl_crystal.colour_modifier _exptl_crystal.colour_primary _exptl_crystal.density_meas _exptl_crystal.density_meas_esd _exptl_crystal.density_meas_gt _exptl_crystal.density_meas_lt _exptl_crystal.density_meas_temp _exptl_crystal.density_meas_temp_esd _exptl_crystal.density_meas_temp_gt _exptl_crystal.density_meas_temp_lt _geom_bond.valence _publ_author.id_iucr _refine.ls_R_factor_gt _refine.ls_goodness_of_fit_gt _refine.ls_goodness_of_fit_ref _refine.ls_shift/esd_max _refine.ls_shift/esd_mean _refine.ls_shift/su_max _refine.ls_shift/su_max_lt _refine.ls_shift/su_mean _refine.ls_shift/su_mean_lt _refine_ls_class.code _refine_ls_class.d_res_high _refine_ls_class.d_res_low _refine_ls_class.R_factor_gt _refine_ls_class.R_factor_all _refine_ls_class.R_Fsqd_factor _refine_ls_class.R_I_factor _refine_ls_class.wR_factor_all _refln.class_code _refln.d_spacing _refln.include_status _refln.mean_path_length_tbar _refln.observed_status _refln.sint/lambda _reflns.Friedel_coverage _reflns.number_gt _reflns_class.code _reflns_class.description _reflns_class.d_res_high _reflns_class.d_res_low _reflns_class.number_gt _reflns_class.number_total _reflns_class.R_factor_all _reflns_class.R_factor_gt _reflns_class.R_Fsqd_factor _reflns_class.R_I_factor _reflns_class.wR_factor_all _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _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 _reflns_shell.Rmerge_I_gt _space_group.crystal_system _space_group.id _space_group.IT_number _space_group.name_Hall _space_group.name_H-M_alt _space_group_symop.id _space_group_symop.operation_xyz _space_group_symop.sg_id _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence _valence_param.B _valence_param.details _valence_param.id _valence_param.ref_id _valence_param.Ro _valence_ref.id _valence_ref.reference Changes (BM): 2005-03-03 Editorial changes to accompany International Tables Volume G publication (B. McMahon): + Fixed broken example loop for _phasing_MAD_ratio.* + Expanded the definitions for _phasing_MIR_der_refln.HL_A_iso (and B, C and D terms) and provided literature reference + Abbreviation .FOM (for figure-of-merit) consistently rendered lowercase + Expanded the definitions for _refine.solvent_model_param_bsol (and *_ksol) and provided literature reference + Rearranged the order of entries in the REFINE_ANALYZE category to preserve strict alphabetisation + Removed _refine_ls_restr_type.U_sigma_weights from example in REFINE_LS_RESTR_TYPE category + Commented out the incorrect example for the CHEM_COMP_LINK category + For the example in the ENTITY_NAME_SYS category supplied the EC number and the systematic name "water"; also trimmed the irrelevant last line of the definition. + Changed the vague 'x,x-pyranoside' example of _entity_name_sys.name to 'hydroquinone-beta-D-pyranoside' and matched this with 'arbutin' for _entity_name_com.name + Removed the CAVEAT and REMARK terms (and PDB code trailers) from the contents pf the _database_PDB_caveat.* and *_remark.* examples in accordance with current PDB practice + Updated reference to Tickle et al. in _refine_analyze.RG_free_work_ratio + Fixed few minor typos + Cosmetic reflowing of textual examples to aid typesetting + Added Engh & Huber and Priestle references to example details + Changed upper enumeration limit of _atom_site_attached_hydrogens to 8 in line with current Core dictionary + Added URL of PDB format description to _database_PDB_rev.mod_type + Extended enumeration list of _publ.requested_category for Acta E papers + Updated definition of _refine.ls_abs_structure_Flack and *_Rogers to reflect the more correct wording of the current Core dictionary. + Added _item_range.maximum and *minimum to _refine.ls_abs_structure_Rogers in line with new wording of definition. Changes (NJA): 2005-03-03 + Commented out duplicate save frames for following items with _item_aliases.version 2.0.1: _atom_site.refinement flags, _database.code_CAS, _database.code_CSD _database.code_ICSD, _database.code_MDF, _database.code_NBS _database.code_PDF, _diffrn.ambient_pressure, _diffrn.ambient_pressure.esd _diffrn_detector.dtime, _exptl_crystal.density.meas _exptl_crystal.density_meas_temp, _refln.mean_path_length_tbar Changes (BM): 2005-03-03 + Fixed erroneous _item.name in save__diffrn.ambient_pressure_esd + Removed erroneous aliases to *_esd quantities in coreCIF 2.3: _cell_reciprocal_angle_alpha_esd, _cell_reciprocal_angle_beta_esd _cell_reciprocal_angle_gamma_esd, _cell_reciprocal_length_a_esd _cell_reciprocal_length_b_esd, _cell_reciprocal_length_c_esd _chemical_temperature_decomposition_esd _chemical_temperature_sublimation_esd _diffrn.ambient_pressure_esd, _diffrn_ambient_temperature_esd _exptl_crystal_density_meas_esd, _exptl_crystal_density_meas_temp_esd + Removed redundant aliases: _cell.special_details ( = _cell.details) _diffrn.ambient_temperature ( = _diffrn.ambient_temp) _refine.ls_shift/esd_max ( = _refine.ls_shift_over_esd_max) _refine.ls_shift/esd_mean ( = _refine.ls_shift_over_esd_mean) _refln.observed_status ( = _refln.status) _refln.sint/lambda ( = _refln.sint_over_lambda) + Changed _refine.ls_shift/su_max to _refine.ls_shift_over_su_max and likewise for *_lt, *_mean and *_max_lt Changes (NJA): 2005-03-07 + Changed _reflns.class_d_res_low to _reflns_class.d_res_low in description of _reflns_class.wR_factor_all + Added [][] to _atom_sites.Cartn_transf_matrix, _diffrn_reflns.transf_matrix and _diffrn_orient_matrix.UB for consistency throughout. + Changed _chem_comp_link.type_1 and _2 to _chem_comp_link.type_comp_1 and 2 in _chem_link_angle.atom_id_1 and _2 + Changed all occurences of _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed _diffrn_reflns.class_code to _diffrn_reflns_class.code in _diffrn_refln.class_code + Changed _geom_bond.distance to _geom_bond.dist in description of _geom_bond.valence. + Changed _refln.observed_status to _refln.status in refln.include_status + Changed _reflns.special_details to _reflns.details in _reflns.number_gt and _reflns_class.number_gt + Created new entry for _reflns.threshold_expression, as no entry existed and many item descriptions referred to _reflns_threshold_expression (these were then changed to _reflns.threshold_expression). + Changed _struct_mon_prot.alt_id, _struct_mon_prot.asym_id, _struct_mon_prot.comp_id and _struct_mon_prot.seq_id to _struct_mon_prot.label_alt_id, _struct_mon_prot.label_asym_id, _struct_mon_prot.label_comp_id and _struct_mon_prot.label_seq_id in Example 1 of _struct_mon_prot. + Changed _struct_site_view.view_id to _struct_site_view.id in Example 1 of _struct_site_view. |
mmcif_std.dic |
| 2.0.05 | 2004-08-04 | Changes (JDW): + Changed data type of _refine.ls_redundancy_reflns_all, _refine.ls_redundancy_reflns_obs, _refine_ls_shell.redundancy_reflns_all, _refine_ls_shell.redundancy_reflns_obs from int to float. |
mmcif_std.dic |
| 2.0.04 | 2004-04-21 | Changes (JDW): + Changed working name and packaging of dictionary. + _reflns_shell_number_possible range data type error fixed + Fix syntax errors in category examples. + Remove nonsense zero value default values + Remove all default values from *_esd items + Make _atom_site.label_* mandatory + Make _atom_site.auth_asym_id mandatory + Make _software.citation_id optional |
mmcif_std.dic |
| 2.0.03 | 2000-11-09 | Changes (JDW): + Relax regular expression for atom names to accept blanks in atom names in order to support nomenclature used in many existing macromolecular data files. Data type "atcode" has been assigned to _chem_comp_atom.atom_id, _atom_site.auth_atom_id and all related items. |
mmcif_std.dic |
| 2.0.02 | 2000-10-24 | Changes (JDW): + Updated enumerations for _database_PDB_rev.mod_type. + Updated enumerations for _struct_conn_type.id + Corrected data type of _refine_ls_shell.percent_reflns_obs from int to float + Updated preliminary description of _database_PDB_rev.status. + Changed regular expression for float to accept trailing decimal (ie. dd.) + Add () to regular expressions for code and ucode. + Added L-saccharide, D-saccharide, saccharide to enumerants for _chem_comp.type to handle monosaccarided components where linking cannot be inferred. |
mmcif_std.dic |
| 2.0.01 | 2000-10-17 | Changes (JDW): + Integrated new definitions and extensions to existing categories. Additional data definitions submitted by Kim Henrick. Content of phasing definitions reviewed by Paula Fitgerald. Content of refinement definitions reviewed by Dale Tronrud. Editorial review by Helen Berman, John Westbrook, and Paula Fitzgerald. New Items included in this version: _phasing_MIR.d_res_high, _phasing_MIR.d_res_low, _phasing_MIR.FOM, _phasing_MIR.FOM_acentric, _phasing_MIR.FOM_centric, _phasing_MIR.reflns, _phasing_MIR.reflns_acentric, _phasing_MIR.reflns_centric, _phasing_MIR.reflns_criterion, _phasing_MIR_der.power_acentric, _phasing_MIR_der.power_centric, _phasing_MIR_der.R_cullis_acentric, _phasing_MIR_der.R_cullis_anomalous, _phasing_MIR_der.R_cullis_centric, _phasing_MIR_der.reflns_acentric, _phasing_MIR_der.reflns_anomalous, _phasing_MIR_der.reflns_centric, _phasing_MIR_der_site.occupancy_anom, _phasing_MIR_der_site.occupancy_anom_su, _phasing_MIR_der_site.occupancy_iso, _phasing_MIR_der_site.occupancy_iso_su, _phasing_MIR_shell.FOM_acentric, _phasing_MIR_shell.FOM_centric, _phasing_MIR_shell.reflns_acentric, _phasing_MIR_shell.reflns_anomalous, _phasing_MIR_shell.reflns_centric, _refine.correlation_coeff_Fo_to_Fc, _refine.correlation_coeff_Fo_to_Fc_free, _refine.overall_SU_B, _refine.overall_SU_ML, _refine.overall_SU_R_Cruickshank_DPI, _refine.overall_SU_R_free, _refine.overall_FOM_free_R_set, _refine.overall_FOM_work_R_set, _refine_analyze.RG_d_res_high, _refine_analyze.RG_d_res_low, _refine_analyze.RG_free, _refine_analyze.RG_work, and _refine_analyze.RG_free_work_ratio. + New categories included in this version: REFINE_FUNCT_MINIMIZED,REFINE_LS_RESTR_TYPE, REFLN_SYS_ABS. + Modification of examples for _refine_ls_restr.type + Contributed editorial and typographical corrections. + Corrected incomplete keys in categories PHASING_MAD_SET and DATABASE_PDB_REV_RECORD. + _exptl.method enumerations moved to examples. + Added database codes for RCSB and EBI. + Fixed item examples in _publ_body.label. |
mmcif_std.dic |
| 1.0.00 | 1997-10-14 | Changes (PMDF): + Editorial changes in light of proof-reading by B. McMahon and I.D. Brown + No data names or enumeration values have changed, with the exception of the addition of the enumeration value 'other' to exptl.method + The bulk of the changes, which are too numerous to list there, were fixing spelling and grammar errors, and providing missing definitions + In a few cases, data definitions were reworded for clarity + Replaced erroneous occurances of Y~calc~ with Y~obs~ in the defintions of weighted R factors (Ian Tickle) |
mmcif_std.dic |
| 0.9.01 | 1997-01-31 | Changes (PMDF): + Removed occurrance of two or more blank lines + Enforced rule of no apostrophes around values for _item_sub_category.id + Enforced rule of no apostrophes around values for_item_default.value + Enforced rule of no apostrophes around values for_item.mandatory_code and fixed one alignment problem + Enforced rule of no apostrophes around values for _item_related.function_code and fixed a few alignment problems + Added _item.mandatory_code for _diffrn_refln.wavelength_id + Changed cifdic.c94 to cif_core.dic in _item_aliases.dictionary everywhere + Changed 2.0 to 2.0.1 in _item_aliases.version everywhere + Changed to consistent usage of kelvins instead of kelvin, got rid of capitalized versions + Removed capitalized usages of angstroms + Enforced rule of no apostrophes around values for _item_units.code + Fixed alignment problems with a few _category_key.name values |
mmcif_std.dic |
| 0.9.0 | 1997-01-30 | Changes (PMDF): + Corrected _reflns_observed_criterion to _reflns.observed_criterion in a number of places + Aligned enumeration lists in this dictionary with those in version 2.0 of the core dictionary. This involved changes in: _citation.coordinate_linkage _diffrn_radiation.xray_symbol _diffrn_refln.scan_mode _diffrn_refln.scan_mode_backgd _exptl.absorpt_correction_type _publ_manuscript_incl.extra_defn _refine.ls_hydrogen_treatment _refine.ls_structure_factor_coef + A number of corrections to errors pointed out by H. Bernstein Added category.id to _database_PDB_tvect.id Fixed spelling of _publ.section_exptl_soltuion Corrected _refine.ls_R_factor_work to _refine.ls_R_factor_R_work in description Corrected spelling of _refine_analyze.Luzaatti_d_res_low_obs in example Corrected spelling of _refine_analyze.Luzzatti_coordinate_error_obs in example Corrected _geom_hbond.atom_site_label_id_D to _geom_hbond.atom_site_id_D in example Corrected _geom_hbond.atom_site_label_id_H to _geom_hbond.atom_site_id_H in example Corrected _geom_hbond.atom_site_label_id_A to _geom_hbond.atom_site_id_A in example Corrected _entry_link.description to _entry_link.details Corrected _DIFFRN_SCALE_GROUP to DIFFRN_SCALE_GROUP in description Corrected _refine_ls_restr_ncs.model_details to _refine_ls_restr_ncs.ncs_model_details in example Corrected _refln.observed_criterion to _reflns.observed_criterion in description Corrected _struct_biol_view.view_id to _struct_biol_view.id in example Corrected _chem_comp_link.id to _chem_comp_link.link_id in example Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _entry_link.link_id to _entry_link.entry_id in description Changes (JDW): Corrections to REFINE_HIST category example and removal of a few misplaced colons. |
mmcif_std.dic |
| 0.8.12 | 1997-01-28 | Changes (JDW): Replaced all tabs with spaces. Fixed instances of lines > 80 characters. Added 'GLX' to the enumeration list for _chem_comp.three_letter_code. Added 'B' and 'Z' to the enumeration list for _chem_comp.one_letter_code. Corrected definition for _cell_measurement.wavelength. Corrected definitions for _atom_type.scat_dispersion_imag and _atom_type.scat_dispersion_real. Corrected examples for categories: CITATION, DIFFRN_DETECTOR, DIFFRN_MEASUREMENT, DIFFRN_SOURCE, GEOM_HBOND, REFINE_ANALYZE, REFINE_LS_RESTR, Corrected definition for _reflns_shell.Rmerge_F_obs. Corrected definition for _reflns_scale.group_code. Changed _refine_ls_restr_ncs.weight_iso_B to _refine_ls_restr_ncs.weight_B_iso. Corrected definitions in: _diffrn_refln.angle_[chi-theta]. Using experimental data kindly provided by Tom Emge, Shri Jain, Rachel Kramer, Jinsong Liu, and Gary Parkinson examples were added for the following categories: DIFFRN_ORIENT_MATRIX, DIFFRN_ORIENT_REFLN, DIFFRN_REFLN, DIFFRN_SCALE_GROUP, EXPTL, EXPTL_CRYSTAL, EXPTL_CRYSTAL_FACE, STRUCT_REF_SEQ, STRUCT_REF_SEQ_DIF, STRUCT_NCS_OPER, STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, REFINE_LS_RESTR_NCS, PHASING_MIR_DER_REFLN, PHASING_SET, PHASING_SET_REFLN, STRUCT_MON_NUCL, STRUCT_MON_PROT, REFINE_HIST, ATOM_SITE_ANISOTROP, CHEM_COMP_LINK, JOURNAL, PUBL, CELL_MEASUREMENT_REFLN, CHEMICAL, CHEMICAL_CONN_ATOM, CHEMICAL_CONN_BOND, STRUCT_BIOL_VIEW, STRUCT_SITE_VIEW, STRUCT_MON_PROT_CIS. Added _exptl_crystal_face.crystal_id. Added items: _reflns.observed_criterion_I_min _reflns.observed_criterion_I_max _reflns.observed_criterion_F_max _reflns.observed_criterion_F_min. Changed dictionary tile and data block name to the conforming name recommended by SRH/BMcM, cif_mm.dic. Restore consistency to the 'arbitrary units' suffix: Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _phasing_mir_der_refln.F_meas_au_sigma to _phasing_mir_der_refln.F_meas_sigma_au Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _refln.F_meas_au_sigma to _refln.F_meas_sigma_au Although data item names and category names are not case sensitive, as a matter of style certain abbreviations are consistently expressed in upper case (e.g. B, MIR, MAD, PDB). Corrected definition for category DATABASE. Added category ENTRY_LINK and corresponding aliases to CIF core category audit_link. Corrected alias name _refine_ls_R_I_factor. Added core CIF alias _diffrn_refln_crystal_id to data item _diffrn.crystal_id. |
mmcif_std.dic |
| 0.8.11 | 1997-01-22 | Changes (PMDF): Enforced style of only one space at the end of a sentence and after a ; Enforced stye in the categories section Enforced style of Need example 1 + More changes to provide compatibility for PDB Remark 3 Added _refine.B_iso_mean Added _refine.ls_percent_reflns_obs Added _refine.ls_R_factor_R_free_error Added _refine.ls_R_factor_R_free_error_details Added _refine_ls_shell.percent_reflns_obs Added _refine_ls_shell.R_factor_R_free_error Added _refine_ls_shell.redundancy_reflns_all Added _refine_ls_shell.redundancy_reflns_obs Added _refine.ls_redundancy_reflns_all Added _refine.ls_redundancy_reflns_obs Added _reflns.observed_criterion_sigma_F Added _reflns.observed_criterion_sigma_I Added REFINE_LS_RESTR_NCS category Added _refine.solvent_model_details Added _refine.solvent_model_param_bsol Added _refine.solvent_model_param_ksol |
mmcif_std.dic |
| 0.8.10 | 1997-01-22 | Changes (PMDF): + Still more changes to align with new core: Added _refine.ls_R_Fsqd_factor_obs Added _refine.ls_R_I_factor_obs Added _atom_site.disorder_assembly Added new definition of _atom_site.disorder_group Many more style and wording changes Changes to provide compatibility with PDB Remark 3 Added _chem_comp_chir_atom.comp_id Added _diffrn.ambient_temp_details Added _exptl_crystal_grow.temp_details Enlarged enumeration list of _phasing.method Added _reflns.Rmerge_F_all Added _reflns.Rmerge_F_obs Added _reflns.B_iso_Wilson_estimate Added _reflns.percent_possible_obs Added _refine_ls_restr.weight Added _refine.aniso_B data items Added _exptl_crystal.density_matthews Added _refine.ls_percent_reflns_R_free Added _refine_ls_shell.percent_reflns_R_free Added _refine.Luzzati_coordinate_error_obs Added _refine.Luzzati_d_res_low_obs Added _refine.Luzzati_sigma_a_obs Added _refine.Luzzati_sigma_a_obs_details Added _refine.Luzzati_coordinate_error_free Added _refine.Luzzati_d_res_low_free Added _refine.Luzzati_sigma_a_free Added _refine.Luzzati_sigma_a_free_details Added _refine.number_disordered_residues Added _refine.occupancy_sum_hydrogen Added _refine.occupancy_sum_non_hydrogen |
mmcif_std.dic |
| 0.8.09 | 1997-01-07 | Changes (PMDF): + More changes to align with new core: Changed _citation.book_coden_ISBN to _citation.book_id_ISBN Changed _citation.journal_coden_ASTM to _citation.journal_id_ASTM Changed _citation.journal_coden_CAS to _citation.abstract_id_ASTM Changed _citation.journal_coden_CSD to _citation.journal_id_CSD Changed _citation.journal_coden_ISSN to _citation.journal_id_ISSN Changed _citation.medline_AN to _citation.database_id_Medline Added _publ.requested_category Corrected alias for _atom_type.scat_length_neutron Added _journal.data_validation_number Changed _diffrn_detector.detector_specific to _diffrn_detector.type Deleted _diffrn_detector.detector_type Added _diffrn_radiation.probe Adjusted definition of _diffrn_radiation.type Changed _diffrn_source.source_specific to _diffrn_source.type Deleted old _diffrn_source.type Changed _diffrn_radiation_wavelength.wavelength_wt to _diffrn_radiation_wavelength.wt Added _diffrn_radiation.xray_symbol Aliased both versions 1.0 and 2.0 of the core for _diffrn_detector.detector _diffrn_detector.dtime _diffrn_source.source |
mmcif_std.dic |
| 0.8.08 | 1997-01-06 | Changes (PMDF): + Added R_work data items to the various REFINE categories + Rewrote definitions for existing R-factor definitions to distinguish between R_work, R_free and conventional R Changes (JDW) (retrieved from earlier, misplaced version): + Added data item _chem_comp.mon_nstd_parent_comp_id to provide explicit reference between a nonstandard component and the parent component. + Changed _item_type.code for _chem_comp.id and all of its children to 'ucode'. + Changed char3 and char1 to uchar3 and uchar1 to be consistent with other case insensitive data type codes. Corrected the regular expressions and primitive codes for these data types. + Added _chem_comp_atom.partial_charge. + Corrected the descriptions for _chem_comp_tor.comp_id, _chem_comp_bond.comp_id and _chem_comp_angle.comp_id. + Added _chem_comp_tor_value.comp_id as a key for category CHEM_COMP_TOR_VALUE. + Added _chem_comp_plane_atom.comp_id as a key in category CHEM_COMP_PLANE_ATOM. + Miscellaneous corrections in item descriptions in CHEM_COMP_GROUP categories. + Added item _chem_comp_plane_atom.dist_esd |
mmcif_std.dic |
| 0.8.07 | 1996-12-18 | Changes (PMDF): + Removed single quote from value of DDL items where they were not needed + Cleaned up style of range minimum/maximum data value + Cleaned up alignment of various DDL items + Deleted _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd |
mmcif_std.dic |
| 0.8.06 | 1996-11-13 | Changes (JDW): + Reorganized categories in the DIFFRN group to formally support multiple diffraction data sets. |
mmcif_std.dic |
| 0.8.05 | 1996-11-11 | Changes (PMDF): + More changes to bring this dictionary into alignement with the extended core + Added _chemical_forumula.iupac + Added _atom_site.B_equiv_geom_mean (and its esd) + Added _atom_site.U_equiv_geom_mean (and its esd) + Added _atom_type.scat_length_neutron |
mmcif_std.dic |
| 0.8.04 | 1996-11-04 | Changes (PMDF): + Changed format of references in data item definitions to match style of extended core. + Changed format of matrices in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Changed format of equivations in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Added aliases to data items where they were missing to establish correspondence with extended core. + Changed frac to fract in _atom_site.frac... data items. + Added _citation_editor_ordinal. + Added JOURNAL_INDEX data items, as well as _journal.language and _journal.paper_category. + Added _diffrn_measurement_specimen_support _diffrn_orient_refln_angle_omega _diffrn_orient_refln_angle_theta + Added PUBL_BODY category and data items. + Added _publ.contact_author_address _publ.contact_author_name + Added _publ.section_exptl_solution _publ.section_synopsis _publ.section_title_footnote + Added AUDIT_CONFORM category and data items. + Added GEOM_HBOND category and data items. |
mmcif_std.dic |
| 0.8.03 | 1996-04-03 | Changes (PMDF): + Began implementing changes to bring this dictionary into alignment with the current version of the CIF core dictionary. These differences were provided by Brian McMahon and I. David Brown. As most of these changes are matters of style and not substance, they will not be noted individually here. Anything that does involve substance will be. + Changed specification of the format of names to included that provision for a dynanastic modifier. |
mmcif_std.dic |
| 0.8.02 | 1996-03-18 | Changes (PMDF): + Changed category from chem_comp to chem_comp_link for data items _chem_comp_link.type_comp_1 and _chem_comp_link.type_comp_1 in the parent/child tree for the chem_comp.type data item. + Added _struct_ref_seq.seq_align_beg and _struct_ref_seq.seq_aling_end to the mandatory code table for _entity_poly_seq.num. + Added _struct_ref_seq_dif.seq_num to both the parent/child and mandatory code tables for _entity_poly_seq.num. + Added data item _struct_ncs_oper.code. + Changed units type to 8pi2_angstroms_squares for _atom_site.B_iso_or_equiv and _atom_site.B_iso_or_equiv_esd. + Moved TVECT vector from DATABASE_PDB_MATRIX to a new category DATABASE_PDB_TVECT and added a identifier and details item to this new category. The matrix component of TVECT has been removed. |
mmcif_std.dic |
| 0.8.01 | 1996-03-12 | Changes (PMDF): + Added missing circumflex to definition of _exptl_crystal.density_percent_sol. + Fixed erroneous reference to _atom_site.entity_seq_num in definition of _atom_site.auth_seq_id. + Changed _chem_comp_link.id to _chem_link.id in definition of _chem_comp_link.link_id. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD in citation category example + Changed _entity_link.id to _chem_link.id in definition of _entity_link.link_id. + Changed _chem_link.type_comp_1 to _chem_comp_link.type_comp_1 in _item_name and parent/child tables for _chem_comp.type. The same change was made for component 2. |
mmcif_std.dic |
| 0.8.0 | 1996-03-06 | Changes (PMDF, HB, JDW): + Added unit type 8pi2_angstroms_squared B anisotropic temperature factors, and added conversion factor for this new unit type in the ITEM_UNITS_CONVERSION category. + Changed _item_type.code for _symmetry_equiv.id to 'code' + Added default value 'no' to _chem_comp.mon_nstd_flag. |
mmcif_std.dic |
| 0.7.34 | 1996-02-20 | Changes (JDW): + Integrated STRUCT_REF, STRUCT_REF_SEQ and STRUCT_REF_SEQ_DIF from PMDF. + Removed ENTITY_REFERENCE and ENTITY_POLY_SEQ_DIF. + Integrated modified categories STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, and STRUCT_NCS_OPER from PMDF. + changed _item_type.code's 'char' and 'uchar' to 'line' and 'uline'. |
mmcif_std.dic |
| 0.7.33 | 1996-02-19 | Changes (JDW): + Replaced category COMP_PROG with category SOFTWARE supplied by P. Bourne. + Fine tuned some values of _item_type.code. Fixed regular expression for code and ucode. |
mmcif_std.dic |
| 0.7.32 | 1996-02-17 | Changes (JDW): + atom_site.entity_id renamed atom_site.label_entity_id. + atom_site.entity_seq_num deleted. + added items _atom_site.auth_asym_id, _atom_site.auth_atom_id, _atom_site.auth_comp_id, and _atom_site.auth_seq_id. These items provide placeholders for alternative nomenclature that may be used by the author. + Set the parentage for _atom_site.label_seq_id to _entity_poly_seq.num. All components of the atom site label (_atom_site.label_*) are now linked to the mmCIF hierarchical description of structure. The data items in _atom_site.auth_* may be used by authors to provide alternative identifiers in the atom site which conform with the scheme that is used in the publication of the structure. + added category group mm_atom_site_auth_label + added auth_asym_id, auth_atom_id, auth_comp_id, and auth_seq_id child data items to the categories: GEOM_ANGLE,GEOM_BOND, GEOM_CONTACT, STRUCT_CONF, STRUCT_CONN, STRUCT_MON_NUCL, STRUCT_PROT, STRUCT_PROT_CIS, STRUCT_NCS_DOM_GEN, STRUCT_SHEET_HBOND, STRUCT_SHEET_RANGE, and STRUCT_SITE_GEN. |
mmcif_std.dic |
| 0.7.31 | 1996-02-12 | Changes (JDW): + Added data items for _database_pdb_matrix.tvect_matrix[][] and _database_pdb_matrix.tvect_vector[]. + Generalized category CHEM_LINK to handle descriptions of a any type of linkage. Created CHEM_COMP_LINK to describe linkages between components, and ENTITY_LINK to describe linkages between entities (and within entities between nonsequential components). Both CHEM_COMP_LINK and ENTITY_LINK reference the linkage description in the CHEM_LINK_* categories. |
mmcif_std.dic |
| 0.7.30 | 1996-01-29 | Changes (PMDF, HB, JDW): + Added data items for pseudorotation in STRUCT_MON_NUCL. + Globally changed future tense usage to present tense (eg. will be -> is) + Added _citation.book_publisher_city. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD. + Added _citation.journal_coden_CAS. + Generalized the defintion of _atom_site.calc_flag. + Corrections to definitions defining beginning and ends of ranges in category STRUCT_SHEET_HBOND. + Added data items _diffrn_refln.scan_rate and _diffrn_refln.scan_time_backgd + Added HELX_LH_27_P and HELX_RH_27_P helix enumeration types. + Added figure of merit data item _refln.fom. |
mmcif_std.dic |
| 0.7.29 | 1995-12-11 | Changes (PMDF): + Changes to my title and Brian's in header information. + Enhanced description of the 'Hill system' of element ordering in the definition of _chem_comp.formula. + Added _item.mandatory_code to _phasing_mir_der.native_set_id + Added DATABASE_PDB_CAVEAT category. + Changed supercedes to superseded in DATABASE category description. + Changed DATABASE_NEW to DATABASE_2 in category description. + Changed SRUCT_SHEET_TOPOLOGY to STRUCT_SHEET_TOPOLOGY in category description. + Changed examples for STRUCT_SHEET_RANGE to contain only _struct_sheet_range.symmetry, not _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry + Added cell.Z_PDB data item + Changed _atoms_sites.Cartn_tran_matrix to atom_sites.Cartn_transf_matrix in definition of _atom_sites.Cartn_transform_axes + Changed _chem_comp.nstd_class to _chem_comp.mon_nstd_class in definition of _chem_comp.mon_nstd_flag + Added data items for _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd + Changed reference to _chemical_formula.appendix to CHEMICAL_FORMULA category description in definition of _chemical_formula.moiety + Changed _comp.prog.version to _comp_prog.version and _comp.prog.citation_id to _comp_prog.citation_id in COMP_PROG example + Changed reference to _computing.phasing_mir in _phasing_mir.method to a reference to the COMP_PROG category. Similarly with _computing.phasing_averaging in _phasing_averaging.method and _computing.phasing_mad in _phasing_mad.method and _computing.save_reduction in _reflns.data_reduction_method + Changed _entity.name_com.name to _entity_name_com.name in ENTITY_NAME_COM example + Changed reference to _exptl_crystal.face_ to data items in the EXPTL_CRYSTAL_FACE category in the definition of _exptl_crystal.description. + Changed _diffrn.attenuator_code to _diffrn_attenuator.code in the definition of _diffrn_refln.attenuator_code + Changed _exptl.crystal_preparation to _exptl_crystal.preparation in the definition of _exptl.details + Changed _geom_bond.distance to _geom_bond.dist in the definition of _geom_bond.dist_esd + Added data items for _refine.ls_d_res_high and _refine.ls_d_res_low + Changed _refine.d_res_high to _refine.ls_d_res_high and _refine.d_res_low to _refine.ls_d_res_low in the definition of _refln.status + Changed _reflns_scale_group.code to _reflns_scale.group_code in the definition of _refln.scale_group_code + Changed _struct_site_view_details to _struct_biol_view.details in the rotation matrix element definitions in the STRUCT_BIOL_VIEW category (even though I realize that this isn't really correct in terms of the definition of _struct_biol_view.details) + Changed _symmetry.equiv_pos_as_xyz to _symmetry_equiv.pos_as_xyz in the definition of _symmetry.space_group_name_H-M + Changed _struct_mon.details_RSSR to _struct_mon_details.RSSR and _struct_mon.details_RSR to _struct_mon_details.RSR in a number of definitions in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories + Changed _reflns_shell.possible_%_obs to _reflns_shell.percent_possible_obs in the REFLNS_SHELL example + Corrected alphabetical order of data items in the REFLNS_SHELL category + Changed _struct_sheet.number_details to _struct_sheet.details in the STRUCT_SHEET examples + Replaced _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry with _struct_sheet_range.symmetry in the STRUCT_SHEET_RANGE category and fixed example itself + Changed _refine.ls_number_reflns to _refine.ls_number_reflns_obs in the definitions of _refine.ls_restrained_S_all and _refine.ls_restrained_S_obs + Changed _refine_ls_shell.reflns to _refine_ls_shell.number_reflns_obs in the REFINE_LS_SHELL example + Removed example from DATABASE category as it was not longer valid |
mmcif_std.dic |
| 0.7.28 | 1995-10-06 | Changes (PMDF): + Removed loop from category example for DATABASE_2 + Fixed data names in category example for STRUCT_KEYWORDS + Rewrote enumeration list for _struct_conf_type.id + Removed references to chemical_formula.appendix and replaced them with reference to the CHEMICAL_FORMULA category description + Added data items _chem_comp.formula and _chem_comp.formula_weight + Changed _chem_link_angle.atom_1_atom_id to _chem_link_angle.atom_id_1 + Changed _chem_link_angle.atom_2_atom_id to _chem_link_angle.atom_id_2 + Changed _chem_link_angle.atom_3_atom_id to _chem_link_angle.atom_id_3 + Changed _chem_link_bond.atom_1_atom_id to _chem_link_bond.atom_id_1 + Changed _chem_link_bond.atom_2_atom_id to _chem_link_bond.atom_id_2 + Realphabetized to accomodation the above changes + Added CHEM_LINK_CHIR category + Added CHEM_LINK_CHIR_ATOM category + Added CHEM_LINK_PLANE category + Added CHEM_LINK_PLANE_ATOM category + Added CHEM_LINK_TOR category + Added CHEM_LINK_TOR_VALUE category + Added entries to parent/child table for _chem_link.id for reflect the addition of the new categories. + Added Engh and Huber/Priestle examples to CHEM_LINK_BOND and CHEM_LINK_ANGLE + Realphabetized categories in PHASING_MAD section Changes (JDW): + Added _item_type.code's for _chem_link_chir*.atom_id and _chem_link_tor.atom_id_*. |
mmcif_std.dic |
| 0.7.27 | 1995-09-27 | Changes (JDW & SH): + Added _item_aliases.dictionary and _item_aliases.version to all alias items. + Added several missing aliases from cifdic.C94. + Added a few missing data type codes in chem_link_* + Modified all _item_range items to reflect the correction in DDL 2.1.1. Checked all of the boundary conditions on ranges. + Made corrections in virtually all of the regular expressions. + Added data types 'ucode' and 'uchar'. These are case insensitive character types for words and single line strings, respectively. The regular expressions for these items will match characters of upper and lower case but the primitive type is uchar so all comparisons are performed in upper case. This avoids problems with case, where case is really not important. + Reviewed all items with character data types and made the following changes (hopefully uniformly): - Data items with single word enumerates were set to type 'ucode'. - Data items with multi word enumerates were set to type 'uchar'. - Any item which could potentially exceed 80 characters was set to type text. - Items which are restricted to single words were set to type 'code'. - Items which are short strings which may not span lines were set to type 'char'. + Moved aliases for anisotropic temperature factors from category ATOM_SITE to ATOM_SITE_ANISOTROP + Added category DATABASE_PDB_MATRIX to hold the SCALE and ORIGX matrices/vectors. + Modified the defintions of data types 'char1' and 'char3' to permit leading '+' to indicate a modification. + Checked dictionary with SIFLIB and returned to Paula ... |
mmcif_std.dic |
| 0.7.26 | 1995-09-25 | Changes (PMDF): + Put single quotes around 5HVP in those examples where they were missing. + Fixed registration of '5VHP' in examples. + Fixed typos in definition of _diffrn_measurement.device_specific. + Added _item.name loop and parent-child tree to _chem_comp.type + Fixed _item.name for _phasing_mir_der.der_set_id + Fixed _item.name for _phasing_mir_der.native_set_id + Added _phasing_mir_der_refln.set_id to _item.name loops and parent-child tree of _phasing_set.id + Fixed two misspellings of reference (refence). |
mmcif_std.dic |
| 0.7.25 | 1995-08-31 | Changes (PMDF): + Eliminated duplicate line in _entry_id parent/child table + Changed the three occurrences of _item_type.code text to char _atom_sites_alt.details _atom_sites_alt_ens.details _database_PDB_remark.text + Fixed Klyne and Prelog reference in GEOM_TORSION category description + Added data item _chem_comp_chir.atom_config + Added hyphen in non-crystallographic in definition sof _struct_ncs_ens.point_group + Changed Data Base to Database when referring to the CSD + Fixed four occurrances of 'the the' in definitions + Added _item_range.maximum and _item_range.minimum DDL items to _refine.ls_abs_structure_Flack and removed discussion of limits from the definition. + Changed two occurances of 'will be' to 'are' in the definition of _entity.type. + Changed ENTITY_NPOL to CHEM_COMP in definition of _entity.type. + Changes ATOM to HETATM for APS coordinates in Example 1 for the ATOM_SITE category + Corrected _item.category_id for _struct_mon_details.prot_cis. + Corrected _item.category_id for _refine_hist.details. + Rewrote header comments to emphasize use of the mmCIF listserver as the forum for the dictionary review process. |
mmcif_std.dic |
| 0.7.24 | 1995-08-21 | Changes (PMDF): + Corrected category.id for data items in the DIFFRN_STANDARDS category + Corrected category.id for data items in the PHASING_MAD_EXPT category + Corrected category.id for selected data items in the PHASING_SET category + Corrected alias for _atom_site.thermal_displace_type + Introduced alias of _atom_site_aniso_label for _atom_site_anistrop.id + Introduced alias of _atom_site_aniso_type_symbol for _atom_site_anisotrop.type_symbol |
mmcif_std.dic |
| 0.7.23 | 1995-08-10 | Changes (PMDF): + Changed _struct_sheet_gen.label_seq_id to _struct_site_gen.label_seq_id in _atom_site.label_seq_id tree + Removed duplicate entry of _phasing_MIR.entry_id in _entry.id tree + Removed alias in definitionof _refln.A_meas_au + Removed _item.category_id from _chem_link.type_comp_1 _chem_link.type_comp_2 _phasing_mad_clust.expt_id _phasing_mad_set.clust_id _phasing_mad_set.expt_id _phasing_mad_set.set_id _phasing_mad_ratio.expt_id _phasing_mad_ratio.clust_id _phasing_mad_ratio.wavelength_1 _phasing_mad_ratio.wavelength_2 + Removed _item_type.code from most of the above (it wasn't there in all of them). + Added _item.mandatory_code to _phasing_mir_der.der_set_id + Corrected _item.name for _phasing_mad_ratio.wavelength_2 |
mmcif_std.dic |
| 0.7.22 | 1995-08-09 | Changes (PMDF): + Added definitions for _chem_link_angle.link_id and _chem_link_bond.link_id + Straighted out spacing inconsistencies with _item.mandatory_code + Another quick pass at spell checking |
mmcif_std.dic |
| 0.7.21 | 1995-08-08 | Changes (PMDF): + Added _citation_author.ordinal and updated examples to reflect this addition. + Changed _item.mandatory_code for _citation_author.name to 'yes'. + First pass at checking the dictionary for spelling - lots of little changes in lots of places. + Removed many occurrences of 'with with' in definitions. |
mmcif_std.dic |
| 0.7.20 | 1995-08-02 | Changes (PMDF): + Enforced 80 character per line limit throughout. + Realphabetized _geom_angle.value and _geom_angle.value_esd. + Realphabetized _geom_torsion.value and _geom_torsion.value_esd. + Removed trailing blanks. + Fixed a couple of problems with missing terminal '. |
mmcif_std.dic |
| 0.7.19 | 1995-07-23 | Changes (JDW & PMDF): + Minor corrections in sheet example and version update. + Removed illegal characters from data item names. Changed any "/" in data item names to "_over_". |
mmcif_std.dic |
| 0.7.18 | 1995-07-20 | Changes (JDW): + Added '_struct_biol_gen.symmetry' to the key on struct_biol_gen. + Changed category block to entry. + Added _dictionary.datablock_id + Replace publ_group and journal_group with category group named iucr_group + Added category group named pdb_group + Removed all the _atom_site.label references and repointed any references to this item to _atom_site.id. + Added optional atom identifiers to all of the GEOM categories. + Added translation vector to transformations in ATOM_SITES + Created subcategories for matrices and vectors + Moved _struct.keywords to a new category STRUCT_KEYWORDS + Added pointer to exptl_crystal.id as part of key in category EXPTL_CRYSTAL_GROW_COMP. + Restructured DATABASE_PDB_REMARK category + Changed alternate_exclusive to replaces and replacedby in DATABASE and DATABASE_2 + Restructured examples in _chem_comp.one_letter_code ... + Added data item _chem_comp.three_letter_code + Made atom_site.label_alt_id and its children an optional item + Changed item names _atom_sites.frac_tran_* _atom_site.frac_transf_* and _atom_sites.Cartn_tran_* _atom_site.Cartn_transf_* + Changed the key of ATOM_SITE_ANISOTROP to _atom_site_anisotrop.id + Added all of the GEOM category atom label items to their appropriate parent data items. + 'arbitrary' added to list of item_units_list.code's + Fixed conflicting mandatory codes... |
mmcif_std.dic |
| 0.7.17 | 1995-05-22 | Changes (PMDF): + Added _phasing_MIR_refln.F_meas_au and _phasing_MIR_refln.F_meas_au_sigma and adjusted appropriate _item.related DDL Added _refln.F_meas_au and _refln.F_meas_au_sigma and adjusted as above Added _phasing_MIR_refln.F_calc_au and adjusted as above Added _refln.F_calc_au and adjusted as above Added _refln.A_calc_au and adjusted as above Added _refln.B_calc_au and adjusted as above Added _refln.A_meas_au and adjusted as above Added _refln.B_meas_au and adjusted as above Changed _item_related.function_code from 'replace' to 'alternate_exclusive' in database_2 data items Added _item_related DDL to appropriate _database data items |
mmcif_std.dic |
| 0.7.16 | 1995-05-18 | Changes (PMDF): + Added _item.name DDL to those data items that didn't have it Wrote program to check that the added names were all correct Fixed problems that turned up (including one missing . in _diffrn_radiation_detector_details |
mmcif_std.dic |
| 0.7.15 | 1995-05-18 | Changes (PMDF): + Added DDL linking data names that are value to the data names that are esds of those values Changed _geom_bond.distance to _geom_bond.dist and _geom_bond.distance_esd to _geom_bond.dist_esd Changed _geom_contact.distance to _geom_contact.dist and _geom_contact.distance_esd to _geom_contact.dist_esd Changed _cell_measurement.temperature to _cell_measurement.temp and _cell_measurement.temperature_esd to _cell_measurement.temp_esd Changed _diffrn.ambient_temperature to _diffrn.ambient_temp and _diffrn.ambient_temperature_esd to _diffrn.ambient_temp_esd |
mmcif_std.dic |
| 0.7.14 | 1995-05-03 | Changes (PMDF): + Fixed definitions of _phasing_MIR_refln.index_k and _phasing_MIR_refln.index_l |
mmcif_std.dic |
| 0.7.13 | 1995-04-20 | Changes (PMDF): + Changed all matrices back to element by element representation. + Reworded definitions of B and U matrices to clarify alternate exclusive relationship + Changed 'miller' to 'Miller' in some definitions, but left it 'miller' in data values. + Changed 'CIF' to 'data bock' where appropriate. + Made changes according to notes from last Rutgers meeting. Mostly this is clearer wording of definitions. Made formal Ref: for scattering factors. Changed atom_site.description to atom_site.details Expanded definitions for the components of the atom site label. Added disclaimer to some records in ATOM_SITE and ATOM_SITES categories. Changed _atom_type.analytical_mass_% to _atom_type.analytical_mass_percent Expanded definition of AUDIT category Added separate esd data items to examples in CELL category Added real formula in definition of _cell.volume Moved disclaimer to the top in CHEMICAL categories Changed enumeration to example in _chem_comp.one_letter_code Changed _phasing_MIR_refln.F_sigma to _phasing_MIR_refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _phasing_MIR_refln.F_meas Changed refln.observed_status to refln.status in example Changed _refln.F_sigma to _refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _refln.F_meas |
mmcif_std.dic |
| 0.7.12 | 1995-02-09 | Changes (JDW): + Changed _atom_site.label_res_id to _atom_site.label_comp_id which is a child of _chem_comp.id. + Changed all children items named label_res_id to label_comp_id + Changed descriptions of many label_comp_id to reference correct parent item. (_atom_site.label_comp_id rather than comp_comp.id). + Changed ENTITY_MON to CHEM_COMP and removed polymer component specific terminology. + Changed ENTITY_LINK to CHEM_LINK and removed polymer component specific terminology. + Added data type for yyyy-mm-dd and applied this where appropriate. + Added chem_comp_group and chem_link_group to the category group list. + Added '_' prefix to all data item save frame names. |
mmcif_std.dic |
| 0.7.11 | 1995-02-07 | Changes (PMDF): + Finished standardizing style of equations in definitions Moved ITEM_TYPE_LIST to bottom of dictionary Moved ITEM_UNITS_LIST to bottom of dictionary Moved ITEM_STRUCTURE_LIST to bottom of dictionary Moved DICTIONARY_HISTORY to bottom of dictionary (it will come back up to the top with version 1.0.0) Rewrote dictionary header comments to reflect this dictionary |
mmcif_std.dic |
| 0.7.10 | 1995-02-03 | Changes (PMDF): + Removed loop_ construction from loop_ or order one, except not for category examples and not for parent/child loops Standardized style of yes/no enumeration lists Made style of all enumeration lists more standard (still not happy here) Standardized style of examples Standardized style of references in definitions Began standardizing style of equations in definitions |
mmcif_std.dic |
| 0.7.9 | 1995-01-30 | Changes (PMDF): + Fixed syntax errors unearthed by checking of JW and PDB |
mmcif_std.dic |
| 0.7.8 | 1995-01-25 | Changes (PMDF): + Added _entity_mon.type, _entity_mon.number_atoms_all, _entity_mon.number_atoms_nh, _entity_mon.one_letter_code Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd, _entity_mon_bond.value_dist_esd Added _entity_mon_atom.type_energy, but since this is intended to be a pointer to a category (_atom_type_energy) that doesn't exist yet, have left it commented out Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and _entity_mon_chir.volume_flag Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh Added _entity_mon_chir_atom.dev Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd Added ENTITY_LINK category Added ENTITY_LINK_ANGLE category Added ENTITY_LINK_BOND category Changes (HB et al.): + Added STRUCT_MON_NUCL category Changes (PMDF): + Added label links from STRUCT_MON_NUCL to rest of dictionary Added label links from STRUCT_MON_PROT as well (forget them initially) |
mmcif_std.dic |
| 0.7.7 | 1995-01-18 | Changes (PMDF): + Added PHASING_MIR_REFLN category |
mmcif_std.dic |
| 0.7.6 | 1995-01-17 | Changes (PMDF): + Added ENTITY_SRC_NAT category Added ENTITY_SRC_GEN category Added ENTITY_NAM_COM category Added ENTITY_NAM_SYS category Added _entity.src_method data item Moved other entity data items to new categories as appropriate |
mmcif_std.dic |
| 0.7.5 | 1995-01-13 | Changes (PMDF): + Provided for sequence microheterogeneity by making _entity_poly_seq.mon_id part of the category key and by adding the data item _entity_poly_seq.hetero as a flag Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer in referenced data items. Added _entity_mon_atom.alt_atom_id. Added COMP_PROG category Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR) |
mmcif_std.dic |
| 0.7.4 | 1995-01-12 | Changes (PMDF): + Finished working on STRUCT_MON_PROT category Added STRUCT_MON_DETAILS category Added STRUCT_MON_PROT_CIS category Added STRUCT_NCS_ENS category Added STRUCT_NCS_ENS_OPER category Added STRUCT_NCS_DOM category Added STRUCT_NCS_DOM_GEN category Added equations to definitions of _phasing_MIR_der_shell.fom and _phasing_MIR_shell.fom Added REFINE_HIST category |
mmcif_std.dic |
| 0.7.3 | 1994-12-22 | Changes (PMDF): + Fixed things turned up by JDW checking of 0.7.2 Couple of small typos Added angstroms_cubed to units list and conversion tables Added _phasing_MIR_site.atom_type_symbol and added this reference to the table until _atom_type.symbol Added _entity_mon_atom.substruct_code Began adding STRUCT_MON_PROT, but this is not yet complete |
mmcif_std.dic |
| 0.7.2 | 1994-12-20 | Changes (PMDF): + Merged JDW changes with version 0.6.12 Changed _item_type.code of numb to either int or float Changed _item_description.description to category.description where appropriate Fixed a bunch of pure syntax errors Removed 'refln_scale_group' from list of category groups. Changed _refln_scale_group_code to _refln.scale_group_code somewhere Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere Reformatted CATEGORY_GROUP_LIST items to match style of other header categories Ensures that all _category data items obey they rule of first alphabetic character is column 34 (most didn't before this check) Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the rest) data items, and added wording to description that these items are only there for compliance via the alias (but left in the one _item_related thing that made the matrix element data item alternate exclusive to the full matrix data item Added language about compliance to _atom_sites.Cartn_tran_matrix Added language about compliance to _diffrn_orient_matrix.UB Added language about compliance to _diffrn_reflns.transf_matrix Removed matrix element data items for _atom_sites.fract_tran_matrix - this wasn't in c91 and so doesn't need aliasing |
mmcif_std.dic |
| 0.7.1 | 1994-12-19 | Changes (JDW): + First pass through SIFLIB checking tools. Corrected syntax errors and missing parent references. |
mmcif_std.dic |
| 0.6.14 | 1994-12-19 | Changes (PMDF): + Changed refine.ls_number_reflns to refine.ls_number_reflns_obs Added refine.ls_number_reflns_all Added refine.ls_number_reflns_R_free Changed _refln.observed_status to refln.status Expanded enumeration list to include resolution limits and R-free flag Rewrote definition Eliminated refln.R_free_status Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs Changed _refine_ls_shell.number_R_free to _refine_ls_shell.number_reflns_R_free Added PHASING category Filled in and reformatted units conversion table |
mmcif_std.dic |
| 0.6.13 | 1994-12-16 | Changes (PMDF): + Added data item _refln.R_free_status Added data item _reflns.R_free_details Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs Added _refine_ls_shell.number_R_free Added _refine_ls_shell.number_all Added _refine_ls_shell.R_factor_R_free Added _refine_ls_shell.wR_factor_R_free Tidied up the count and R-factor descriptions in REFINE_LS_SHELL Added appropriate item_related names to the R-factors in REFINE_LS_SHELL Changed 'count' to 'number' in several data names Changed _reflns.number_total to _reflns.number_all Changed _reflns.number_observed to _reflns.number.obs Added _refine.ls_R_factor_R_free Added _refine.ls_wR_factor_R_free Edited descriptions of the other R-factor data items in the REFINE category to conform to the style in REFINE_LS_SHELL Re-alphabetized the things I changed yesterday from special_details to details - I had forgotten to do that yesterday |
mmcif_std.dic |
| 0.6.12 | 1994-12-15 | Changes (PMDF): + Changed _enumeration_default.code to _item_default.value Changed _enumeration_default.value to _item_default.value Changed _enumeration.code to _item_enumeration.value Changed _enumeration.detail to _item_enumeration.detail Changed _enumeration.case to _item_enumeration.value Changed _enumeration_limit.maximum to _item_range.maximum Changed _enumeration_limit.minimum to _item_range.minimum Checked that matrix were properly labeled as either rw_rowwise or just plan rowwise. Reworded matrix descriptions for consistency. Got rid of the last of the a.b_* constructions in descriptions Added cell_length, cell_length_esd, cell_angle and cell_angle_esd subcategories Changed special_details to details for core items - original names retained in aliases Added atom_site.id Added mm_atom_site_label subcategory Commented out _atom_site.label_component until it can be dealt with properly Changed 'SIF' to 'data block' in a number of descriptions. |
mmcif_std.dic |
| 0.6.11 | 1994-12-14 | Changes (PMDF): + Fixed R-Kraut reference Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol Included full formula for this calculation in description Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target Improved wording of all definitions in REFINE_LS_RESTR Explained sums in _reflns_shell.Rmerge_I_obs and related data items |
mmcif_std.dic |
| 0.6.10 | 1994-12-13 | Changes (PMDF): + Established check-list for unfinished tasks and began dealing with them Added enumeration limits of 0 and 1 and enumeration default of 1.0 to occupancy data items Left heavy-atom maximum with an enumeration of ? Added enumeration default of 1_555 to all _symmetry data items where it was missing Changed 'connect type' to 'interaction' in _struct_conn_type data items. Filled out sub_category ddl items for cartesian coordinates, fractional coordinates, cartesian coordinates esds, and Miller indices. |
mmcif_std.dic |
| 0.6.9 | 1994-12-09 | Changes (PMDF): + Added _esd data items where needed Rationalized descriptions for all of the coordinate data items |
mmcif_std.dic |
| 0.6.8 | 1994-12-08 | Changes (PMDF): + Created ATOM_SITE_ANISOTROP category to provide for ability to have anisotropic data is a separate loop, if desired. Checked and fixed a bunch of style things Added item_units.code of degrees in data items with degrees in the description but not in the ddl Added item_units.code of kelvin in data items with kelvin in the description but not in the ddl (and added 'in degrees kelvin' to the description of those with item_units.code of kelvin but no corresponding phrase in the description) Added item_units.code of microseconds to _diffrn_radiation.detector_dtime (added to units list at same time) Added 'in minutes' to description of _diffrn_refln.elapsed_time Added 'in kilopascals' to to the description of those with item_units.code of kilopascals but no corresponding phrase in the description Added BLOCK category Added appropriate pointers (in category key, and with a data item pointing to _data_block.id) in all categories that needed them |
mmcif_std.dic |
| 0.6.7 | 1994-12-07 | Changes (PMDF): + Created DATABASE_NEW category to solve logical problems with old DATABASE category. Need to think some more about how old data items are handled. Added aliases for remaining c91 data items Changed geom_angle to geom_angle.value (aliased to original name) Changed geom_torsion to geom_torsion.value (aliased to original name) Returned ATOM_SITE items taken out during ATOM_SITE_MM transition |
mmcif_std.dic |
| 0.6.6 | 1994-12-06 | Changes (PMDF): + Finished conversion of _list_link_parent items to appropriate new DDL relationships Filled out category_key.id items in each category Had to add diffrn_refln.id item, as cannot use h k l in that category (perfectly valid to measure same reflection more than once). Used _diffrn_standard_refln.code in that category - this may cause a problem with old files, as example file did not give this data item Moved _entity_poly items back to _entity category Moved _entity_poly.formula_weight to entity.formula_weight Used _exptl_crystal.id in that category - this may cause a problem with old files, as example file did not give this data item Added _exptl_crystal_grow.crystal_id in that category Added _symmetry_equiv.id in that category - this may cause a problem with old files, as this is a new data item |
mmcif_std.dic |
| 0.6.5 | 1994-12-02 | Changes (PMDF): + Began implementation of new scheme for relationships in the entity category All entities will be treated as polymers - non-polymers will have a number of monomers of 1 All data items in ENTITY_NPOL categories are eliminated All data items in ENTITY_POLY category are moved to ENTITY |
mmcif_std.dic |
| 0.6.4 | 1994-12-01 | Changes (PMDF): + Began conversion of _list_link_parent items to appropriate new DDL relationships |
mmcif_std.dic |
| 0.6.3 | 1994-11-30 | Changes (PMDF): + Finished conversion of units data items Added a number of unit types to the table Conversation table still need to be fleshed out Removed _list_mandatory and changed _item_mandatory.code to yes for those data items |
mmcif_std.dic |
| 0.6.2 | 1994-11-28 | Changes (PMDF): + Made loop_ _item.name data items into separate data items This involved rewriting the definitions of most of them. In doing so I continued to eliminate the a.b_* construction. Added unit type of degrees. Added unit type of minutes. Added unit type of electrons. |
mmcif_std.dic |
| 0.6.1 | 1994-11-21 | Changes (JDW): + Converted dictionary and dictionary_history categories. Incorporated core dictionary history list into the new history list in the revision 0.5.1 where the dictionary merger is firsted discussed. |
mmcif_std.dic |
| 0.5.5 | 1994-11-15 | Implementation of DDL 2.0.7 dictionary wide - PMDF Finished putting .'s in itme names Changed _diffrn_measure_ to _diffrn_measurement. Changed _diffrn_rad_ to _diffrn_radiation. <saved newddl_all_4 at this point> Implemented category and ID pointers for entity category. Found all sorts of errors while doing this, and attempted to fix them consistently. Did not remove child data Items, even though they don't have to be specified - they should help keep all of this straight during the transition. Some silly reformatting to ensure that data values always have the first alphabetic character in column 33. More silly reformatting to put each example in an example loop on a separate line. <saved newddl_all_4 at this point and sent copy to JW> |
mmcif_std.dic |
| 0.5.4 | 1994-11-14 | Implementation of DDL 2.0.7 dictionary wide - PMDF Changed _enumeration to _enumeration.code Changed _enumeration_detail to _enumeration.code_detail Changed _enumeration_default to _enumeration_default.code Put .'s in item names (incomplete) Moved _PDB back to appropriate place in item names in the _database_remark_PDB_ and _database_rev_PDB_ and _database_rev_record_PDB_ categories Changed database_rev_PDB to database_PDB_rev Changed database_remark_PDB to database_PDB_remark Changed database_rev_record_PDB to database_PDB_rev_record Changed category items from item to category Began getting rid of *_whatever construction in category and item descriptions <saved newddl_all_3 at this point> |
mmcif_std.dic |
| 0.5.3 | 1994-11-13 | Implementation of DDL 2.0.7 dictionary wide - PMDF Finished merging [] and [mm] sections <Saved newddl_all_1 at this point> Changed data_ to save_ everywhere Changed _name to _item.name everywhere Added _item.mandatory_code everywhere Added save_ everywhere Moved _description to top of _save frame everywhere Changed _example to _item_examples.case everywhere Changed _example_detail to _item_examples.detail everywhere Changed _description to _item.description.description everywhere Removed _list yes everywhere Removed _list_reference everywhere Changed _enumeration_range to enumeration_limit.minimum and enumeration_limit.maximum everywhere <saved newddl_all_2 at this point> |
mmcif_std.dic |
| 0.5.2 | 1994-11-09 | Implementation of DDL 2.0.7 in CITATION category - PMDF & JW |
mmcif_std.dic |
| 0.5.1 | 1994-10-10 | Implementation of Treaty of Brussels - PMDF Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary dated 1994-05-20. The history records for the core dictionary are included here to identify the version of the core that was merged: _dictionary_name cifdic.c94 _dictionary_version 2.0 _dictionary_update 1994-03-01 _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 fine tuning 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 -------------- Removed all mm sections that enumeration items present in core but not present in mm dictionary. Fixed errors with missing trailing _'s in some category headers Also unbalanced ##'s in same place Removed "End of Example" statement everywhere Standardized syntax for missing examples Standardized syntax and style for category _definition data items. Added a bunch of ending dashed lines where they were missing. <Saved Brussels_airplane_1 at this point and began new file.> Merged [] and [mm] category explanation sections. Made HIV example always example 1, moved examples from core (where they were different from the HIV example) to higher numbers. <Saved Bussels_airplane_2 at this point - [] and [mm] sections not yet completely merged.. |
mmcif_std.dic |
| 0.4.3 | 1994-03-28 | Various changes following suggestions by IDB - PMDF Changed _entity_mon_angle_value to _entity_mon_angle_value_angle in example Changed _entity_npol_bond_value to _entity_npol_bond_value_dist Changed nonp to npol in _entity_npol_tor_value category Reworded angle _enumeration_details in _refine_ls_restr_type Reworded definitions in _struct_asym_[mm] and _struct_biol_[mm] Reworded definitions of _struct_conn_symmetry_* _struct_site_gen_symmetry _struct_biol_gen_symmetry Split _struct_conn_symmetry_* into _struct_conn_ptnr1_symmetry and _struct_conn_ptnr2_symmetry Split _struct_conn_role_* into _struct_conn_ptnr1_role and _struct_conn_ptnr2_role Removed _list_link_child from _struct_conn_conn_type_id Added _list_link_child to _struct_conn_type_id |
mmcif_std.dic |
| 0.4.2 | 1994-02-25 | Corrected spelling errors found by BMcM - PMDF |
mmcif_std.dic |
| 0.4.1 | 1994-02-04 | Major modifications of _entity_ subcategories - PMDF Added angles, planes, torsion angles and chiral centers to _entity_mon_ and _entity_npol_ Added many missing definitions Added many missing examples |
mmcif_std.dic |
| 0.3.14 | 1994-01-26 | Lots more re-alphabetization - PMDF Changed non_s to nstd throughout - PMDF Changed nonp to npol throughout - PMDF Removed all multiple spaces - PMDF Fixed a couple of alignment problems - PMDF |
mmcif_std.dic |
| 0.3.13 | 1994-01-13 | Rationalization of categories between mm and core dicts - BMcM Deleted _diffrn_crystal_environment (same as core _diffrn_ambient_environment) and moved other _diffrn_crystal items to core - BMcM Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM Some re-alphabetization - BMcM |
mmcif_std.dic |
| 0.3.12 | 1993-12-23 | Broke out examples from intro sections to loop_ _item_examples.case _example_detail construction - BMcM |
mmcif_std.dic |
| 0.3.11 | 1993-12-22 | Made a number of fixes relayed by PEB from MS AND RH _type of _atom_site_footnote_id (numb->char) - PMDF _type of _database_rev_record_rev_num_PDB (char->numb) - PMDF _type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF _atom_sites_fract_tran_matrx to _matrix - PMDF _type of _phasing_MIR_site_details (numb->char) - PMDF _example of _struct_conf_type_reference - PMDF |
mmcif_std.dic |
| 0.3.10 | 1993-12-15 | Various changes following suggestions from BMcM Refined definition of _atoms_site_label_atom_id - PMDF Removed _atom_sites_fract_tran (moved to core) - PMDF Changed _diffrn_crystal_physical_device to _diffrn_crystal_support - PMDF Changed _diffrn_measure_device_part to _diffrn_measure_device_specific - PMDF Changed _diffrn_rad_detector_part to _diffrn_rad_detector_specific - PMDF Changed _diffrn_rad_source_part to _diffrn_rad_source_specific - PMDF Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF Fixed several occurrences of \&A instead of \%A - PMDF |
mmcif_std.dic |
| 0.3.9 | 1993-12-02 | Deleted section summarizing categories - PMDF Returned definitions for most *_[mm] sections - PMDF Added _list and _list_level to global - PMDF Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF Checked lists of data items in core, fixing some problems with missing names and alphabetization - PMDF Resorted some categories to correct alphabetization - PMDF Changed form and definitions of _database_remark_num_PDB and _database_remark_text_PDB - PMDF Added data item _database_rev_replaced_by_PDB - PMDF Reordered data items in _citation example - PMDF Added data item _exptl_crystal_density_%_sol - PMDF |
mmcif_std.dic |
| 0.3.8 | 1993-11-30 | Moved _audit_author_, _citation_ categories to CIF core Definitions and small-molecule examples removed from *_[mm] sections that don't extend core categories - BMcM |
mmcif_std.dic |
| 0.3.7 | 1993-11-16 | Changed form of dates in _update_history to CIF style Changed ? to . in examples, where appropriate Added _example_detail to _refine_ls_restr_type Expanded definition of _refine_ls_restr_type |
mmcif_std.dic |
| 0.3.6 | 1993-10-10 | Changed *_appendix to *_[mm] throughout Removed 'Need example here' from _chemical_[mm] Removed 'Need example here' from _chemical_conn_atom_[mm] Removed 'Need example here' from _chemical_conn_bond_[mm] Moved _PDB to end of all relevant data names (except _[mm]) Added _database_rev_record_details_PDB data name Changed _refine_occupancy_limit_high to _refine_occupancy_max Changed _refine_occupancy_limit_low to _refine_occupancy_min Changed _refine_B_iso_limit_high to _refine_B_iso_max Changed _refine_B_iso_limit_low to _refine_B_iso_min Changed all definitions and examples in _refine_iso_B_ category to _refine_B_iso_ equivalents |
mmcif_std.dic |
| 0.3.5 | 1993-09-08 | Added missing _diffrn_orient_matrix_UB_33 (in appendix) Added missing _phasing_MIR_der_shell_der_id to appropriate example |
mmcif_std.dic |
| 0.3.4 | 1993-09-01 | Added _struct_conn_ptnr1_label_alt_id and _struct_conn_ptnr2_label_alt_id Corrected definitions for _struct_conn_ptnr2_ items Added _struct_site_gen_label_alt_id Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis Change _database_PDB_rev_ example to _loop construction Added _PDB_remark category (data items _PDB_remark_num and _PDB_remark_text) Added 'obsolete' to enumeration list for _database_PDB_rev_status Added _database_PDB_rev_replaces data item |
mmcif_std.dic |
| 0.3.3 | 1993-08-12 | Syntax and consistency checks - SRH Added _type of null for appendix items. |
mmcif_std.dic |
| 0.3.2 | 1993-08-11 | Cleaning up of stray notes |
mmcif_std.dic |
| 0.3.1 | 1993-08-08 | Began implementing DDL v0.7 |
mmcif_std.dic |
| 0.2.8 | 1993-08-03 | More work on phasing_MIR Created phasing_MIR_der and phasing_MIR_der_shell categories |
mmcif_std.dic |
| 0.2.7 | 1993-08-01 | Redesigned phasing_MIR definitions |
mmcif_std.dic |
| 0.2.6 | 1993-06-02 | Fixed _atom_site_ example (_entity_poly_seq_num) Removed _list_link_parent from _entity_mon_atom_atom_id a _entity_nonp_atom_atom_id Added real APS coordinates to _atom_site_ example Rewrote _atom_sites_footnote_ example |
mmcif_std.dic |
| 0.2.5 | 1993-05-20 | A general merging of updates from PMR, BMcM and SRH Fixed typographical and stylistic problems a la BMcM |
mmcif_std.dic |
| 0.2.4 | 1993-05-20 | DDL adjustment from down under ):-(> |
mmcif_std.dic |
| 0.2.3 | 1993-05-19 | Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon |
mmcif_std.dic |
| 0.2.2 | 1993-05-18 | Style consistency and proof reading changes throughout Make page numbers general to articles and chapters in citation Added *_method to all phasing categories Looped out keywords from _struct_site_ list Added _atom_site_label_ definitions as per H. Berman Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne Added _atom_sites_alt_ data items to formally handle alternative conformations Verified with Cyclops and RGB tools |
mmcif_std.dic |
| 0.2.1 | 1993-05-13 | Major rethinking of _entity_ data based following discussions of 1993-05-10 meeting |
mmcif_std.dic |
| 1.1.18 | 1993-05-12 | Looped out authors and editors in citation list Verified with RGB tools Some style consistency imposed Fleshed out category definitions and imposed style Updated "sets of data item" at beginning of document Checked alphabetical order of data names - moved id's |
mmcif_std.dic |
| 0.1.17 | 1993-05-11 | Changed _atom_site_label_component_? to new nomenclature Introduced category DDL throughout Introduced refers_to DDL throughout Introduced part_of_key DDL throughout Mandated that _list must be in each data definition Standardized 'need not be unique' statements Standardized example headers |
mmcif_std.dic |
| 0.1.16 | 1993-05-10 | Made corrections based on written comments from K. Watenpaugh Made corrections/additions based on discussions at Rutgers |
mmcif_std.dic |
| 0.1.15 | 1993-05-09 | Reconciled nonconcurrent versions Removed trailing blanks Made corrections based on email suggestions from P. Bourne |
mmcif_std.dic |
| 0.1.14 | 1993-04-07 | Experiment with refers_to, category and part_of_key in entity_conn_atom_ and entity_conn_bond_ sections. Discovered horror show with nonconcurrent versions on different computers - not yet resolved. |
mmcif_std.dic |
| 0.1.13 | 1993-04-07 | Introduced _exptl_crystal_grow_ data names |
mmcif_std.dic |
| 0.1.12 | 1993-04-06 | More syntax problems fixed a la Peter Murray-Rust |
mmcif_std.dic |
| 0.1.11 | 1993-04-03 | Syntax checked using tools of Peter Murray-Rust - many problems fixed |
mmcif_std.dic |
| 0.1.10 | 1993-03-28 | Filled in examples for several data categories |
mmcif_std.dic |
| 0.1.9 | 1993-03-26 | Removed _struct_topol_ section until it gets straightened out |
mmcif_std.dic |
| 0.1.8 | 1993-03-25 | Still testing for Cyclops compliance - reveal many additional syntax problems Also verified with new tool by RG Ball - still more errors fixed Dealt with issue raised by PE Bourne - amongst changes Rewrote _database_ section completely Changed _audit_contact_author_ to _audit_contact_author_name _audit_contact_author_address |
mmcif_std.dic |
| 0.1.7 | 1993-03-24 | Tested for Cyclops compliance - most problems are names that are too long. Changed crystal_preparation to crystal_prep Changed d_resolution to d_res Many other such changes |
mmcif_std.dic |
| 0.1.6 | 1993-03-24 | Dealt with many issues raised by SR Hall. Some were merely typographical. Changed temp to B_iso Changed occ to occupancy Changed special_details to details. Changed asl to label everywhere. Shuffled data names in _struct_conf_ and _struct_conn_ |
mmcif_std.dic |
| 0.1.5 | 1993-03-24 | Finished moving examples to *_appendix data items |
mmcif_std.dic |
| 0.1.4 | 1993-02-11 | Added example for _symmetry_ |
mmcif_std.dic |
| 0.1.3 | 1993-02-11 | Started moving core data names to the *_appendix data items |
mmcif_std.dic |
| 0.1.2 | 1993-02-11 | Started moving examples to *_appendix data items. |
mmcif_std.dic |
| 0.1.1 | 1993-02-11 | Highlighted all notes with # %%%%% surrounds. |
mmcif_std.dic |