Supporting Data mmcif_pdbx.dic
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 1.05241 | 2008-12-11 | + Changes: (jdw) Corrected Typographical errors in category name for - _item.category_id for _pdbx_construct_feature.entry_id _item.category_id for _struct_ncs_dom_lim.pdbx_ens_id Add definition for _ndb_original_ndb_coordinates.coord_section |
mmcif_pdbx.dic |
| 1.0524 | 2008-10-23 | Changes: (jdw) + _chem_comp.type add 'peptide linking' |
mmcif_pdbx.dic |
| 1.0523 | 2008-10-15 | Changes: (jdw) + Added item _reflns.pdbx_number_measured_all |
mmcif_pdbx.dic |
| 1.0522 | 2008-10-04 | Changes: (jdw) BRANCH REVISION + add _pdbx_nmr_exptl_sample.concentration_range |
mmcif_pdbx.dic |
| 1.0521 | 2008-08-08 | Changes: (jdw) BRANCH REVISION + update enumeration for _pdbx_database_related.content_type + add _chem_comp_atom.pdbx_component_atom_id + add _chem_comp_atom.pdbx_component_comp_id + add _chem_comp_atom.pdbx_subcomponent_list + added _pdbx_chem_comp_feature.comp_id, _pdbx_chem_comp_feature.type, _pdbx_chem_comp_feature.value and _pdbx_chem_comp_feature.source + _chem_comp.type added enumeration - 'peptide-like' |
mmcif_pdbx.dic |
| 1.052 | 2008-05-29 | Changes: (jdw) + Added- _refine_ls_restr_ncs.pdb_ens_id, _struct_ncs_dom.pdbx_ens_id, _struct_ncs_dom_lim.pdbx_ens_id. + Removed parent-child references to the atom_site category from categories pdbx_unobs_or_zero_occ_atoms/residues. ** Note this is the last main version of the dictionary supporting version PDB 3.1 files. |
mmcif_pdbx.dic |
| 1.051 | 2008-02-10 | Changes: (jw): + Added contributed item from Acta Cryst. editors by way of Brian McMahon, _reflns.pdbx_d_opt. |
mmcif_pdbx.dic |
| 1.050 | 2008-01-24 | Changes (jdw,zf): + make _pdbx_validate_close_contact.symm_as_xyz_1,2 optional |
mmcif_pdbx.dic |
| 1.049 | 2008-01-09 | + Added _entity_poly.rcsb_build_self_reference, _refine.pdbx_overall_phase_error and _refine_ls_shell.pdbx_phase_error + Added contributed items from Howard Einsphar and Manfred Weiss - _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all |
mmcif_pdbx.dic |
| 1.048 | 2007-11-18 | Changes: (jdw/kh) + allow leading '+' for data type int + add '[]' to allowed characters for data types code and ucode - + make items other than the category key in ENTITY_SRC_NAT optional. |
mmcif_pdbx.dic |
| 1.047 | 2007-08-24 | Changes: (jdw/kh/zf) + Add categories pdbx_struct_ref_seq_insertion and pdbx_struct_ref_seq_deletion. |
mmcif_pdbx.dic |
| 1.046 | 2007-08-14 | Changes: (jdw/kh/zf) + Replace ebi_validate_* categories with pdbx_validate_* categories including categories describing planar deviations. These categories provide placeholder definitions for mapping PDB REMARK 500 validation data and other PDB remarks - Added categories: pdbx_validate_close_contact,pdbx_validate_symm_contact,pdbx_validate_rmsd_bond, pdbx_validate_rmsd_angle,pdbx_validate_torsion,pdbx_validate_peptide_omega, pdbx_validate_chiral,pdbx_validate_planes,pdbx_validate_planes_atom, pdbx_validate_main_chain_plane, pdbx_struct_conn_angle, pdbx_unobs_or_zero_occ_residues pdbx_unobs_or_zero_occ_atoms, pdbx_struct_mod_residue, and pdbx_entry_details + Add 'identity operation' to enums for _pdbx_struct_oper_list.type + _chem_comp.pdbx_processing_site added. |
mmcif_pdbx.dic |
| 1.045 | 2007-06-23 | Changes: (jdw) + change data type for _pdbx_database_PDB_obs_spr.replace_pdb_id to line + remove parent/child relationship for - _chem_comp.mon_nstd_parent_comp_id + extend enumerations for _pdbx_SG_project + data type _diffrn_detector.pdbx_collection_date made yyyy-mm-dd:hh:mm-flex + extend enumerations for _pdbx_nmr_exptl_sample.concentration_units + make pdbx_database_status - author_release_status and recvd_initial_deposition_date items optional + adjust enumeration case for _pdbx_chem_comp_descriptor.type + supress parent relationship for _phasing_MIR_der_site.atom_type_symbol + uchar3 adjusted to accept all possible 3-letter-code values - + extended enumeration for _software.language + data type for _chem_comp.mon_nstd_parent_comp_id changed to uline |
mmcif_pdbx.dic |
| 1.044 | 2007-05-30 | Changes: (jdw/as) + added _citation_author.ordinal to category key + remove duplicate data item specifications in category entity_src_gen + miscellaneous corrections to data item references in definitions + make all 'replaces/replacedby' relationships reciprocal + make all key items mandatory. + add program and program_version to the key of category pdbx_chem_comp_identifier + suppress aliases to the ebi_extension dictionary. |
mmcif_pdbx.dic |
| 1.043 | 2007-05-28 | Changes: (jdw) + adjust child data types for consistency with parent types. + removed aliases to local status items in pdbx_database_status. |
mmcif_pdbx.dic |
| 1.042 | 2007-05-20 | Changes: (jdw) + Add _software.classification to category key. + Change enumerations for _pdbx_chem_comp_descriptors.program and _pdbx_chem_comp_identifiers.program to examples. + Make category keys in audit_conform mandatory + remove incorrect parent-child link to _pdbx_struct_assembly_gen.oper_expression + Added _pdbx_struct_assembly_gen.asym_id_list and replaced _pdbx_struct_assembly_gen.entity_inst_id with this item in the key for this category. Suppressed parent child relationships between _pdbx_struct_entity_inst.id and categories outside the _pdbx_struct_* group. + Added _chem_comp.pdbx_model_coordinates_db_code, _chem_comp.pdbx_initial_date, _chem_comp.pdbx_modified_date. + Data types changed to int for - _atom_site.pdbx_PDB_model_num, _struct_conf.pdbx_PDB_helix_length, _pdbx_poly_seq_scheme.ndb_seq_num, _pdbx_struct_sheet_hbond.range_1_label_seq_id, _pdbx_struct_sheet_hbond.range_2_label_seq_id, _atom_site_anisotrop.pdbx_label_seq_id, _struct_conn.pdbx_ptnr3_label_seq_id. + _em_vitrification.humidity data type changed to float. + category key for refine_ls_restr_ncs changed to _refine_ls_restr_ncs.dom_id, _refine_ls_restr_ncs.pdbx_type, _refine_ls_restr_ncs.pdbx_asym_id. |
mmcif_pdbx.dic |
| 1.041 | 2007-04-04 | Changes: (jdw) Adjust category key for PDBX_VERSION category. Update definition of _pdbx_struct_oper_list.id |
mmcif_pdbx.dic |
| 1.040 | 2007-03-20 | Changes: (jdw) + skip version 1.039 to sync with remediation dictionary version. + Updated enumerations and boundary values for _pdbx_database_status.deposit_site *.isotopic_labeling, _citation.pdbx_database_id_PubMed. |
mmcif_pdbx.dic |
| 1.038 | 2007-02-02 | Changes: (jdw) + Added category PDBX_VERSION. |
mmcif_pdbx.dic |
| 1.037 | 2006-12-15 | Changes: (jdw) + corrected type in _chem_comp.pdbx_ideal_coordinates_details _chem_comp.pdbx_model_coordinates_details definitions. + added _chem_comp.pdbx_ideal_coordinates_missing_flag + added _chem_comp.pdbx_model_coordinates_missing_flag + In chem_comp_atom /bond - added missing enumerations for atom/bond stereo_config and aromatic flags. + added PUBCHEM_SID and PUBCHEM_CID to pdbx_chem_comp_identifier.type. |
mmcif_pdbx.dic |
| 1.036 | 2006-11-14 | Changes: (jdw) + revise category keys in pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit. + removed unused category pdbx_chem_comp_protonation_site + added _chem_comp.pdbx_model_coordinates_details and _chem_comp.pdbx_ideal_coordinates_details. |
mmcif_pdbx.dic |
| 1.035 | 2006-11-05 | Changes: (jdw) + missing data types in pdbx_struct_msym/asym_gen. + _citation.pdbx_unpublished enum typo |
mmcif_pdbx.dic |
| 1.034 | 2006-11-01 | Changes: (jdw) + Adjust mandatory codes for pdbx_entity_inst_id. |
mmcif_pdbx.dic |
| 1.033 | 2006-10-16 | Changes: (jdw) + Correct typos pdbx_chem_comp_descriptors/identifiers + add ordinal data items to these cateogories. + added _pdbx_refine.free_R_error_no_cutoff |
mmcif_pdbx.dic |
| 1.032 | 2006-10-12 | Changes: (jdw) +Added Categories: pdbx_helical_symmetry pdbx_point_symmetry pdbx_struct_entity_inst pdbx_struct_oper_list pdbx_struct_assembly pdbx_struct_assembly_gen pdbx_struct_asym_gen pdbx_struct_msym_gen pdbx_struct_legacy_oper_list pdbx_reflns_twin pdbx_struct_info pdbx_re_refinement pdbx_struct_assembly_prop pdbx_struct_ref_seq_feature pdbx_struct_ref_seq_feature_prop pdbx_struct_chem_comp_diagnostics +Added items: _pdbx_helical_symmetry.entry_id _pdbx_helical_symmetry.number_of_operations _pdbx_helical_symmetry.rotation_per_n_subunits _pdbx_helical_symmetry.rise_per_n_subunits _pdbx_helical_symmetry.n_subunits_divisor _pdbx_helical_symmetry.dyad_axis _pdbx_helical_symmetry.circular_symmetry _pdbx_point_symmetry.entry_id _pdbx_point_symmetry.Schoenflies_symbol _pdbx_point_symmetry.H-M_notation _pdbx_point_symmetry.circular_symmetry _pdbx_struct_entity_inst.details _pdbx_struct_entity_inst.entity_id _pdbx_struct_entity_inst.id _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] _pdbx_struct_assembly.details _pdbx_struct_assembly.id _pdbx_struct_assembly_gen.entity_inst_id _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_asym_gen.entity_inst_id _pdbx_struct_asym_gen.asym_id _pdbx_struct_asym_gen.oper_expression _pdbx_struct_msym_gen.entity_inst_id _pdbx_struct_msym_gen.msym_id _pdbx_struct_msym_gen.oper_expression _pdbx_struct_legacy_oper_list.id _pdbx_struct_legacy_oper_list.name _pdbx_struct_legacy_oper_list.matrix[1][1] _pdbx_struct_legacy_oper_list.matrix[1][2] _pdbx_struct_legacy_oper_list.matrix[1][3] _pdbx_struct_legacy_oper_list.matrix[2][1] _pdbx_struct_legacy_oper_list.matrix[2][2] _pdbx_struct_legacy_oper_list.matrix[2][3] _pdbx_struct_legacy_oper_list.matrix[3][1] _pdbx_struct_legacy_oper_list.matrix[3][2] _pdbx_struct_legacy_oper_list.matrix[3][3] _pdbx_struct_legacy_oper_list.vector[1] _pdbx_struct_legacy_oper_list.vector[2] _pdbx_struct_legacy_oper_list.vector[3] _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction _pdbx_reflns_twin.mean_I2_over_mean_I_square _pdbx_reflns_twin.mean_F_square_over_mean_F2 _struct_conn.pdbx_dist_value _pdbx_struct_info.type _pdbx_struct_info.value _pdbx_struct_assembly_prop.details _pdbx_re_refinement.entry_id _pdbx_re_refinement.citation_id _pdbx_re_refinement.details _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details _struct_biol.pdbx_aggregation_state _struct_biol.pdbx_assembly_method _entry.pdbx_DOI _citation.unpublished_flag _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_nat.pdbx_ncbi_taxonomy_id _pdbx_struct_ref_seq_feature.feature_id _pdbx_struct_ref_seq_feature.align_id _pdbx_struct_ref_seq_feature.type _pdbx_struct_ref_seq_feature.details _pdbx_struct_ref_seq_feature.pdb_strand_id _pdbx_struct_ref_seq_feature.asym_id _pdbx_struct_ref_seq_feature.beg_auth_seq_id _pdbx_struct_ref_seq_feature.end_auth_seq_id _pdbx_struct_ref_seq_feature.beg_seq_num _pdbx_struct_ref_seq_feature.end_seq_num _pdbx_struct_ref_seq_feature.beg_auth_mon_id _pdbx_struct_ref_seq_feature.end_auth_mon_id _pdbx_struct_ref_seq_feature.beg_pdb_ins_code _pdbx_struct_ref_seq_feature.end_pdb_ins_code _pdbx_struct_ref_seq_feature_prop.feature_id _pdbx_struct_ref_seq_feature_prop.property_id _pdbx_struct_ref_seq_feature_prop.type _pdbx_struct_ref_seq_feature_prop.value _pdbx_struct_ref_seq_feature_prop.details _pdbx_struct_ref_seq_feature_prop.beg_db_mon_id _pdbx_struct_ref_seq_feature_prop.end_db_mon_id _pdbx_struct_ref_seq_feature_prop.beg_db_seq_id _pdbx_struct_ref_seq_feature_prop.end_db_seq_id |
mmcif_pdbx.dic |
| 1.031 | 2006-08-10 | Changes: (jdw) + Correct typo in new definitions - change _chem_comp_atom.pdbx_model_Cartn_[xyz]_2 to [xyz]_ideal + Add enum for NYSGXRC + Add enum for HOLD FOR 8 WEEKS. |
mmcif_pdbx.dic |
| 1.030 | 2006-06-27 | Changes: (zf) + fixed the alias for _pdbx_refine_tls_group.beg_auth_seq_id item |
mmcif_pdbx.dic |
| 1.029 | 2006-06-12 | Changes: (jdw) + More additions to enumerations for SG sites. + revise enumerations for status codes. |
mmcif_pdbx.dic |
| 1.028 | 2006-05-11 | Changes: (jdw) + Make _chemp_comp.pdbx_replaces a comma separated list. + Adjust enumerations for SG sites |
mmcif_pdbx.dic |
| 1.027 | 2006-05-01 | Changes: (jdw) + add _chemp_comp.pdbx_replaces/pdbx_replaced_by |
mmcif_pdbx.dic |
| 1.026 | 2006-04-27 | Changes: (jdw) + add 4 week enumeration/example for HOLD status items + add pdbx_ordinal items for chem_comp_atom/bond and pdbx_ambiguous_flag to chem_comp. |
mmcif_pdbx.dic |
| 1.025 | 2006-04-18 | Changes: (jdw) + fix data type for _entity_poly.type |
mmcif_pdbx.dic |
| 1.024 | 2006-04-13 | Changes: (jdw) + Correct alias for _struct_site_gen.pdbx_auth_ins_code. + Add enum 'polydeoxyribonucleotide/polyribonucleotide hybrid' to entity_poly.type. + update enums in pdbx_SG_project. |
mmcif_pdbx.dic |
| 1.023 | 2006-03-01 | Changes: (jdw) + Add _pdbx_contact_author.continent + Remove enums for _pdbx_contact_author.country + Added EMDB, TARGETDB, PEPCDB to _pdbx_database_related.db_name examples and associated EM volume, associated NMR restraints, associated structure factors, and associated protein target sequence/protocol data to _pdbx_database_related.content_type. |
mmcif_pdbx.dic |
| 1.022 | 2006-02-24 | Changes: (jdw) + Fixed syntax issues (ie. extra loop_) in items in _pdbx_construct.* + Added missing category groups in standard dictionary section 1. + Fixed category error for item _chem_comp_atom.pdbx_align |
mmcif_pdbx.dic |
| 1.021 | 2005-10-12 | Changes: (jdw) + added categories pdbx_refine_component, pdbx_chem_comp_descriptor, pdbx_chem_comp_identifier, pdbx_chem_comp_import,pdbx_chem_comp_atom_edit, pdbx_chem_comp_bond_edit, and pdbx_chem_comp_audit. + added stereochemistry and aromaticity flags to chem_comp_atom and chem_comp_bond. + added alternate component and atom nomenclature to chem_comp_atom. + added alternate model coordinates to chem_comp_atom category |
mmcif_pdbx.dic |
| 1.020 | 2005-08-23 | Changes: (jdw) + Correct typos in pdbx_feature_monomer. + Correct typos in examples in categories refine and publ_manuscript_incl |
mmcif_pdbx.dic |
| 1.019 | 2005-07-21 | Changes: (jdw) + Added _struct.pdbx_formula_weight and _struct.pdbx_formula_weight_method + Added _refln.pdbx_HL_A_iso, _refln.pdbx_HL_B_iso, _refln.pdbx_HL_C_iso, and _refln.pdbx_HL_D_iso + Added _phasing_set.pdbx_d_res_low/high _pdbx_phasing_MR.native_data_set_id + Added category pdbx_feature_monomer |
mmcif_pdbx.dic |
| 1.018 | 2005-07-14 | Changes: (jdw) + Added PDB_SOLN_SCATTER* definitions + Added _refln.pdbx_[F,I]_[minus,plus] and _refln.pdbx_[F,I]_[minus,plus]_sigma + Extend enumeration for _pdbx_database_status.status_code_sf |
mmcif_pdbx.dic |
| 1.017 | 2005-06-27 | Changes: (BMcM) + added _reflns.threshold_expression and _publ_author.email + numerous minor changes to wordings of definitions to align with mmcif version 2.0.09 as released on International Tables G CD-ROM |
mmcif_pdbx.dic |
| 1.016 | 2005-06-24 | Changes: (jdw) + aliases repointed for items in category pdbx_database_remark + Added the following items: _diffrn_detector.pdbx_frames_total _diffrn_detector.pdbx_collection_time_total _refine.pdbx_ls_sigma_Fsqd _reflns.pdbx_Rmerge_I_all _reflns.pdbx_netI_over_sigmaI _reflns.pdbx_res_netI_over_av_sigmaI_2 _reflns.pdbx_res_netI_over_sigmaI_2 _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _struct_biol.pdbx_formula_weight _struct_biol.pdbx_formula_weight_method _struct_biol_gen.pdbx_PDB_order _phasing_MAD.pdbx_number_data_sets _phasing_MAD.pdbx_anom_scat_method _phasing_MIR.pdbx_number_derivatives _phasing_set.pdbx_temp_details + miscellaneous editorial changes in descriptions and enumerations. |
mmcif_pdbx.dic |
| 1.015 | 2005-04-15 | Changes: (jdw) + remove _entity_keywords.text from category key |
mmcif_pdbx.dic |
| 1.014 | 2005-04-08 | Changes: (jdw) + remove _struct_keywords.text from category key |
mmcif_pdbx.dic |
| 1.013 | 2005-04-05 | Changes: (jdw) + Temporarily remove definitions from Image CIF dictionary + Added mandatory code for _cell.reciprocal_angle_beta + Added mandatory code for _pdbx_entity_nonpoly.entity_id + Fixed category attribute for _reflns_shell.pdbx_chi_squared + Changed mandatory code for _software.citation_id |
mmcif_pdbx.dic |
| 1.012 | 2005-03-29 | Changes: (kh/jdw) + added preliminary set of extensions for macromolecular powder diffraction experiments, including: _pdbx_exptl_pd (category) _pdbx_exptl_pd.entry.id _pdbx_exptl_pd.spec_preparation_pH _pdbx_exptl_pd.spec_preparation_pH_range _pdbx_exptl_pd.spec_preparation _diffrn_radiation.pdbx_analyzer _refine.pdbx_pd_number_of_powder_patterns _refine.pdbx_pd_number_of_points _refine.pdbx_pd_meas_number_of_points _refine.pdbx_pd_proc_ls_prof_R_factor _refine.pdbx_pd_proc_ls_prof_wR_factor _refine.pdbx_pd_Marquardt_correlation_coeff _refine.pdbx_pd_Fsqrd_R_factor _refine.pdbx_pd_ls_matrix_band_width Changes: (fzk) removed 'National Project on Protein Structural and Functional Analyses' from _pdbx_SG_project.full_name_of_center, added 'National Project on Protein Structural and Functional Analyses' to _pdbx_SG_project.project_name |
mmcif_pdbx.dic |
| 1.011 | 2005-03-08 | Changes: (jdw) + Included extensions from mmCIF dictionary... Changes: (fzk) + add _pdbx_refine_tls_group.beg_auth_asym_id + add _pdbx_refine_tls_group.end_auth_asym_id + add enumeration values 'SGC' and 'NPPSFA' for _pdbx_SG_project.initial_of_center + add enumeration values 'Structural Genomics Consortium' and 'National Project on Protein Structural and Functional Analyses' for _pdbx_SG_project.full_name_of_center + fix _item_description.description for _entity_poly.pdbx_target_identifier |
mmcif_pdbx.dic |
| 1.010 | 2005-01-25 | Changes: (jdw) + change mandatory doc for _pdbx_database_status.SG_entry + fix key in category pdbx_database_PDB_obs_spr |
mmcif_pdbx.dic |
| 1.009 | 2005-01-13 | Changes: (zkf) + add _pdbx_database_status.status_code_sf item + add _pdbx_database_status.date_of_sf_release item + add _pdbx_database_status.status_code_mr item + add _pdbx_database_status.date_of_mr_release item + add _pdbx_database_status.SG_entry item + add _entity_poly.pdbx_target_identifier item + add pdbx_SG_project category + fixed enumeration values for _software.language |
mmcif_pdbx.dic |
| 1.008 | 2004-11-15 | Changes: (jdw) + fix typo in category save frame name pdbx_exptl_crystal_grow_comp. |
mmcif_pdbx.dic |
| 1.007 | 2004-11-02 | Changes: (jdw) + added pdbx_entity_prod_protocol, pdbx_exptl_crystal_grow_sol, pdbx_exptl_crystal_grow_comp, and pdbx_exptl_crystal_cryo_treatment categories + relax enumerations in cryo-em dictionary. + remove upper-bound for refine.occupancy_max |
mmcif_pdbx.dic |
| 1.006 | 2004-10-10 | Changes: (jdw) + Update enumerations in cryo-em dictionary. |
mmcif_pdbx.dic |
| 1.005 | 2004-09-28 | Changes: (zkf,jdw) + Add missing pdbx_contact_author.postal_code item + Add missing pdbx_contact_author.city item + Add missing pdbx_contact_author.state_province item + Add enumerations in pdbx_contact_author.id + Modify enumerations in pdbx_contact_author.role |
mmcif_pdbx.dic |
| 1.004 | 2004-08-04 | Changes: (jdw) + Fix many data type errors in phasing section. + Add pdbx_contact_author |
mmcif_pdbx.dic |
| 1.003 | 2004-06-16 | Changes: (jdw) + Fix miscellaneous unresolved links. |
mmcif_pdbx.dic |
| 1.002 | 2004-06-09 | Changes: (jdw) + Added categories PDBX_DOMAIN, PDBX_SEQUENCE_RANGE, PDBX_FEATURE_ENTRY, PDBX_FEATURE_ASSEMBLY, PDBX_FEATURE_DOMAIN, and PDBX_FEATURE_SEQUENCE_RANGE. |
mmcif_pdbx.dic |
| 1.001 | 2004-05-21 | Changes: (jdw) + Fixed incorrect category in _pdbx_audit_author.address + Added _citation.pdbx_database_id_DOI + Fixed placement of _chem_comp.pdbx_align. Moved this item to _chem_comp_atom.pdbx_align |
mmcif_pdbx.dic |
| 1.000 | 2004-04-22 | Changes: (jdw) + New packaging and naming + Integrate 3d em definitions + Relax enumerations to comply with existing legacy data. + Version to 1.000 |
mmcif_pdbx.dic |
| 0.020 | 2003-10-30 | Changes: (jdw/zf) + Fix cases where category keys are not flagged as mandatory + Add category PDBX_AUDIT_AUTHOR |
mmcif_pdbx.dic |
| 0.019 | 2003-09-21 | Changes: (jdw/hy) + Added additional phasing items for PDB_EXTRACT. |
mmcif_pdbx.dic |
| 0.018 | 2003-07-07 | Changes: (jdw) + Integrated protein production data items. |
mmcif_pdbx.dic |
| 0.017 | 2002-10-05 | Changes: (jdw) + Final corrections of recommendations for NMR and X-ray deposition for structural genomics. |
mmcif_pdbx.dic |
| 0.016 | 2002-08-05 | Changes: (jdw) + Add PDBX_AUDIT category. |
mmcif_pdbx.dic |
| 0.015 | 2002-05-22 | Changes: (jdw) + Add PDBX_ENTITY_NONPOLY and fix missing data type codes. |
mmcif_pdbx.dic |
| 0.014 | 2002-02-28 | Changes: (jdw) + Add items for NMR model and PDB insert code to GEOM_BOND, GEOM_ANGLE, GEOM_CONTACT, and GEOM_TORSION categories. |
mmcif_pdbx.dic |
| 0.013 | 2001-07-12 | Changes: (jdw) + enumerations->examples for _pdbx_nmr_representative.selection_criteria and _pdbx_database_related.db_name. + add regex for int and float ranges |
mmcif_pdbx.dic |
| 0.012 | 2001-06-28 | Changes: (jdw) + _atom_site_anisotrop.pdbx_auth_* aliases corrected. + adjust regex for date:time type |
mmcif_pdbx.dic |
| 0.011 | 2001-06-14 | Changes: (jdw) + Moved enumerations to examples for _pdbx_nmr_spectrometer.field_strength + _atom_site.pdb_auth_atom_name data type changed from code to atcode. |
mmcif_pdbx.dic |
| 0.010 | 2001-04-18 | Changes: (jdw) + Added missing _item_type.codes for _refine_hist.number_atoms_solvent _refine_hist.number_atoms_total _refine.overall_SU_B _refine.overall_SU_ML _refine.pdbx_overall_ESU_R + Added CCP4 data items output from REFMAC V5. |
mmcif_pdbx.dic |
| 0.009 | 2001-03-02 | Changes: (jdw) + Added missing mandatory codes and reset aliases for _diffrn_radiation.pdbx_wavelenth_list. |
mmcif_pdbx.dic |
| 0.008 | 2001-01-22 | Changes: (jdw) + Added item _pdbx_database_status.dep_release_code_sequence |
mmcif_pdbx.dic |
| 0.007 | 2000-11-09 | Changes: (jdw) + Added mandatory codes for _exptl_crystal_grow.pdbx_details and _exptl_crystal_grow.pdbx_pH_range. + Added missing data types and category ids in category pdbx_struct_sheet_hbond. + Updated data type for atom name references to atcode. + Updated aliases for _refine.overall_SU_B and _refine.overall_SU_ML. + Trimmed line lengths > 80 characters. |
mmcif_pdbx.dic |
| 0.006 | 2000-10-26 | Changes: (jdw) + Added _exptl_crystal_grow.rcsb_pH_range. + Added category PDBX_STRUCT_SHEET_HBOND to hold single hydrogen bond registration between beta sheet strands. |
mmcif_pdbx.dic |
| 0.005 | 2000-10-25 | Changes: (jdw) + drop category PDBX_DATABASE_REMARK |
mmcif_pdbx.dic |
| 0.004 | 2000-10-24 | Changes: (jdw) + Added optional timestamps to data items. + Repositioned parent items in PDBX_POLY_SEQ_SCHEME. |
mmcif_pdbx.dic |
| 0.003 | 2000-10-16 | Changes: (jdw) + Move enumerations to examples for: _pdbx_nmr_exptl.type _pdbx_nmr_ensemble.conformer_selection_criteria _pdbx_nmr_software.name _struct_keywords.pdbx_keywords + Added _atom_site_anisotrop.pdbx_auth_* items + Added _struct_mon_prot_cis.pdbx_ + Added _struct_conn.pdbx_ptnr3_auth_* items. |
mmcif_pdbx.dic |
| 0.002 | 2000-06-06 | Changes: (jdw) + Added items in refine_hist and exptl_crystal_grow |
mmcif_pdbx.dic |
| 0.001 | 2000-05-23 | Initial revision based on RCSB local dictionaries and EBI database schema. J. Westbrook and J. Ionides |
mmcif_pdbx.dic |
Data Type List
| Data Type Code | Primitive Type Code | Regular Expression | Description |
|---|---|---|---|
| any | char | .* | A catch all for items that may take any form... |
| atcode | char | [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | Character data type for atom names ... |
| binary | char | \n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION---- |
binary items are presented as MIME-like ascii-encoded sections in an imgCIF. In a CBF, raw octet streams are used to convey the same information. |
| code | char | [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words ... |
| code30 | char | .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? | A string value, not allowed to exceed 30 characters. |
| uchar | [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... | |
| fax | uchar | [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... |
| float | numb | -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? | float item types are the subset of numbers that are the floating numbers. |
| float-range | numb | -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)? | int item types are the subset of numbers that are the floating numbers. |
| idname | uchar | [_A-Za-z0-9]+ | idname item types take the form... |
| int | numb | [+-]?[0-9]+ | int item types are the subset of numbers that are the negative or positive integers. |
| int-range | numb | -?[0-9]+(--?[0-9]+)? | int item types are the subset of numbers that are the negative or positive integers with optional range. |
| line | char | [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | char item types / multi-word items ... |
| name | uchar | _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ | name item types take the form... |
| operation_expression | char | [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | sequence of parenthetical integer ranges and character codes |
| phone | uchar | [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... |
| symop | char | ([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])? | symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. |
| text | char | [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | text item types / multi-line text ... |
| uchar1 | uchar | [+]?[A-Za-z0-9] | data item for 1 character codes |
| uchar3 | uchar | [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]? | data item for 3 character codes |
| ucode | uchar | [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... |
| uline | uchar | [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | char item types / multi-word items (case insensitive)... |
| yyyy-mm-dd | char | [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9] | Standard format for CIF dates. |
| yyyy-mm-dd:hh:mm | char | [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])? | Standard format for CIF dates with optional time stamp. |
| yyyy-mm-dd:hh:mm-flex | char | [0-9][0-9][0-9][0-9](-[0-9]?[0-9])?(-[0-9][0-9])?(:[0-9]?[0-9]:[0-9][0-9])? | Flexible date-time format. |
SubCategory List
| SubCategory Identifier | Description |
|---|---|
| cartesian_coordinate | The collection of x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. |
| cartesian_coordinate_esd | The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. |
| cell_angle | The collection of alpha, beta, and gamma angles of a unit cell. |
| cell_angle_esd | The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. |
| cell_length | The collection of a, b, and c axis lengths of a unit cell. |
| cell_length_esd | The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. |
| fractional_coordinate | The collection of x, y, and z components of a position specified with reference to unit cell directions. |
| fractional_coordinate_esd | The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to unit cell directions. |
| matrix | The collection of elements of a matrix. |
| miller_index | The collection of h, k, and l components of the Miller index of a reflection. |
| mm_atom_site_auth_label | The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. |
| mm_atom_site_label | The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. |
| vector | The collection of elements of a vector. |
Units List
| Units Identifier | Description |
|---|---|
| 8pi2_angstroms_squared | 8pi2 * angstroms squared (metres * 10(-10))2 |
| angstroms | angstroms (metres * 10(-10)) |
| angstroms_cubed | angstroms cubed (metres * 10(-10))3 |
| angstroms_degrees | angstroms * degrees |
| angstroms_squared | angstroms squared (metres * 10(-10))2 |
| arbitrary | arbitrary system of units. |
| celsius | degrees (of temperature) Celsius |
| centimetres | centimetres (metres * 10( -2)) |
| counts | counts |
| counts_per_photon | counts per photon |
| degrees | degrees (of arc) |
| degrees_per_minute | degrees (of arc) per minute |
| degrees_squared | degrees squared |
| electron_volts | electron volts |
| electrons | electrons |
| electrons_angstrom_squared | electrons square angstrom |
| electrons_per_angstroms_cubed | electrons per angstroms cubed (electrons/(metres * 10(-10))(-3)) |
| electrons_per_nanometres_cubed | electrons per nanometres cubed (electrons/(metres * 10( -9))(-3)) |
| electrons_per_picometres_cubed | electrons per picometres cubed (electrons/(metres * 10(-12))(-3)) |
| electrons_squared | electrons squared |
| femtometres | femtometres (metres * 10(-15)) |
| gigapascals | gigapascals |
| hours | hours |
| kelvins | degrees (of temperature) Kelvin |
| kilopascals | kilopascals |
| kilovolts | kilovolts |
| kilowatts | kilowatts |
| megadaltons | megadaltons |
| megagrams_per_cubic_metre | megagrams per cubic metre |
| metres | metres (metres) |
| mg_per_ml | milliliter per milligram |
| microns | microns |
| microns_squared | microns squared |
| microseconds | microseconds |
| milliamperes | milliamperes |
| milligrams | grams / 1000 |
| milliliters | liter / 1000 |
| millimetres | millimetres (metres * 10( -3)) |
| millimolar | millimolar |
| minutes | minutes |
| ml_per_min | milliliter per minute |
| nanometres | nanometres (metres * 10( -9)) |
| nanometres_cubed | nanometres cubed (metres * 10( -9))3 |
| nanometres_squared | nanometres squared (metres * 10( -9))2 |
| picometres | picometres (metres * 10(-12)) |
| picometres_cubed | picometres cubed (metres * 10(-12))3 |
| picometres_squared | picometres squared (metres * 10(-12))2 |
| pixels_per_millimetre | pixels per millimetre |
| reciprocal_angstroms | reciprocal angstroms ((metres * 10(-10))(-1)) |
| reciprocal_centimetres | reciprocal centimetres ((metres * 10( -2))(-1)) |
| reciprocal_metres | reciprocal metres (metres(-1)) |
| reciprocal_millimetres | reciprocal millimetres ((metres * 10( -3))(-1)) |
| reciprocal_nanometres | reciprocal nanometres ((metres * 10( -9))(-1)) |
| reciprocal_picometres | reciprocal picometres ((metres * 10(-12))(-1)) |
| seconds | seconds |
Units Conversion List
| From Units&Identifier | To Units&Identifier | Operator | Conversion Factor |
|---|---|---|---|
| metres | centimetres | * | 1.0E+02 |
| metres | millimetres | * | 1.0E+03 |
| metres | nanometres | * | 1.0E+09 |
| metres | angstroms | * | 1.0E+10 |
| metres | picometres | * | 1.0E+12 |
| metres | femtometres | * | 1.0E+15 |
| centimetres | millimetres | * | 1.0E+01 |
| centimetres | nanometres | * | 1.0E+07 |
| centimetres | angstroms | * | 1.0E+08 |
| centimetres | picometres | * | 1.0E+10 |
| centimetres | femtometres | * | 1.0E+13 |
| millimetres | centimetres | * | 1.0E-01 |
| millimetres | nanometres | * | 1.0E+06 |
| millimetres | angstroms | * | 1.0E+07 |
| millimetres | picometres | * | 1.0E+09 |
| millimetres | femtometres | * | 1.0E+12 |
| nanometres | centimetres | * | 1.0E-07 |
| nanometres | millimetres | * | 1.0E-06 |
| nanometres | angstroms | * | 1.0E+01 |
| nanometres | picometres | * | 1.0E+03 |
| nanometres | femtometres | * | 1.0E+06 |
| angstroms | centimetres | * | 1.0E-08 |
| angstroms | millimetres | * | 1.0E-07 |
| angstroms | nanometres | * | 1.0E-01 |
| angstroms | picometres | * | 1.0E+02 |
| angstroms | femtometres | * | 1.0E+05 |
| picometres | centimetres | * | 1.0E-10 |
| picometres | millimetres | * | 1.0E-09 |
| picometres | nanometres | * | 1.0E-03 |
| picometres | angstroms | * | 1.0E-02 |
| picometres | femtometres | * | 1.0E+03 |
| femtometres | centimetres | * | 1.0E-13 |
| femtometres | millimetres | * | 1.0E-12 |
| femtometres | nanometres | * | 1.0E-06 |
| femtometres | angstroms | * | 1.0E-05 |
| femtometres | picometres | * | 1.0E-03 |
| reciprocal_centimetres | reciprocal_millimetres | * | 1.0E-01 |
| reciprocal_centimetres | reciprocal_nanometres | * | 1.0E-07 |
| reciprocal_centimetres | reciprocal_angstroms | * | 1.0E-08 |
| reciprocal_centimetres | reciprocal_picometres | * | 1.0E-10 |
| reciprocal_millimetres | reciprocal_centimetres | * | 1.0E+01 |
| reciprocal_millimetres | reciprocal_nanometres | * | 1.0E-06 |
| reciprocal_millimetres | reciprocal_angstroms | * | 1.0E-07 |
| reciprocal_millimetres | reciprocal_picometres | * | 1.0E-09 |
| reciprocal_nanometres | reciprocal_centimetres | * | 1.0E+07 |
| reciprocal_nanometres | reciprocal_millimetres | * | 1.0E+06 |
| reciprocal_nanometres | reciprocal_angstroms | * | 1.0E-01 |
| reciprocal_nanometres | reciprocal_picometres | * | 1.0E-03 |
| reciprocal_angstroms | reciprocal_centimetres | * | 1.0E+08 |
| reciprocal_angstroms | reciprocal_millimetres | * | 1.0E+07 |
| reciprocal_angstroms | reciprocal_nanometres | * | 1.0E+01 |
| reciprocal_angstroms | reciprocal_picometres | * | 1.0E-02 |
| reciprocal_picometres | reciprocal_centimetres | * | 1.0E+10 |
| reciprocal_picometres | reciprocal_millimetres | * | 1.0E+09 |
| reciprocal_picometres | reciprocal_nanometres | * | 1.0E+03 |
| reciprocal_picometres | reciprocal_angstroms | * | 1.0E+01 |
| nanometres_squared | angstroms_squared | * | 1.0E+02 |
| nanometres_squared | picometres_squared | * | 1.0E+06 |
| angstroms_squared | nanometres_squared | * | 1.0E-02 |
| angstroms_squared | picometres_squared | * | 1.0E+04 |
| angstroms_squared | 8pi2_angstroms_squared | * | 78.9568 |
| picometres_squared | nanometres_squared | * | 1.0E-06 |
| picometres_squared | angstroms_squared | * | 1.0E-04 |
| nanometres_cubed | angstroms_cubed | * | 1.0E+03 |
| nanometres_cubed | picometres_cubed | * | 1.0E+09 |
| angstroms_cubed | nanometres_cubed | * | 1.0E-03 |
| angstroms_cubed | picometres_cubed | * | 1.0E+06 |
| picometres_cubed | nanometres_cubed | * | 1.0E-09 |
| picometres_cubed | angstroms_cubed | * | 1.0E-06 |
| kilopascals | gigapascals | * | 1.0E-06 |
| gigapascals | kilopascals | * | 1.0E+06 |
| hours | minutes | * | 6.0E+01 |
| hours | seconds | * | 3.6E+03 |
| hours | microseconds | * | 3.6E+09 |
| minutes | hours | / | 6.0E+01 |
| minutes | seconds | * | 6.0E+01 |
| minutes | microseconds | * | 6.0E+07 |
| seconds | hours | / | 3.6E+03 |
| seconds | minutes | / | 6.0E+01 |
| seconds | microseconds | * | 1.0E+06 |
| microseconds | hours | / | 3.6E+09 |
| microseconds | minutes | / | 6.0E+07 |
| microseconds | seconds | / | 1.0E+06 |
| celsius | kelvins | - | 273.0 |
| kelvins | celsius | + | 273.0 |
| electrons_per_nanometres_cubed | electrons_per_angstroms_cubed | * | 1.0E+03 |
| electrons_per_nanometres_cubed | electrons_per_picometres_cubed | * | 1.0E+09 |
| electrons_per_angstroms_cubed | electrons_per_nanometres_cubed | * | 1.0E-03 |
| electrons_per_angstroms_cubed | electrons_per_picometres_cubed | * | 1.0E+06 |
| electrons_per_picometres_cubed | electrons_per_nanometres_cubed | * | 1.0E-09 |
| electrons_per_picometres_cubed | electrons_per_angstroms_cubed | * | 1.0E-06 |