Supporting Data mmcif_pdbx.dic
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 5.336 | 2020-11-10 | Changes (ep): + Create category _em_virus_synthetic + Add 'TFE' to _pdbx_nmr_chem_shift_ref.mol_common_name enumeration + Update funding enumerations + Make _diffrn_refln.standard_code and _diffrn_refln.scale_group_code non-mandatory |
mmcif_pdbx.dic |
| 5.335 | 2020-10-27 | Changes (ep): + add STOPGAP and novaSTA to _emd_software.name and _em_software.name enumerations + add PRIME and ULTIMA to _software.name enumeration + Update funding enumerations + Set upper limits for _reflns_shell.Rmerge_I_obs and _reflns.pdbx_Rmerge_I_obs + Change code for _pdbx_depui_entry_details.replace_pdb_id to pdbx_PDB_obsoleted_db_id + Add SYNTHETIC to _em_entity_assembly.source enumeration + Add category _em_entity_assembly_synthetic + Add attribute _atom_site.pdbx_atom_ambiguity + Add category pdbx_database_doi |
mmcif_pdbx.dic |
| 5.334 | 2020-10-05 | Changes (ep): + Remove trailing newlines from dictionary + Update funding enumerations + Add 'TMSP' to _pdbx_nmr_chem_shift_ref.mol_common_name enumeration + Add 'CRISpy' to _software.name enumeration + Add pdbx_PDB_obsoleted_db_id for list of PDB ids that are obsoleted + Add AUCO to enumeraion for _pdbx_database_status.status_code_cs and _pdbx_database_status.status_code_mr |
mmcif_pdbx.dic |
| 5.333 | 2020-09-08 | Changes (ep): + Update funding enumerations + Add advisory limits for _em_focused_io_beam.final_thickness and _emd_sectioning_focused_ion_beam.final_thickness + Add 'methylene carbons' to _pdbx_nmr_chem_shift_ref.atom_group enumeraton + Change type of struct_ncs_oper.id, struct_ncs_end_gen.oper_id, pdbx_struct_ncs_virus_gen.oper_id to int to match current PDB practice + Change _pdbx_struct_assembly.details mandatory based on current use. + Change type of pdbx_database_released.db_id type from line to pdbx_related_db_id |
mmcif_pdbx.dic |
| 5.332 | 2020-08-19 | Changes (ep): + Create enumeration for pdbx_chem_comp_feture.type + Remove ranges for _diffrn_source.pdbx_wavelength_list as not compatible with code type 'line' + Update funding enumerations + Add SHELXT to _software.name enumeration + Remove obsolete enumberations from chem_comp.type 'D-saccharide 1,4 and 1,6 linking', 'L-saccharide 1,4 and 1,4 linking', 'L-saccharide 1,4 and 1,6 linking', 'D-saccharide 1,4 and 1,4 linking' + Close the enumerations for _pdbx_nmr_constraint_file.constraint_subtype and _pdbx_nmr_systematic_chem_shift_offset.type + Add 'NMR relaxation study' to _pdbx_struct_assembly_auth_evidence.experimental_support eumeration |
mmcif_pdbx.dic |
| 5.331 | 2020-07-20 | Changes (ep): + Add "Synthetic opioid" and "Transition state mimetic' to _pdbx_reference_molecule.class and _pdbx_molecule_features.class enumerations. + Add "The Mark Foundation", "Canada Research Chairs" and "The Swedish Foundation for Strategic Research" to _pdbx_audit_support.funding_organization" + Add 'PELCO Ultrathin Carbon with Lacey Carbon' to _em_sample_support.grid_type enumeration |
mmcif_pdbx.dic |
| 5.330 | 2020-07-11 | Changes (ep): + Add "MANACA" to _diffrn_source.pdbx_synchrtron_beamline, "LNLS SIRUS BEAMLINE MANACA" to _diffrn_source.type and "LNLS SIRUS" to _diffrn_source.pdbx_synchrotron enumerations. + Update descripion of _atom_site.id to reflect current PDB usage + Document that attributes in _reflns_shell category apply to multiple shells and not just highest resolution shell + Add "The Mark Foundation" to _pdbx_audit_support.funding_organization" + Correct "deposition_email" type to be POSIX compliant |
mmcif_pdbx.dic |
| 5.329 | 2020-06-23 | Changes (ep): + Add 'Transport activator' to _pdbx_reference_molecule.class and _pdbx_molecule_features.class + Remove 'ELETTRA BEAMLINE XRD2' to _diffrn_source.type and _diffrn_source.pdbx_synchrotron_beamline. 'ELETTRA BEAMLINE 11.2C' is the same one. + Add 'S-Glycosylation' to enumeration for _struct_conn.pdbx_role + Add 'eTasED' to em_software.name enumeration + Restrict type of em_single_particle_entity.id to integer + Add 'Remediation' to pdbx_audit_revision_details.type enumeration |
mmcif_pdbx.dic |
| 5.328 | 2020-06-08 | Changes (ep): + Add new funding agency: 'Consortia for HIV/AIDS Vaccine Development' and 'Tower Cancer Research Foundation' + Synchronize pdbx_molecule_features.class enumeration from _pdbx_reference_molecule.class + _em_software.name enumeration add DIALS + Add 'SSRL BEAMLINE BL12-1' to _diffrn_source.type enumeration |
mmcif_pdbx.dic |
| 5.327 | 2020-06-05 | Changes (ep): + Remove local contexts from the following categories: _pdbx_chem_comp_synonyms, _pdbx_chem_comp_related, _pdbx_chem_comp_atom_related, _pdbx_entity_branch_list, _pdbx_entity_branch_link, _pdbx_entity_branch, _pdbx_branch_scheme + Remove local contexts from the following attributs: _struct_conn.pdbx_ptnr1_atom_stereo_config, _struct_conn.pdbx_ptnr1_leaving_atom_id, _struct_conn.pdbx_ptnr2_atom_stereo_config, _struct_conn.pdbx_ptnr2_leaving_atom_id, _entity_name_com.pdbx_provenance |
mmcif_pdbx.dic |
| 5.326 | 2020-05-26 | Changes (ep): + Incorpoate branch chain dictionary extension + Extend enumeration of pdbx_audit_support.funding_organization + Correct diffrn_source.type for "ORNL Spallation Neutron Source BEAMLINE MANDI" to indicate spallation source. + Add "oligosaccharide" to _pdbx_reference_entity_poly.type + Add 'cxi.merge' to _software.name enumeration + Extend enumeration of _pdbx_reference_molecule.class |
mmcif_pdbx.dic |
| 5.325 | 2020-04-13 | Changes (jt/ep): + Add 'ELETTRA BEAMLINE XRD2' to _diffrn_source.type and _diffrn_source.pdbx_synchrotron_beamline + Add _pdbx_audit_support.funding_organization enumeration + Add "GOLD" enumeration to em_support_film.material + Add "FEI Falcon IV (4k X 4k)" to _em_image_recording.film_or_detector_model + Add "JADAS" and "crYOLO" to em_software.name + Remove local contet from _pdbx_database_status.status_code_nmr_data |
mmcif_pdbx.dic |
| 5.324 | 2020-03-03 | Changes (pkeller/ep): + Changes to pdbx_refine_tls_group to enforce consistency between TLS group definitions and structure: Make the following items children of the corresponding items in atom_site: _pdbx_refine_tls_group.beg_auth_asym_id, _pdbx_refine_tls_group.beg_auth_seq_id, _pdbx_refine_tls_group.end_label_asym_id, _pdbx_refine_tls_group.end_auth_seq_id Add new items _pdbx_refine_tls_group.beg_PDB_ins_code, _pdbx_refine_tls_group.end_PDB_ins_code + Add _atom_type.pdbx_scat_Cromer_Mann_a6 and _atom_type.pdbx_scat_Cromer_Mann_b6 + Add PDBC to examples/enumerations for _pdbx_database_status.deposit_site, _pdbx_database_status.process_site, pdbx_chem_comp_audit.processing_site, _chem_comp.pdbx_processing_site, _pdbx_prd_audit.processing_site, pdbx_family_prd_audit.processing_site, em_admin.deposition_site, _pdbx_chem_comp_model_audit.processing_site + Set upper limit for _refine.ls_R_factor_obs, refine.ls_R_factor_R_free, refine.ls_R_factor_R_work to 1.0 + Change hard limits to soft for _em_imaging.accelerating_voltage + Extend pdbx_audit_support enumeration + Add CoMAND to _pdbx_nmr_software.name enumeration + Add 'mg' to _pdbx_nmr_exptl_sample.concentration_units + Make _pdbx_reference_entity_sequence.type and _pdbx_reference_entity_list.type into enumerations. |
mmcif_pdbx.dic |
| 5.323 | 2020-02-04 | Changes (ep): + Add "branched" to pdbx_reference_molecule.represent_as + Add 'HITACHI H3000 UHVEM' to _em_imaging.microscope_model + Extend pdbx_audit_support enumeration |
mmcif_pdbx.dic |
| 5.322 | 2020-01-26 | Changes (ep): + Extend deposition enumeration for pdbx_database_related to include 'split' and 'complete structure' + Extend pdbx_nmr_software.name (I-PINE) + Limit _reflns.pdc_Rrim_I_all to be less than 5 + Extend pdbx_audit_support enumeration + Add 'ICON' and 'ISOLDE' to _em_software.name enumeration. Remove duplicate 'CryoSPARC' + Improve description of _em_buffer.pH + Add 'NICKEL/TITANIUM' to _em_sample_support.grid_material + Create deposition enumeration for _em_imaging_optics.phase_plate + Add "TFS TALOS F200C" and "TFS TALOS L120C" to em_imaging.microscope_model + Add pdbx_chem_comp_synonyms + Add "Model orientation/position" add to _pdbx_depui_status_flags.post_rel_replacement_reason enumeration. |
mmcif_pdbx.dic |
| 5.321 | 2019-12-18 | Changes (ep): + Extend _diffrn_detector.type enumeration to include BIX-3, BIX-4 and iBIX |
mmcif_pdbx.dic |
| 5.320 | 2019-11-26 | Changes (ep): + Extend _pdbx_audit_support.funding_organization + Add alpha and beta linking D/L saccharide to _chem_comp.type + Add 'CONDENSED IUPAC CARBOHYDRATE SYMBOL','IUPAC CARBOHYDRATE SYMBOL' 'SNFG CARBOHYDRATE SYMBOL' to _pdbx_chem_comp_identifier.type + Add 'CARBOHYDRATE ANOMER', 'CARBOHYDRATE ISOMER', 'CARBOHYDRATE RING' to examples for pdbx_chem_comp_feature.type |
mmcif_pdbx.dic |
| 5.319 | 2019-11-12 | Changes (ep): + Extend pdbx_database_status to include nmr_data contents. + Reorganize _pdbx_audit_support.funding_organization such that details will include the country. + Extend em_software.name to include ERRASER + Set upper limit for _diffrn.ambient_temp to 450 + Add TFA to _pdbx_nmr_chem_shift_ref.mol_common_name. Add fluorine to _pdbx_nmr_chem_shift_ref.atom_group + Add 'TFS TAOLS' to _em_imaging.microscope_model + Correct soft limits for _reflns.percent_possible_obs + Make _struct_keywords.pdbx_keywords mandatory for deposition + Add soft limits for _reflns.pdbx_CC_half |
mmcif_pdbx.dic |
| 5.318 | 2019-10-28 | Changes (ep): + Remove duplicate enumerations from _diffrn_detector.type + Correct deposition_email type name |
mmcif_pdbx.dic |
| 5.317 | 2019-10-21 | Changes (ep): + Add newer DECTRIS EIGER detectors to _diffrn_detector.type + Extend _pdbx_audit_support.funding_organiation enumerations + _em_imaging.specimen_holder_model add 'GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' and 'FISCHIONE 2550' to enumeration + _em_imaging.microscope_model add 'TFS GLACIOS' and ' TFS KRIOS' to enumeration. |
mmcif_pdbx.dic |
| 5.316 | 2019-10-10 | Changes (ep): + Adjust range limits for _reflns.pdbx_CC_star, _reflns_shell.pdbx_CC_star + Adjust range limits for _reflns.pdbx_R_split, _reflns_shell.pdbx_R_split + Create internal enumeration for struct_ref_seq_dif.details + Expand _pdbx_audit_support.funding_organiation enumerations + Use a new type deposition_email for pdbx_contact_author.email |
mmcif_pdbx.dic |
| 5.315 | 2019-09-11 | Changes (ep): + Expand _pdbx_audit_support.funding_organiation enumerations + Added _pdbx_depui_status_flags.post_rel_replacement_reason_details and _pdbx_audit_revision_details.details + Update description of _atom_site.label_alt_id + Add _refine.pdbx_R_complete and _refine_ls_shell.pdbx_R_complete |
mmcif_pdbx.dic |
| 5.314 | 2019-08-19 | Changes (ep/jmb): + Correct capitalization in _pdbx_nmr_spectrometer.model + Expand _diffrn_detector.type, _pdbx_audit_support.funding_organiation enumerations + Adjust advisory limits for _reflns.pdbx_Rrim_I_all, _reflns.pdbx_Rpim_I_all, _reflns.pdbx_R_split + Add _atom_type.pdbx_scat_Z, _atom_type.pdbx_N_electrons + Add _reflns.pdbx_CC_star and _reflns_shell.pdbx_CC_star definitions |
mmcif_pdbx.dic |
| 5.313 | 2019-07-10 | Changes (ep): + Expand _diffrn_detector.type, _software.name, _pdbx_audit_support.funding_organiation enumerations + Make _pdbx_refine_tls_group.pdbx_refine_id and _pdbx_refine_tls.pdbx_refine_id mandatory |
mmcif_pdbx.dic |
| 5.312 | 2019-06-11 | Changes (ep/jmb): + Adjust descriptions involving country to include region. + Rename pdbx_entity_descriptor to pdbx_entity_branch_descriptor + Adjust limits of _em_image_recording.avg_electron_dose_per_image" + Add DECTRIS EIGER2 detectors to _diffrn_detector.type + Increase high soft limit for _reflns_shell.pdbx_Rsym_value |
mmcif_pdbx.dic |
| 5.311 | 2019-05-21 | Changes (ep): + Add _pdbx_entry_details.has_ligand_of_interest + Add Fragon to software.name enumeration + Make pdbx_nmr_chem_shift_software.software_label non-mandatory |
mmcif_pdbx.dic |
| 5.310 | 2019-05-16 | Changes (ep/jb): + Add PDB-REDO to software.name enumeration + Set upper limit for _exptl_crystal_grow.pH to 14.0 + Update examples for exptl_crystal_grow.method to match enumeration + Add newer AVANCE spectrometers to _pdbx_nmr_spectrometer.model |
mmcif_pdbx.dic |
| 5.309 | 2019-04-24 | Changes (ep): + Make _em_depui.obsolete_instructions and em_admin.replace_existing_entry_flag non-mandatory. + Extend _pdbx_audit_support.funding_organization enumeration + Incorporate enumeration/examples for branch change carbohydrates including _entity.type, _pdbx_chem_comp_identifier.type, _pdbx_entity_descriptor.type. + Increase soft upper limit for _reflns_shell.Rmerge_I_obs + Add _pdbx_depui_status_flags.post_rel_replacement_reason + Add _pdbx_database_status.post_rel_recvd_coord_date, _pdbx_database_status.post_rel_recvd_coord, _pdbx_database_status.post_rel_status. + Create type 'id_list_spc' for an id list with spaces. Use for pdbx_struct_assembly_gen_depositor_info.chain_id_list |
mmcif_pdbx.dic |
| 5.308 | 2019-04-11 | Changes (ep): + Add Amber to _em_software.name enumeration + Extend _pdbx_audit_support.funding_organization + Change type of _pdbx_struct_assembly_gen.asym_id_list to text |
mmcif_pdbx.dic |
| 5.307 | 2019-04-01 | Changes (ep): + Add 'carbonyl carbon' to _pdbx_nmr_chem_shift_ref.atom_group enumeration + Extend _pdbx_audit_support.funding_organization + Create deposition enumeration for _pdbx_nmr_software.name |
mmcif_pdbx.dic |
| 5.306 | 2019-03-20 | Changes (ep): + Extend _pdbx_audit_support.funding_organization + Restrict _entity.pdbx_number_of_molecules to integers + Remove polysaccharide(D) and polysaccharide(L) type from entity_poly.type + Update example for _audit_author.identifier_ORCID and _citation_author.identifier_ORCID with an invalid checksum + Add "LaB6 thermoionic" to _diffrn_source.type enumeration + Add emClairity to em_software.name enumeration + Change lower limit for _refine.ls_d_res_low, _refine_ls_shell.d_res_low, _refine_ls_shell.d_res_high to not include 0.0 |
mmcif_pdbx.dic |
| 5.305 | 2019-02-03 | Changes (ep): + Revert change for _refine.pdbx_starting_model being mandatory in deposition + Add enumeration for struct_conn.conn_type_id + Extend _pdbx_audit_support.funding_organization with KU Leuven and Lundbeckfonden |
mmcif_pdbx.dic |
| 5.304 | 2019-01-29 | Changes (ep): + Adjust contexts for _pdbx_chem_comp_audit.annotator and _pdbx_chem_comp_audit.details + Extend _pdbx_audit_support.funding_organization enumeration + Set maximum for _em_imaging.accelerating_voltage to 400 + For deposition, make _refine.pdbx_method_to_determine_struct, _refine.pdbx_starting_model, _reflns_shell.number_unique_obs mandatory + Add 'Excillum MetalJet D2 70 kV' and 'ELETTRA BEAMLINE 11.2C to _diffrn_source.type enumeration + Change _em_3d_fitting_list.pdb_chain_id type to asym_id |
mmcif_pdbx.dic |
| 5.303 | 2018-12-03 | Changes (ep): + Change ec-type to support new enzyme classifications + Add TRANSLOCASE to _struct_keywords.pdbx_keywords enumeration |
mmcif_pdbx.dic |
| 5.302 | 2018-11-19 | Changes (ep): + Add various em_* categories to em_group + Add 'Science and Technology Funding Council' and 'Global Challenges Research Fund' to _pdbx_audit_support.funding_organization + _pdbx_audit_support.funding_organization mandatory for deposition + _em_imaging.c2_aperture_diameter units changed to microns and lower limit changed to 1 + _pdbx_nmr_chem_shift_ref.mol_common_name add glucose to enumeration |
mmcif_pdbx.dic |
| 5.301 | 2018-11-08 | Changes (ep): + Add Buccaneer to _em_software.name enumeration + Add enumeration to _pdbx_prd_audit.processing_site + Add CHESS BEAMLINE G3, PAL-XFEL BEAMLINE NCI beamlines + Add Rigaku HyPic-6000HE detector + Add newer AVANCE spectrometers to _pdbx_nmr_spectrometer.model + Adjust limits for _refine.ls_d_res_high to not include 0 + Remove use of non_negative_int as regular expression incorrect + Add citation_doi and exp_data_doi for use in citation and pdbx_related_exp_data_set |
mmcif_pdbx.dic |
| 5.300 | 2018-10-15 | Changes (ep/jmb): + Correct examples for _pdbx_related_exp_data_set + _diffrn_detector.type correct type for 'BRUKER PHOTON 100' + Extend audit content types to support 'Chemical component' + Add cisTEM and Topaz to em_software.name + Update _pdbx_audit_support.funding_organization enumeration |
mmcif_pdbx.dic |
| 5.299 | 2018-09-04 | Changes (ep): + Correct _diffrn_source.type enumeration for 'MICROMAX-003' + Extend _pdbx_audit_support.funding_organization enumeration + Incorporate XFEL extension + Add Diamond beamlines VMXi and VMXm to _diffrn_source.type + Add "Gorgon" and "Pathwalking" to _em_software.name |
mmcif_pdbx.dic |
| 5.298 | 2018-08-01 | Changes (ep): + Extend _pdbx_audit_support.funding_organization enumeration |
mmcif_pdbx.dic |
| 5.297 | 2018-07-23 | Changes (ep): + Extend _software.language enumeration + Extend _pdbx_audit_support.funding_organization enumeration + Add COUNTER-DIFFUSION to deposition enumeration for _exptl_crystal_grow.method + Add 'JEOL CRYOSPECPORTER' to _em_imaging.specimen_holder_model enumeration + Extend deposition enumerations for _software.name + Require _atom_site.pdbx_PDB_model_num non-zero positive integer + For deposition, require _pdbx_nmr_representative.conformer_id to be positive integer |
mmcif_pdbx.dic |
| 5.296 | 2018-06-25 | Changes (ep): + Update point_group regular expression type + Add beamline 'SACLA BEAMLINE BL2' and 'APS BEAMLINE 34-ID' to _diffrn_source.type enumeration + Change context of _citation_author.identifier_ORCID to make public + Extend enumerations with _pdbx_audit_support.funding_organization + Provide deposition specific help text for _pdbx_nmr_representative.conformer_id + Make _pdbx_contact_author.identifier_ORCID mandatory during deposition |
mmcif_pdbx.dic |
| 5.295 | 2018-06-07 | Changes (ep): + Update pdbx_deposit_group.group_type enumeration + Extend ranges to match EMDB schema for em_imaging.calibrated_defocus_max _em_start_model.random_conical_tilt_angle, _em_imaging.nominal_cs + Change units for emd_fiducial_markers.diameter, _em_fiducial_markers.diameter + Change units, range, and mandatory flag for _em_focused_ion_beam.dose_rate and _emd_sectioning_focused_ion_beam.dose_rate + Add 'JEOL 3100FEF' to em_imaging.microscope_model |
mmcif_pdbx.dic |
| 5.294 | 2018-05-12 | Changes (ep): + Update pdbx_item_enumeration.detail for _pdbx_nmr_spectrometer.model + Extend enumeration for _pdbx_audit_support.funding_organization |
mmcif_pdbx.dic |
| 5.293 | 2018-04-17 | Changes (ep): + Allow any number of digits for emd_id + Add "PSI JUNGFRAU 1M" to diffn_detector.type enumeration + Add pdbx_depui_status_flags.merged_fail |
mmcif_pdbx.dic |
| 5.292 | 2018-03-22 | Changes (ep): + Add "MAXIMUM LIKELIHOOD" to _emd_angle_assignment.type enumeration + Extend range for _em_image_recording.average_exposure_time + Update diffrn_source category deposition related enumerations |
mmcif_pdbx.dic |
| 5.291 | 2018-03-06 | Changes (ep): + Ensure _diffrn_detector.type, _diffrn_source.pdbx_synchrotron_beamline, _diffrn_source.pdbx_synchrotron_site enumerations complete + Extend _pdbx_audit_support.funding_organization enumeration + Add RNA-Puzzles to _pdbx_database_status.methods_development_category enumeration + Add _pdbx_audit_support.details |
mmcif_pdbx.dic |
| 5.290 | 2018-02-07 | Changes (ep): + Add SIMBAD to _software.name enumeration + Add 'Sculptor', 'SUPER' and 'FOCUS' to em_software.name enumeration + Extend _pdbx_audit_support.funding_organization enumeration + Extend _pdbx_struct_assembly_auth_evidence_depositor_info.experimental_support enumeration + Remove 4x3_matrix and implement 3x4_matrices + Add enumeration for _pdbx_deposit_group.group_type + Add _em_imaging_optics.energyfilter_slit_width + Switch to closed enumeration for _pdbx_audit_support.funding_organization. + Change type of _pdbx_depui_validation_status_flags.adp_outliers_zero to text |
mmcif_pdbx.dic |
| 5.289 | 2018-01-11 | Changes (ep): + Add "SLAC LCLS BEAMLINE AMO" to _diffrn_source.type, add "AMO" to _diffrn_source.pdbx_synchrotron_breamline to deposition enumerations. + Correct _diffrn_source.type for "BRUKER D8 QUEST" - is a SEALED TUBE. + Update/add range limits for _em_imaging.nominal_defocus_max, _em_imaging.nominal_defocus_min, _em_image_recording.average_exposure_time, _em_imaging.nominal_magnification, _em_focused_ion_beam.initial_thickness, _em_focused_ion_beam.current, _em_imaging.nominal_cs, _em_imaging.c2_aperature_diameter, _em_imaging.calibrated_defocus_max + Add 'ISOLDE" to enumeration for _software.name + Add "JEOL CRYO ARM 200" and "JEOL CRYO ARM 300" to _em_imaging.microscope_model + Improve date_dep regular expression to prevent zero dates + Extend _pdbx_audit_support.funding_organization enumeration + Add 'HOLD FOR 8 WEEKS' to enumeration pdbx_database_status.dep_release_code_struct_fact + Add 'Bruker PHOTON III' and correct type of 'Bruker PHOTON II' in _diffrn_detector.type enumeration. + Add 'GRAPHENE OXIDE' to _em_sample_support.grid_material enumeration |
mmcif_pdbx.dic |
| 5.288 | 2017-11-27 | Changes (ep/ar/cl): + Correct spelling errors in category_group_list.description + Add item_sub_category.id for TLS definitions in pdbx_refine_tls + Add _citation_author.identifier_ORCID with WWPDB_LOCAL context + Add SPOTITON to em_virtification.instrument enumeration + Add GATAN K3 detectors to _emd_image_recording.film_or_detector_model enumeration + Add 'GIF Bioquantum' to _em_imaging_optics.energyfilter_name enumeration + Update deposition description for citation_author.name + Add SwissFEL and PAL-XFEL enumerations to diffrn_source category enumerations + Set maximum of 30 seconds for _em_image_recording.average_exposure_time + Add 'HOLD FOR 4 WEEKS' to enumeration pdbx_database_status.dep_release_code_struct_fact |
mmcif_pdbx.dic |
| 5.287 | 2017-10-18 | Changes (ep/jmb): + Add _pdbx_depui_validation_status_flags.tls_no_aniso to flag TLS records without anisotropic ones during deposition + Add _pdbx_depui_validation_status_flags.adp_outliers_zero to flag zero B factors during deposition + Update _pdbx_audit_support.funding_organization enumeration + Add European XFEL site and beamlines to diffrn_source.type, diffrn_source.pdbx_synchrotron_beamline and diffrn_source.pdbx_synchrotron_site + pdbx_database_related.db_name deposition enumeration extended to include matching content_type context. + Add upper range limit for reflns.percent_possible_obs and reflns_shell.percent_possible_obs + Require reflns.pdbx_R_split and reflns_shell.pdbx_R_split to be positive and create advisory limits for deposition. + Make reflns_shell.d_res_low and reflns_shell.d_res_high mandatory for deposition system. + Add 'LIQUID ANODE' to Deposition enumeration for diffrn_source.source. Change METALJET generators in diffrn_source.type to match. + Extend enumeration for pdbx_struct_assembly_auth_evidence.experimental_support |
mmcif_pdbx.dic |
| 5.286 | 2017-09-10 | Changes (ep): + Add 'RMVD' to enumeration for pdbx_database_status.status_code, pdbx_database_status.status_code_sf, pdbx_database_status.status_code_mr, pdbx_database_status.status_code_cs + Add enumeration for em_sample_support.grid_type + Add enumeration for em_imaging_optics.energyfilter_name + Correct capitalization of BRUKER METALJET in diffrn_source.type + To support entity_branch_extension, extend deposition entity.type |
mmcif_pdbx.dic |
| 5.285 | 2017-08-30 | Changes (ep): + Add 'FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER' to em_imaging.specimen_holder_model enumeration + Add soft and hard limits for reflns.pdbx_Rrim_I_all, reflns_shell.pdbx_Rrim_I_all, reflns.pdbx_Rpim_I_all, reflns_shell.pdbx_Rpim_I_all, reflns_shell.pdbx_Rrim_I_all_anomalous, reflns_shell.pdbx_Rpim_I_all_anomalous, reflns.pdbx_Rrim_I_all_anomalous, reflns.pdbx_Rpim_I_all_anomalous + Add DepUI enumeration for em_software.name + Make pdbx_struct_assembly_auth_evidence.details and pdbx_struct_assembly_depositor_info.details mandatory at deposition + Update enumeration for _pdbx_audit_support.funding_organization + Add _pdbx_deposit_group.group_type + Remove ESRF BEAMLINE ID30A from diffrn_source.type + Update software.name enumeration with role software used (for deposition) |
mmcif_pdbx.dic |
| 5.284 | 2017-08-03 | Changes (ep): + Merge in all deposition interface enumerations, descriptions and mandatory codes + Add 'PDB_ACC' to database_2.database_id enumeration + Correct type for pdbx_nmr_exptl_sample.concentration_units to match enumeration + Add MCMR (Midwest Center for Macromolecular Research) to pdbx_SG_project.initial_of_center and pdbx_SG_project.full_name_of_center |
mmcif_pdbx.dic |
| 5.283 | 2017-07-08 | Changes (ep): + Add 'carbohydrate dihedral angle' to _pdbx_nmr_constraint_file.constraint_type + Extend soft limit range for em_image_recording.avg_electron_dose_per_image + Set pdbx_depui_status_flags.is_grant_funded mandatory for deposition |
mmcif_pdbx.dic |
| 5.282 | 2017-07-01 | Changes (ep): + Add pdbx_depui_status_flags.use_sas_refine |
mmcif_pdbx.dic |
| 5.281 | 2017-06-27 | Changes (ep): + Add pdbx_contact_author.legacy_address to replace audit_contact_author.address. + Change type for pdbx_database_status.recvd_initial_deposition_date to yyyy-mm-dd from yyyy-mm-dd:hh:mm for xsd type checking + Add 'FEI FALCON III (4k x 4k)' to enumeration for emd_image_recording.film_or_detector_model |
mmcif_pdbx.dic |
| 5.280 | 2017-05-10 | Changes (ep): + Add pdbx_supporting_exp_data_set category + Remove deposition only related enumerations + Add _pdbx_depui_status_flags.has_sas_data and _pdbx_depui_status_flags.is_sas_deposited |
mmcif_pdbx.dic |
| 5.279 | 2017-04-20 | Changes (ep): + Add 'Data processing' to _pdbx_audit_revision_group.group enumeration + Add 'Obsolete' to _pdbx_audit_revision_details.type + Change enumeration in _emd_map.endian_type and _em_map.endian_type from 'small' to 'little' |
mmcif_pdbx.dic |
| 5.278 | 2017-04-18 | Changes (ep): + Add WWPDB_LOCAL context for entry.pdbx_DOI + Add 'Direct Drive' to _pdbx_nmr_spectrometer.model deposition enumeration + For v50: Mark as WWPDB_LOCAL context for database_PDB_rev and database_PDB_rev_record |
mmcif_pdbx.dic |
| 5.277 | 2017-04-08 | Changes (ep): + For v50: correct WWPDB_LOCAL context for _pdbx_database_status.date_begin_release_preparation, and remove context for _pdbx_database_status.status_code_cs |
mmcif_pdbx.dic |
| 5.276 | 2017-04-06 | Changes (ep/mrs): + Correct capitalization of enumerations in pdbx_contact_author.contry and pdbx_audit_support.country. + Correct capitalization of enumerations of _ pdbx_SG_project.full_name_of_center + Update archive enumerations for pdbx_nmr_exptl_sample.concentration_units to match deposition enumeration + For deprecated em_* categories, in which a forward reference is provided to new item in dictonary, provide the reverse mapping as well. + For v5rc: For deprecated computing category provide forward references to software category + For v5rc: export _pdbx_database_status.recvd_initial_deposition_date and indicate replaces database_PDB_rev.date_original + For v5rc: remove pdbx_binding_assay category + Extend enumeration for _pdbx_nmr_constraint_file.constraint_subtype ('PRE', 'PRE solvent', 'CSP') + For v5rc: For deprecated pdbx_version category provide replacement items names |
mmcif_pdbx.dic |
| 5.275 | 2017-03-28 | Changes (ep/mg): + Move 'Bruker METLJET' from diffrn_detector.type enumeration to diffrn_source.type + Change 'SSRF BEAMLINE BL17U' ine diffrn_source.type enumerate to 'SSRF BEAMLINE BL17U1' + Add 'Agrovata', 'DIMPLE', 'SHELXL-97' to software.name deposition enumeration |
mmcif_pdbx.dic |
| 5.274 | 2017-03-20 | Changes (ep): + For v5rc: Remove category context for database_PDB_rev and database_PDB_rev_record + Add 'Force Field X' to deposition enumeration for software.name |
mmcif_pdbx.dic |
| 5.273 | 2017-03-20 | Changes (ep): + For v5rc: Set category context to WWPDB_LOCAL for computing + For v5rc: Remove context on the following due to existing data in archive _atom_site.Cartn_x_esd, _atom_site.Cartn_y_esd, _atom_site.Cartn_z_esd, _atom_site.occupancy_esd, _atom_site.B_iso_or_equiv_esd, _atom_site_anisotrop.U[1][1]_esd, _atom_site_anisotrop.U[2][2]_esd, _atom_site_anisotrop.U[3][3]_esd, _atom_site_anisotrop.U[1][2]_esd, _atom_site_anisotrop.U[1][3]_esd, _atom_site_anisotrop.U[2][3]_esd + Add 'Bruker METALJET' to _diffrn_detector.type enumeration + Flag _pdbx_audit_revision_details.type as mandatory for deposition. + Add _pdbx_crystal_alignment.ybeam_esd + Make _refine_B_iso.pdbx_residue_num, _refine_B_iso.pdbx_strand, _refine_B_iso.pdbx_residue_name non-mandatory + Correct examples for pdbx_audit_revision_history and pdbx_audit_revision_group + Update enumeration for _pdbx_audit_revision_group.group + Create/update examples for emd_molecular_mass, emd_vitrification, emd_angle_assignment, emd_particle, emd_volume, emd_modelling_initial_model |
mmcif_pdbx.dic |
| 5.272 | 2017-03-14 | Changes (ep): + For v5rc: Set category context to WWPDB_LOCAL for pdbx_version, database_PDB_rev and database_PDB_rev_record + Add ssbond to enumeration for pdbx_data_processing_status.status + Set WWPDB_LOCAL context for em_2d_crystal_entity.c_sampling_length in v5_next but not v5rc. |
mmcif_pdbx.dic |
| 5.271 | 2017-03-09 | Changes (ep): + Add category group assignments for pdbx_unobs_or_zero_occ_residues, pdbx_unobs_or_zero_occ_atoms, pdbx_struct_mod_residue, pdbx_distant_solvent_atoms, _pdbx_struct_special_symmetry, pdbx_pdb_compnd, pdbx_pdb_source + Update context values to WWPDB_LOCAL for pdbx_remediation_atom_site_mapping + Parent for _pdbx_remediation_atom_site_mapping.auth_alt_id removed. + Add MIRAS, SIR to deposition enumeration for _refine.pdbx_method_to_determine_struct + Change type for pdbx_hybrid.residue_names to line based on usage + Add category keys for pdbx_source and pdbx_refine_ls_restr_ncs + To support data from pdb_extract, added pdbx_crystal_alignment category and updates to exisitin pdbx_phasing_MR, reflns_shell, reflns categories + For 4x3 matrix - require space between columns + Add new categories to support versioning: pdbx_audit_revision_history, pdbx_audit_revision_category, pdbx_audit_revision_group, pdbx_audit_revision_item, pdbx_audit_revision_details + For v5rc: Set item context on the following to WWPDB_LOCAL: _atom_site.Cartn_x_esd, _atom_site.Cartn_y_esd, _atom_site.Cartn_z_esd, _atom_site.occupancy_esd, _atom_site.B_iso_or_equiv_esd, _atom_site_anisotrop.U[1][1]_esd, _atom_site_anisotrop.U[2][2]_esd, _atom_site_anisotrop.U[3][3]_esd, _atom_site_anisotrop.U[1][2]_esd, _atom_site_anisotrop.U[1][3]_esd, _atom_site_anisotrop.U[2][3]_esd |
mmcif_pdbx.dic |
| 5.270 | 2017-03-01 | Changes (ep): + Update pdbx_struct_assembly_auth_evidence_depositor_info.experimental_support enumeration to include 'immunoprecipitation' |
mmcif_pdbx.dic |
| 5.269 | 2017-02-27 | Changes (ep): + Add STARANISO to deposition software.name enumeration list + Add NSRRC BEAMLINE TPS 05A synchrotron beamline to diffrn.source.type + Update deposition example for refins.pdbx_starting_model + Add "MAATEL BIODIFF" to diffrn_detector.type + Update pdbx_struct_assembly_auth_evidence.experimental_support enumeration to include 'immunoprecipitation' |
mmcif_pdbx.dic |
| 5.268 | 2017-02-17 | Changes (ep): + Add internal pdbx_binding_assay.auth_comp_id + Provide limits for pdbx_binding_assay.assay_pH and pdbx_binding_assay.assay_temperature + Make pdbx_binding_assay.assay_type, pdbx_binding_assay.assay_value and pdbx_binding_assay.assay_value_type non-mandatory |
mmcif_pdbx.dic |
| 5.267 | 2017-02-15 | Changes (ep): + Export pdbx_entity_instance_feature to public in v5rc + For pdbx_entity_instance_feature.comp_id change parent to atom_site.label_comp_id + Add parent atom_site.auth_comp_id to pdbx_entity_instance_feature.auth_comp_id |
mmcif_pdbx.dic |
| 5.266 | 2017-02-11 | Changes (ep): + For 4x3_matrix - allow spaces at start of row + add pdbx_struct_assembly_auth_evidence_depositor_info. Change parent of pdbx_struct_assembly_gen_depositor_info to pdbx_struct_assembly_depositor_info + export pdbx_binding_assay to public in v5rc |
mmcif_pdbx.dic |
| 5.265 | 2017-02-05 | Changes (ep): + Add BRUKER TURBO X-RAY SOURCE and OXFORD DIFFRACTION NOVA to list of X-ray sources for deposition system. + Define 4x3_matrix, id_list, symmetry_operation as regular expressions for use in deposition system to validate pdbx_struct_assembly_gen_depositor_info + Add pdbx_struct_assembly_gen_depositor_info.symmetry_operation |
mmcif_pdbx.dic |
| 5.264 | 2017-01-05 | Changes (ep/M. Hekkelman): + Change _pdbx_struct_assembly_gen_depositor_info.chain_id_list non-mandatory + Correct inconsistent mandatory setting for _atom_site.label_alt_id, _atom_site.label_comp_id, _atom_site.label_atom_id, _diffrn_refln.wavelength_id, _atom_site.label_entity_id, _atom_site.label_seq_id, _refln.wavelength_id, _atom_site.label_asym_id, _struct_conn.ptnr1_label_atom_id, _struct_conn.ptnr2_label_atom_id, _struct_mon_prot_cis.label_alt_id, _struct_site_gen.label_alt_id + Split up pdbx_struct_assembly_auth_evidence into pdbx_struct_assembly_auth_classification. Export categories to v5rc + Make _pdbx_struct_assembly_gen_depositor_info.chain_id_list, _pdbx_struct_assembly_gen_depositor_info.full_matrices, _pdbx_struct_assembly_gen_depositor_info.at_unit_matrix, non-mandatory for archive, but mandatory depui + Make pdbx_nmr_refine.software_ordinal a key for category internally + Add adamantane to _pdbx_nmr_chem_shift_ref.mol_common_name enumeration |
mmcif_pdbx.dic |
| 5.263 | 2017-01-03 | Changes (jw/ep): + add units micrometres, micrometres_squared, teraphotons_per_pulse, kiloelectron_volts, microjoules, hertz, femtoseconds, microliters_per_min + add category group xfel_group + incorporate draft xfel dictionary extension + incorporate draft diffraction data extension and supporting category group + Add _pdbx_struct_assembly_gen_depositor_info.all_chains |
mmcif_pdbx.dic |
| 5.262 | 2016-12-19 | Changes (ep/jb): + Update pdbx_struct_assembly_gen_depositor_info category for better support of assemblies. + Add pdbx_entity_instance_feature.auth_seq_num and auth_comp_id + Add DECTRIS EIGER X 500K to diffrn_detector.type + Add "FRM II BEAMLINE BIODIFF" to diffrn_source.type + Remove context for audit_author.identifier_ORCID + Item context added for audit_author.address |
mmcif_pdbx.dic |
| 5.261 | 2016-12-06 | Changes (ep/esg/cl): + Allow 0.0 in range for emd_crystallography_stats.overall_phase_error + emd_recombinant_expression.plasmid: make non-mandatory + Reclassify the category_group for em_ categories + Add pdbx_biocurator_comment and pdbx_depositor_comment |
mmcif_pdbx.dic |
| 5.260 | 2016-11-30 | Changes (jdw): + Add item _audit_author.identifier_ORCID + Add category pdbx_entity_instance_feature |
mmcif_pdbx.dic |
| 5.259 | 2016-11-30 | Changes (ep): + Allow 0.0 in range for em_diffraction_stats.overall_phase_error + _em_entity_assembly_recombinant.plasmid: make non-mandatory + Flag _em_helical_entity, em_helical_entity.hand, _em_single_particle_entity, _em_virus_entity.ictvdb_id, as deprecated in V5RC and provide forward reference possible. |
mmcif_pdbx.dic |
| 5.258 | 2016-11-29 | Changes (ep): + Add missing detectors to em_image_recording.file_or_detector_model + Add HITACHI EF3000 to em_imaging.microscope_model + For deprecated em_* categories, change context to WWPDB_DEPRECATED and provide mapping to replacement |
mmcif_pdbx.dic |
| 5.257 | 2016-11-22 | Changes (ep): + struct_keywords.pdbx_keywords add documented enumerations + pdbx_released_exp_data_set.data_set_type add EMPIAR + diffrn_detector.type: Add Bruker PHOTON II, TVIPS TEMCAM-F416 + diffrn_source.type add Excillum MetalJet sealed tube generators + pdbx_data_processing_status.task_name: update examples and provide annotation enumeration + make pdbx_nmr_refine.software_ordinal a key for category + em_entity_assembly_molwt: Make units and value non-mandatory |
mmcif_pdbx.dic |
| 5.256 | 2016-10-18 | Changes (ep): + em_vitrification.instrument add ZEISS PLUNGE FREEZER CRYOBOX + Add em_3d_reconstruction/emd_final_reconstruction refinement_type attribute to replace fsc_type. + _emd_admin.hold_expiry_date renamed _emd_admin.map_hold_date |
mmcif_pdbx.dic |
| 5.255 | 2016-09-28 | Changes (ep): + Add range limits for reflns.pdbx_CC_half and reflns_shell.pdbx_CC_half + Add pdbx_deposit_group.group_title and pdbx_deposit_group.group_description + emd_microscopy.microscope add FEI/PHILIPS CM10 + em_imaging.microscope_model add FEI/PHILIPS CM10, JEOL 100B, SIEMENS SULEIKA + Enhanced EM extension dictionary + Add_ndb_struct_na_base_pair.propel as alias for _ndb_struct_na_base_pair.propeller |
mmcif_pdbx.dic |
| 5.254 | 2016-09-19 | Changes (ep): + Extend enumeration for pdbx_nmr_chem_shift_ref.mol_common_name to include 'methionine' and 'deuterium oxide' + Add SLAC sector MFX + Correct example for pdbx_reference_linked_entity_link + Enhanced EM extension dictionary |
mmcif_pdbx.dic |
| 5.253 | 2016-08-26 | Changes (ep): + Add enumeration for emd_map.contour_level_source and em_map.contour_level_source |
mmcif_pdbx.dic |
| 5.252 | 2016-07-27 | Changes (ep): + emd_virus_shell.triangulation and _em_virus_shell.triangulation, changle value to positive integer + Add DECTRIS PILATUS3 R CdTe detectors to diffrn_detector.type |
mmcif_pdbx.dic |
| 5.251 | 2016-07-05 | Changes (ep): + Change description of reflns.pdbx_CC_half and reflns_shell.pdbx_CC_half to refer to a decimal value. + Remove local context for _pdbx_deposit_group.group_id + Update enumerations for _pdbx_nmr_chem_shift_ref.atom_group and _pdbx_nmr_exptl_sample_conditions.pH_units + Description updates to several emd related categories + Deposition updates to BRUKER IMUS MICROFOCUS source and RAYONIX MX225-HS/MX170-HS detectors + Range limits for reflns.pdbx_CC_half + _pdbx_item_linked_group and _pdbx_item_linked_group_list updates for pdbx_chem_comp_model_*, em_*, emd_* and_pdbx_struct_special_symmetry categories |
mmcif_pdbx.dic |
| 5.250 | 2016-06-04 | Changes (ep): + Reduce _pdbx_nmr_exptl_sample_conditions.temperature_units enumeration for deposition system + Add deposition system enumeration _diffrn_detector.type with numerous DECTRIS detectors + Update examples for: _em_author_list _em_depui _em_grid_pretreatment _em_diffraction _em_diffraction_shell _em_diffraction_stats _em_final_classification _em_euler_angle_assignment _em_ctf_correction _em_image_processing _em_fsc_curve _emd_microscopy _emd_image_recording _pdbx_deposit_group_index _pdbx_entity_src_gen_depositor_info + Create parent/child definitions for: _em_imaging.specimen_id _em_image_scans.image_recording_id _em_3d_reconstruction.image_processing_id _em_diffraction_stats.image_processing_id _em_image_recording.imaging_id _em_final_classification.image_processing_id _em_startup_model.image_processing_id _em_euler_angle_assignment.image_processing_id _em_ctf_correction.image_processing_id _em_volume_selection.image_processing_id _em_image_processing.image_recording.id _emd_microscopy.emd_specimen_id _emd_image_recording.emd_microscopy_id _emd_image_digitization.emd_image_recording_id' _emd_image_processing.emd_image_recording_id' _emd_startup_model.emd_image_processing_id _emd_angle_assignment.emd_image_processing_id _emd_final_reconstruction.emd_image_processing_id _emd_final_classification.emd_image_processing_id _emd_particle_selection.emd_image_processing_id _emd_volume_selection.emd_image_processing_id _emd_ctf_correction.emd_image_processing_id _emd_crystallography_stats.emd_image_processing_id |
mmcif_pdbx.dic |
| 5.249 | 2016-05-24 | Changes (ep): + deposition _software.name enumerations updated (CRANK, CRANK2, EVAL15, KYLIN) + Add AichiSR synchrotron and beamline BL2S1 to deposiiton diffrn_source + Add 'dipolar recoupling' and 'spin diffusion' to _pdbx_nmr_constraint_file.constraint_subtype + Add DECTRIS PILATUS3 R 300K detector + Update examples to include correct items: _pdbx_audit_conform_extension _pdbx_chem_comp_depositor_info _pdbx_chem_comp_instance_depositor_info _pdbx_depui_upload _pdbx_deposition_message_info _pdbx_deposition_message_file_reference _pdbx_struct_ref_seq_depositor_info _em_db_reference _em_entity_assembly_molwt _em_entity_assembly_naturalsource _em_image_recording _em_interpret_figure _em_structure_factors_depositor_info _em_volume_selection _em_particle_selection _em_mask_depositor_info _pdbx_struct_special_symmetry _pdbx_reference_publication_list _pdbx_nmr_chem_shift_ref _pdbx_nmr_chem_shift_reference _pdbx_reference_entity_poly_link |
mmcif_pdbx.dic |
| 5.248 | 2016-05-03 | Changes (ep): + CAPRI added to _pdbx_database_status.methods_development_category + Correct pdbx_nmr_chem_shift_ref.mol_common_name enumeration + Add RDC to pdbx_nmr_constraint_file.constraint_subtype enumeration + Correct limits of em_3d_crystal_entity.space_group_num + EMD updates to status (HOLD8W), remove 'JEM3400FSC CRYOHOLDER', add new microscopes |
mmcif_pdbx.dic |
| 5.247 | 2016-04-27 | Changes (ep): + deposition beamline enumeration updates + add extensions to support pdbx_struct_assembly evidence |
mmcif_pdbx.dic |
| 5.246 | 2016-04-11 | Changes (ep): + deposition beamline enumeration updates |
mmcif_pdbx.dic |
| 5.245 | 2016-04-02 | Changes (PDBj): + _diffrn_source.type/_diffrn_source.pdbx_synchrotron_beamline deposition enumeration update BL-21 -> PX-BL21 |
mmcif_pdbx.dic |
| 5.244 | 2016-03-31 | Changes (jw): + add extensions to capture results from ligand binding assays |
mmcif_pdbx.dic |
| 5.243 | 2016-03-25 | Changes (jy,zf): + add extensions for group depositions |
mmcif_pdbx.dic |
| 5.242 | 2016-03-21 | Changes (jw): + add regular expression for ORCID |
mmcif_pdbx.dic |
| 5.241 | 2016-03-08 | Changes (ep): + Update local context for selected em_* categories. + Update internal enumerations for detectors and secondary structure types. |
mmcif_pdbx.dic |
| 5.240 | 2016-02-24 | Changes (cl,ep): + Update local context for selected em_* categories. + Add internal data item _pdbx_database_status.auth_req_rel_date |
mmcif_pdbx.dic |
| 5.239 | 2016-02-09 | Changes (cl,ap): + enumeration update for item _em_imaging.specimen_holder_model and _emd_microscopy.specimen_holder_model + set local context for categories em_virus_natural_host and em_virus_shell |
mmcif_pdbx.dic |
| 5.238 | 2016-02-03 | Changes (jy): + enumeration update for item _pdbx_database_status.methods_development_category |
mmcif_pdbx.dic |
| 5.237 | 2016-02-01 | Changes (es): + update enumerations and descriptions for EMD data items - |
mmcif_pdbx.dic |
| 5.236 | 2016-01-26 | Changes (cl,ep): + update enumerations and descriptions for EM data items - |
mmcif_pdbx.dic |
| 5.235 | 2016-01-21 | Changes (jw): + update context for EM data items - + add _em_admin.map_hold_date |
mmcif_pdbx.dic |
| 5.234 | 2016-01-06 | Changes (ep): + description text updates |
mmcif_pdbx.dic |
| 5.233 | 2015-12-08 | Changes (cl,ep): + EM extension update |
mmcif_pdbx.dic |
| 5.232 | 2015-12-07 | Changes (ep): + enumeration updates |
mmcif_pdbx.dic |
| 5.231 | 2015-12-04 | Changes (cl): + EM extension update |
mmcif_pdbx.dic |
| 5.230 | 2015-12-03 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.229 | 2015-12-03 | Changes (jdw): + Category context changed for pdbx_nmr_spectral_peak_list |
mmcif_pdbx.dic |
| 5.228 | 2015-11-28 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.227 | 2015-11-24 | Changes (ep): + DCC extension update |
mmcif_pdbx.dic |
| 5.226 | 2015-11-24 | Changes (cl): + EM extension update |
mmcif_pdbx.dic |
| 5.225 | 2015-11-24 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.224 | 2015-11-19 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.223 | 2015-11-11 | Changes (jw): + Adjust local context for selected NMR and EM data categories. |
mmcif_pdbx.dic |
| 5.222 | 2015-11-11 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.221 | 2015-11-02 | Changes (ep): + Enumeration updates |
mmcif_pdbx.dic |
| 5.220 | 2015-10-30 | Changes (ep): + Enumeration updates |
mmcif_pdbx.dic |
| 5.219 | 2015-10-22 | Changes (cl): + EM extension update |
mmcif_pdbx.dic |
| 5.218 | 2015-10-22 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.217 | 2015-10-15 | Changes (jw): + add item _pdbx_depui_entry_details.wwpdb_site_id |
mmcif_pdbx.dic |
| 5.216 | 2015-10-14 | Changes (cl): + Add _emd_admin.header_release_date, _emd_admin.obsoleted_date and _em_admin.header_release_date |
mmcif_pdbx.dic |
| 5.215 | 2015-10-13 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.214 | 2015-10-08 | Changes (ep): + Enumeration updates + regex update for type author |
mmcif_pdbx.dic |
| 5.213 | 2015-10-01 | Changes (jdw): + _pdbx_nmr_systematic_chem_shift_offset.ordinal replaces the natural category key for this category. + Enumeration updates |
mmcif_pdbx.dic |
| 5.212 | 2015-09-08 | Changes (cl): + EM extension update |
mmcif_pdbx.dic |
| 5.211 | 2015-09-08 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.210 | 2015-08-31 | Changes (cl,jw): + EM extension update |
mmcif_pdbx.dic |
| 5.209 | 2015-08-30 | Changes (ep,jw): + Enumeration updates |
mmcif_pdbx.dic |
| 5.208 | 2015-08-14 | Changes (cl,jw): + EM extension update |
mmcif_pdbx.dic |
| 5.207 | 2015-08-06 | Changes (ep,jw): + enumeration updates |
mmcif_pdbx.dic |
| 5.206 | 2015-07-20 | Changes (jw): + add new category pdbx_audit_conform_extension |
mmcif_pdbx.dic |
| 5.205 | 2015-07-17 | Changes (ep,jw): + enumeration updates |
mmcif_pdbx.dic |
| 5.204 | 2015-07-06 | Changes (es,cl): + EMD data type refinement |
mmcif_pdbx.dic |
| 5.203 | 2015-06-30 | Changes (es): + EMD data type refinement |
mmcif_pdbx.dic |
| 5.202 | 2015-06-26 | Changes (es): + EMD regular expression update |
mmcif_pdbx.dic |
| 5.201 | 2015-06-24 | Changes (es): + EMD extension update |
mmcif_pdbx.dic |
| 5.200 | 2015-06-19 | Changes (cl): + EMD extension update |
mmcif_pdbx.dic |
| 5.199 | 2015-06-09 | Changes (cl): + EMD extension update |
mmcif_pdbx.dic |
| 5.198 | 2015-06-03 | Changes (es,cl,jdw): + EMD extension update |
mmcif_pdbx.dic |
| 5.197 | 2015-05-06 | Changes (ep,ms,jdw): + enumeration updates |
mmcif_pdbx.dic |
| 5.196 | 2015-04-30 | Changes (ep,jdw): + enumeration updates |
mmcif_pdbx.dic |
| 5.195 | 2015-04-28 | Changes (es,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.194 | 2015-04-22 | Changes (ep,jdw): + enumeration updates + add item _pdbx_contact_author.identifier_ORCID. + add chem_comp_model_group extensions. |
mmcif_pdbx.dic |
| 5.193 | 2015-03-31 | Changes (cs,jdw): + remove relationship between _pdbx_reference_entity_subcomponents.prd_id and _pdbx_reference_molecule_list.prd_id |
mmcif_pdbx.dic |
| 5.192 | 2015-03-18 | Changes (ep,jdw): + Add item _pdbx_depui_entry_details.replace_pdb_id + Enumeration updates |
mmcif_pdbx.dic |
| 5.191 | 2015-03-10 | Changes (es,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.190 | 2015-02-28 | Changes (ep,jdw): + Enumeration updates - + removed _pdbx_poly_seq_scheme.hetero relationship with _entity_poly_seq.hetero |
mmcif_pdbx.dic |
| 5.189 | 2015-02-20 | Changes (es,ep,jdw): + EMD extension dictionary update + Enumeration updates |
mmcif_pdbx.dic |
| 5.188 | 2015-02-10 | Changes (es,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.187 | 2015-02-03 | Changes (es,cl,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.186 | 2015-02-01 | Changes (zf,jdw): + NMR updates for deposition system |
mmcif_pdbx.dic |
| 5.185 | 2014-12-17 | Changes (ag,ep,jdw): + NMR updates for deposition system |
mmcif_pdbx.dic |
| 5.184 | 2014-12-02 | Changes (es,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.183 | 2014-11-21 | Changes (es,cl,jdw): + EMD extension dictionary update |
mmcif_pdbx.dic |
| 5.182 | 2014-11-07 | Changes (ag,ez,jdw): + NMR updates for deposition system - |
mmcif_pdbx.dic |
| 5.181 | 2014-10-28 | Changes (ag,ez,jdw): + NMR updates for deposition system - |
mmcif_pdbx.dic |
| 5.180 | 2014-10-21 | Changes (es,cl,jdw): + EMD dictionary update - make all categories optional -- |
mmcif_pdbx.dic |
| 5.179 | 2014-10-20 | Changes (es,cl,jdw): + EMD dictionary update |
mmcif_pdbx.dic |
| 5.178 | 2014-10-14 | Changes (ep,jdw): + update enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.177 | 2014-09-25 | Changes (ep,jdw): + update detector enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.176 | 2014-09-11 | Changes (to,jdw): + add _pdbx_depui_validation_status_flags.residual_B_factors_flag |
mmcif_pdbx.dic |
| 5.175 | 2014-09-10 | Changes (ep,jdw): + update of NMR alternative mandatory codes and examples |
mmcif_pdbx.dic |
| 5.174 | 2014-09-02 | Changes (cl,ep,jdw): + update of EM extensions definitions, examples and enumerations |
mmcif_pdbx.dic |
| 5.173 | 2014-08-28 | Changes (cl,jdw): + update of EM extensions definitions, examples and enumerations |
mmcif_pdbx.dic |
| 5.172 | 2014-07-30 | Changes (cl,jdw): + update of EM extensions definitions, examples and enumerations |
mmcif_pdbx.dic |
| 5.171 | 2014-07-21 | Changes (jdw): + _pdbx_depui_status_flags.has_viewed_validation_report made optional |
mmcif_pdbx.dic |
| 5.170 | 2014-07-17 | Changes (cl,ep,jdw): + update of enumerations for 3DEM and other deposition forms. |
mmcif_pdbx.dic |
| 5.169 | 2014-07-16 | Changes (ep,jdw): + update of enumerations for deposition forms. |
mmcif_pdbx.dic |
| 5.168 | 2014-07-10 | Changes (cl,ep,jdw): + update of EM extensions definitions, examples and enumerations + update of enumerations for deposition forms. |
mmcif_pdbx.dic |
| 5.167 | 2014-06-15 | Changes (jdw): + added _pdbx_depui_status_flags.validated_model_file_name, _pdbx_depui_status_flags.merge_prior_model_file_name, _pdbx_depui_status_flags.merge_replace_model_file_name, _pdbx_depui_status_flags.merge_output_model_file_name + Corrected/removed item-linked relation to _struct_ref_seq_dif.db_mon_id. + Updated _refine.pdbx_method_to_determine_structure + Update examples in category pdbx_data_processing_status |
mmcif_pdbx.dic |
| 5.166 | 2014-06-06 | Changes (jdw): + Add item _pdbx_struct_conn_angle.ptnr3_symmetry + Add category pdbx_database_status_history |
mmcif_pdbx.dic |
| 5.165 | 2014-06-05 | Changes (cl/jdw): + Update em extensions and add deposition specific em categories - + Add save__pdbx_depui_status_flags.has_viewed_validation_report |
mmcif_pdbx.dic |
| 5.164 | 2014-06-03 | Changes (jdw): + Update mandatory codes in category pdbx_database_status |
mmcif_pdbx.dic |
| 5.163 | 2014-05-30 | Changes (jdw): + remove redundant mandatory code for _pdbx_database_status.data_hold_nmr_contraints |
mmcif_pdbx.dic |
| 5.162 | 2014-05-08 | Changes (ep/jdw): + update enumerations in category software |
mmcif_pdbx.dic |
| 5.161 | 2014-05-07 | Changes (jdw): + update enumerations in category pdbx_SG_project |
mmcif_pdbx.dic |
| 5.160 | 2014-05-02 | Changes (jdw): + Items _entity_src_gen.pdbx_src_id, _entity_src_nat.pdbx_src_id _pdbx_entity_src_syn.pdbx_src_id added to category key and set to mandatory code = yes. + Update internal enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.159 | 2014-04-10 | Changes (cl/jdw): + Update in EM extension dictionary in support of new deposition system. |
mmcif_pdbx.dic |
| 5.158 | 2014-04-03 | Changes (jdw): + Make context for _entity_poly.pdbx_explicit_linking_flag local. + extend enumeration for _pdbx_contact_author.id. |
mmcif_pdbx.dic |
| 5.157 | 2014-03-28 | Changes (ep/jdw): + Update internal enumerations and boundary values for deposition system - |
mmcif_pdbx.dic |
| 5.156 | 2014-03-24 | Changes (ep/jdw): + Update detector enumerations |
mmcif_pdbx.dic |
| 5.155 | 2014-03-12 | Changes (hy/jdw): + Add preliminary items for _reflns.pdbx_CC_half,_reflns.pdbx_R_split,_reflns_shell.pdbx_CC_half and _reflns_shell.pdbx_R_split. |
mmcif_pdbx.dic |
| 5.154 | 2014-03-10 | Changes (ag/eu/jdw): + Update deposition closed enumeration flags for NMR extension definitions. |
mmcif_pdbx.dic |
| 5.153 | 2014-03-07 | Changes (eu/jdw): + add item _pdbx_nmr_refine.software_ordinal + update enumeration for _pdbx_database_status.dep_release_code_struct_fact |
mmcif_pdbx.dic |
| 5.152 | 2014-03-04 | Changes (ep/jdw): + change type of _pdbx_struct_assembly_depositor_info.oligomeric_count to line + update deposition specific enumerations in category software |
mmcif_pdbx.dic |
| 5.151 | 2014-03-01 | Changes (ep/jdw): + update deposition specific enumerations in category pdbx_database_related |
mmcif_pdbx.dic |
| 5.150 | 2014-02-25 | Changes (cl/ep/jdw): + update EM deposition specific metadata items. |
mmcif_pdbx.dic |
| 5.149 | 2014-02-20 | Changes (jdw): + update deposition mandatory codes and enumerations. |
mmcif_pdbx.dic |
| 5.148 | 2014-02-19 | Changes (jdw): + update regular expressions one-letter code sequences + add mandatory codes to pdbx_nmr_chem_shift_ref and pdbx_nmr_constraint_file |
mmcif_pdbx.dic |
| 5.147 | 2014-02-18 | Changes (jdw): + update diffraction detector enumerations/ |
mmcif_pdbx.dic |
| 5.146 | 2014-02-11 | Changes (eu/jdw): + new items _pdbx_nmr_software.details,_pdbx_nmr_exptl_sample.concentration_err,_pdbx_nmr_spectrometer.name, _pdbx_nmr_assigned_chem_shift_list.conditions_label,_pdbx_nmr_spectral_dim.sweep_width_units, _pdbx_nmr_spectral_dim.center_frequency_offset,_pdbx_nmr_spectral_dim.under_sampling_type, _pdbx_nmr_chem_shift_software.software_label + updates for deposition enumerations and mandator codes for NMR extensions. |
mmcif_pdbx.dic |
| 5.145 | 2014-02-10 | Changes (cl/jdw): + Update of enumerations for 3DEM extension dictionary. + Add categories pdbx_depui_entry_details and pdbx_data_processing_status. + Added definitions _atom_type.pdbx_scat_Cromer_Mann_a5,_atom_type.pdbx_scat_Cromer_Mann_b5,_refine.pdbx_average_fsc_overall, _refine.pdbx_average_fsc_work,_refine.pdbx_average_fsc_free,_refine_ls_shell.pdbx_fsc_work,_refine_ls_shell.pdbx_fsc_free, _refine_hist.pdbx_number_residues_total,_refine_hist.pdbx_B_iso_mean_ligand,_refine_hist.pdbx_B_iso_mean_solvent, _atom_site_anisotrop.pdbx_PDB_model_num |
mmcif_pdbx.dic |
| 5.144 | 2014-02-06 | Changes (cl/jdw): + Update of enumerations for save__em_experiment.reconstruction_method |
mmcif_pdbx.dic |
| 5.143 | 2014-01-24 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.142 | 2014-01-23 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.141 | 2014-01-21 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.140 | 2014-01-20 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.139 | 2014-01-17 | Changes (jdw): + Update enumerations for item _pdbx_database_status.status_code + add category pdbx_related_exp_data_set + In pdbx_related_exp_data_set limit references to DOI types + Update item descriptions and examples for _pdbx_depui_entity_features.type,_entity_poly.pdbx_target_identifier,_reflns.pdbx_Rsym_value, _refine.pdbx_solvent_vdw_probe_radii,_refine.pdbx_solvent_ion_probe_radii,_citation.pdbx_database_id_DOI,_entity.pdbx_description, and _exptl_crystal_grow.pdbx_details. + Update of internal descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.138 | 2013-12-20 | Changes (jdw): + Update mandatory codes for category pdbx_contact_author. + Update enumerations for category software. |
mmcif_pdbx.dic |
| 5.137 | 2013-12-10 | Changes (jdw): + Update mandatory codes for category pdbx_contact_author. + Update enumerations for category software. |
mmcif_pdbx.dic |
| 5.136 | 2013-11-22 | Changes (cl/jdw): + new EMD mapping extension dictionary added. + local context of _pdbx_database_status.status_code_sf removed. + Update context to WWPDB_LOCAL for item _entity_poly.pdbx_sequence_evidence_code + Update context values to WWPDB_LOCAL for categories database_PDB_remark and pdbx_contact_author + multiple updates of EMD/EM extensions. + category group updates |
mmcif_pdbx.dic |
| 5.135 | 2013-10-17 | Changes (jdw): + added _pdbx_depui_upload.file_content_type and remove enumeration from _pdbx_depui_upload.file_type. + includes any local meta-data changes coded into the deposition system. + update internal metadata for deposition system + add data categories for messaging pdbx_deposition_message_file_reference and pdbx_deposition_message_info + update mandatory codes and category group assignments + Reassign context RCSB_LOCAL to WWPDB_LOCAL + update software application enumerations. + Update category and item item context values in categories audit_contact_author, pdbx_database_proc, pdbx_entity_name, struct_biol_gen, atom_site and pdbx_database_status. + add internal items _pdbx_database_status.date_begin_processing, _pdbx_database_status.date_end_processing, _pdbx_database_status.date_begin_deposition, _pdbx_database_status.date_begin_release_preparation, _pdbx_database_status.date_author_release_request |
mmcif_pdbx.dic |
| 5.134 | 2013-08-27 | Changes (jdw): + Added status flags -- _pdbx_depui_status_flags.is_ligand_processing_complete _pdbx_depui_status_flags.sample_xyz_sequence_alignments_valid _pdbx_depui_entity_status_flags.sample_xyz_sequence_alignments_valid + Added local category context to all internal categories. |
mmcif_pdbx.dic |
| 5.133 | 2013-06-18 | Changes (jdw): + updated advisory limits for _reflns_shell.d_res_low and _refine_ls_shell.d_res_low |
mmcif_pdbx.dic |
| 5.132 | 2013-06-16 | Changes (jdw): + add _pdbx_seq_map_depositor_info.entity_id _pdbx_seq_map_depositor_info.auth_asym_id _pdbx_seq_map_depositor_info.one_letter_code _pdbx_seq_map_depositor_info.one_letter_code_mod |
mmcif_pdbx.dic |
| 5.131 | 2013-06-14 | Changes (jdw): + update enumerations for _pdbx_struct_ref_seq_depositor_info.db_name |
mmcif_pdbx.dic |
| 5.130 | 2013-06-14 | Changes (jdw): + added _pdbx_depui_status_flags.has_accepted_terms_and_conditions + updated advisory and hard limits to include equivalence on the boundary endpoints. |
mmcif_pdbx.dic |
| 5.129 | 2013-05-29 | Changes (jdw): + _pdbx_database_status.pdbx_annotator replaces _pdbx_database_status.rcsb_annotator |
mmcif_pdbx.dic |
| 5.128 | 2013-05-23 | Changes (jdw): + add item _entity_poly.pdbx_sequence_evidence_code |
mmcif_pdbx.dic |
| 5.127 | 2013-04-27 | Changes (jdw): + Update alternate descriptions and enumerations for deposition system. |
mmcif_pdbx.dic |
| 5.126 | 2013-04-16 | Changes (jdw): + Set _pdbx_contact_author.role and _pdbx_contact_author.role internally mandatory. + Set _pdbx_contact_author.name_mi optional + Relax regular expression for _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code + Set _entity_poly.pdbx_seq_one_letter_code, _entity_src_gen.pdbx_gene_src_scientific_name, _entity_src_nat.pdbx_organism_scientific internally mandatory. + Add _pdbx_depui_status_flags.has_helical_symmetry, _pdbx_depui_status_flags.has_point_symmetry, _pdbx_depui_status_flags.has_cyclic_symmetry + |
mmcif_pdbx.dic |
| 5.125 | 2013-04-08 | Changes (jdw): + add items _pdbx_struct_ref_seq_dif_depositor_info.entity_id and _pdbx_chem_comp_instance_depositor_info.formula |
mmcif_pdbx.dic |
| 5.124 | 2013-03-15 | Changes (jdw): + add optional items _pdbx_validate_main_chain_plane.label_alt_id, _pdbx_validate_planes.lable_alt_id, _pdbx_validate_torsion.label_alt_id |
mmcif_pdbx.dic |
| 5.123 | 2013-03-12 | Changes (jdw): + add category pdbx_depui_entity_features |
mmcif_pdbx.dic |
| 5.122 | 2013-03-11 | Changes (jdw): + add items _pdbx_depui_status_flags.primary_citation_status, _pdbx_depui_status_flags.reference_citation_status, _pdbx_depui_status_flags.corresponding_author_status |
mmcif_pdbx.dic |
| 5.121 | 2013-03-07 | Changes (jdw): + bulk import of RCSB local enumerations into internal pdbx_item_enumeration containers, |
mmcif_pdbx.dic |
| 5.120 | 2013-03-01 | Changes (jdw): + consolidated pdbx_struct_ref_depositor_info into pdbx_struct_ref_seq_depositor_info |
mmcif_pdbx.dic |
| 5.119 | 2013-02-20 | Changes (jdw): + restore main public version of mmcif_pdbx-def-2.dic + added _pdbx_depui_status_flags.prediction_target and category pdbx_depui_entity_status_flags |
mmcif_pdbx.dic |
| 5.118 | 2013-02-20 | Changes (jdw): + Added internal category pdbx_chem_comp_upload_depositor_info to hold potentially multiple data files per chemical component. |
mmcif_pdbx.dic |
| 5.117 | 2013-02-13 | Changes (jdw): + Added internal categories -depui_validation_status_flags, pdbx_depui_upload, pdbx_depui_status_flags |
mmcif_pdbx.dic |
| 5.116 | 2013-02-13 | Changes (jdw): + added _pdbx_helical_symmetry_depositor_info.status_flag and _pdbx_point_symmetry_depositor_info.status_flag + updated the collection of advisory boundary values -- |
mmcif_pdbx.dic |
| 5.115 | 2013-02-06 | Changes (jdw,kh): + Add categories pdbx_chem_comp_subcomponent_struct_conn and pdbx_chem_comp_subcomponent_entity_list. + For item _pdbx_chem_comp_subcomponent_entity_list.type change data type to uline and extend enumeration. + Set mandatory codes to optional for categories emd, emd_map and pdbx_nmr_software_task |
mmcif_pdbx.dic |
| 5.114 | 2012-12-14 | Changes (eu,ag): + Added items _pdbx_nmr_assigned_chem_shift_list.label, _pdbx_nmr_assigned_chem_shift_list.conditions_label, _pdbx_nmr_spectral_peak_list.label, and _pdbx_nmr_spectral_peak_list.conditions_label |
mmcif_pdbx.dic |
| 5.113 | 2012-12-04 | Changes (eu,ag): + Add _pdbx_nmr_exptl.sample_state |
mmcif_pdbx.dic |
| 5.112 | 2012-11-12 | Changes (cl,jdw): + Update to the 3DEM data categories - |
mmcif_pdbx.dic |
| 5.111 | 2012-11-08 | Changes (cl,jdw): + Update to the 3DEM data categories - |
mmcif_pdbx.dic |
| 5.110 | 2012-11-07 | Changes (ss,sv,jdw): +Added item _pdbx_entity_src_gen_depositor_info.entity_id +Removed item _pdbx_entity_src_gen_depositor_info.alt_source_flag and _pdbx_entity_src_gen_depositor_info.gene_src_strain +Items _pdbx_entity_src_gen_depositor_info.beg_seq_num and _pdbx_entity_src_gen_depositor_info.end_seq_num set to mandatory +Data types for _pdbx_entity_src_gen_depositor_info.host_org_ncbi_taxonomy_id set to int |
mmcif_pdbx.dic |
| 5.109 | 2012-10-15 | Changes (jdw): + pdbx_chem_comp_instance_depositor_info + Update joint enumerations for _pdbx_reference_molecule.class. + Update enumeration list for _em_imaging.specimen_holder_model |
mmcif_pdbx.dic |
| 5.108 | 2012-10-03 | Changes (jdw): + Adjust mandatory codes for items in the pdbx_contact_author category. + Update all current extension dictionaries in + Correct version number typo. |
mmcif_pdbx.dic |
| 5.107 | 2012-09-19 | Changes (jdw): + Rename categories to: pdbx_reference_linked_entity, pdbx_reference_linked_entity_comp_list, pdbx_reference_linked_entity_link, and pdbx_reference_linked_entity_comp_link and distinguish inter and intra entity linkages. + Revised enumeration for _pdbx_reference_linked_entity.link_to_entity_type |
mmcif_pdbx.dic |
| 5.106 | 2012-09-18 | Changes (jdw): + remove existing EM dictionary which duplicates new EM item definitions + add categories pdbx_reference_linked_entity, pdbx_reference_linked_entity_list, pdbx_reference_linked_entity_link. |
mmcif_pdbx.dic |
| 5.105 | 2012-09-06 | Changes (jdw): + Revised definition of _struct_conn.pdbx_leaving_atom_flag. + Add definition _pdbx_solvent_atom_site_mapping.symmetry/symmetry_as_xyz |
mmcif_pdbx.dic |
| 5.104 | 2012-09-01 | Changes (jdw): + Added category pdbx_audit_support extension. + Incorporated D&A alternate descriptions and boundary values. |
mmcif_pdbx.dic |
| 5.103 | 2012-08-29 | Changes (jdw/jy): + Update enumerations for _pdbx_family_prd_audit.action_type and _pdbx_prd_audit.action_type + Update enumerations for _pdbx_reference_molecule.class/type, _pdbx_molecule_features.class/type + Added category for publication reference data - PDBX_REFERENCE_PUBLICATION_LIST |
mmcif_pdbx.dic |
| 5.102 | 2012-08-28 | Changes (jdw/cl): + added category group em_group_da + added EM extension dictionaries for D&A project. _em_experiment.entry_id _em_experiment.reconstruction_method _em_experiment.specimen_type _em_software.ordinal _em_software.classification _em_software.name _em_software.version _em_assembly.entry_id _em_assembly.name _em_assembly.composition _em_assembly.num_components _em_assembly.mol_wt_exp _em_assembly.mol_wt_theo _em_assembly.mol_wt_method _em_assembly.details _em_entity_assembly.id _em_entity_assembly.type _em_entity_assembly.name _em_entity_assembly.details _em_entity_assembly.organism_scientific _em_entity_assembly.organism_common _em_entity_assembly.strain _em_entity_assembly.tissue _em_entity_assembly.cell _em_entity_assembly.organelle _em_entity_assembly.cellular_location _em_entity_assembly.engineered_flag _em_entity_assembly.expression_system _em_entity_assembly.expression_system_plasmid _em_entity_assembly.go_id _em_entity_assembly.ipr_id _em_entity_assembly.ncbi_taxonomy_id _em_entity_assembly.synonym _em_entity_assembly.mutant_flag _em_entity_assembly.number_of_copies _em_entity_assembly.oligomeric_details _em_entity_assembly.entity_list _em_entity_assembly.mol_wt _em_entity_assembly.mol_wt_method _em_entity_assembly.entity_parent_id _em_virus_entity.id _em_virus_entity.virus_host_category _em_virus_entity.virus_host_species _em_virus_entity.virus_host_ncbi_taxonomy_id _em_virus_entity.virus_host_growth_cell _em_virus_entity.virus_type _em_virus_entity.virus_isolate _em_virus_entity.entity_assembly_id _em_virus_entity.enveloped _em_virus_entity.empty _em_virus_entity.details _em_icos_virus_shells.virus_entity_id _em_icos_virus_shells.id _em_icos_virus_shells.shell_diameter _em_icos_virus_shells.triangulation_num _em_specimen.id _em_specimen.sample_state _em_specimen.num_grids _em_specimen.cryoprotectant _em_specimen.embedding_material _em_specimen.details _em_sample_preparation.id _em_sample_preparation.specimen_id _em_sample_preparation.entity_assembly_id _em_sample_preparation.ph _em_sample_preparation.buffer_id _em_sample_preparation.sample_concentration _em_sample_preparation.details _em_specimen_support.id _em_specimen_support.specimen_id _em_specimen_support.method _em_specimen_support.grid_model _em_specimen_support.grid_material _em_specimen_support.grid_mesh_size _em_specimen_support.grid_type _em_specimen_support.pretreatment _em_specimen_support.details _em_specimen_support.film_material _em_specimen_support.film_topology _em_specimen_support.film_thickness _em_array_formation.id _em_array_formation.specimen_id _em_array_formation.method _em_array_formation.apparatus _em_array_formation.atmosphere _em_array_formation.pH _em_array_formation.temp _em_array_formation.time _em_array_formation.buffer_id _em_array_formation.details _em_array_formation.number_arrays _em_array_formation.mean_2d_crystal_size _em_stain.id _em_stain.specimen_id _em_stain.type _em_stain.material _em_stain.details _em_buffer.id _em_buffer.name _em_buffer.details _em_buffer_components.id _em_buffer_components.buffer_id _em_buffer_components.name _em_buffer_components.conc _em_buffer_components.conc_units _em_buffer_components.details _em_vitrification.id _em_vitrification.specimen_id _em_vitrification.cryogen_name _em_vitrification.freezing_technique _em_vitrification.humidity _em_vitrification.temp _em_vitrification.ambient_temp _em_vitrification.instrument _em_vitrification.method _em_vitrification.time_resolved_state _em_vitrification.details _em_imaging.id _em_imaging.astigmatism _em_imaging.electron_beam_tilt_params _em_imaging.specimen_id _em_imaging.detector_id _em_imaging.scans_id _em_imaging.microscope_model _em_imaging.specimen_holder_model _em_imaging.details _em_imaging.date _em_imaging.accelerating_voltage _em_imaging.illumination_mode _em_imaging.mode _em_imaging.nominal_cs _em_imaging.nominal_defocus_min _em_imaging.nominal_defocus_max _em_imaging.tilt_angle_min _em_imaging.tilt_angle_max _em_imaging.tilt_angle_increment _em_imaging.second_tilt_axis_flag _em_imaging.nominal_magnification _em_imaging.calibrated_magnification _em_imaging.electron_source _em_imaging.electron_dose _em_imaging.energy_filter _em_imaging.energy_window_min _em_imaging.energy_window_max _em_imaging.temperature _em_imaging.cryogen _em_imaging.detector_distance _em_imaging.recording_temperature_minimum _em_imaging.recording_temperature_maximum _em_imaging.c2_aperture_diameter _em_imaging.alignment_procedure _em_imaging.Cs_corrector _em_imaging.Cc_corrector _em_imaging.phase_plate _em_detector.id _em_detector.details _em_detector.class _em_detector.type _em_detector.detective_quantum_efficiency _em_image_scans.id _em_image_scans.number_digital_images _em_image_scans.details _em_image_scans.scanner_model _em_image_scans.scanner_sampling_size _em_image_scans.apix_sampling _em_image_scans.od_range _em_image_scans.quant_bit_size _em_image_scans.width _em_image_scans.height _em_image_scans.sampling_size _em_image_scans.frames_per_image _em_2d_crystal_symmetry.id _em_2d_crystal_symmetry.length_a _em_2d_crystal_symmetry.length_b _em_2d_crystal_symmetry.angle_gamma _em_2d_crystal_symmetry.details _em_2d_crystal_symmetry.angle_alpha _em_2d_crystal_symmetry.angle_beta _em_2d_crystal_symmetry.length_c _em_2d_crystal_symmetry.thickness_c _em_2d_crystal_symmetry.space_group_name_H-M _em_point_symmetry.entry_id _em_point_symmetry.symmetry_type _em_point_symmetry.cyclic_symmetry _em_helical_symmetry.id _em_helical_symmetry.entity_assembly_id _em_helical_symmetry.details _em_helical_symmetry.dyad _em_helical_symmetry.axial_symmetry _em_helical_symmetry.angular_rotation_per_subunit _em_helical_symmetry.axial_rise_per_subunit _em_helical_symmetry.hand _em_2d_projection_selection.entry_id _em_2d_projection_selection.num_particles _em_2d_projection_selection.method _em_2d_projection_selection.details _em_3d_reconstruction.entry_id _em_3d_reconstruction.entity_assembly_id _em_3d_reconstruction.method _em_3d_reconstruction.spatial_filtering _em_3d_reconstruction.masking _em_3d_reconstruction.details _em_3d_reconstruction.resolution _em_3d_reconstruction.resolution_method _em_3d_reconstruction.magnification_calibration _em_3d_reconstruction.ctf_correction_method _em_3d_reconstruction.ctf_correction_type _em_3d_reconstruction.nominal_pixel_size _em_3d_reconstruction.actual_pixel_size _em_3d_reconstruction.num_particles _em_3d_reconstruction.num_class_averages _em_3d_reconstruction.software _em_3d_reconstruction.initial_model_type _em_3d_reconstruction.initial_model_details _em_euler_assignment.id _em_euler_assignment.name _em_euler_assignment.method _em_euler_assignment.num_reference_projections _em_euler_assignment.merit_function _em_euler_assignment.angular_sampling _em_euler_assignment.details _em_electron_crystallography.entry_id _em_electron_crystallography.num_meas_intensities _em_electron_crystallography.num_structure_factors _em_electron_crystallography.details _em_electron_crystallography.d_res_high _em_electron_crystallography.overall_phase_residual _em_electron_crystallography.overall_phase_error _em_electron_crystallography.rejection_criteria_phase_error _em_electron_crystallography.Fourier_space_coverage _em_electron_crystallography.r_merge _em_electron_crystallography.r_sym _em_electron_crystallography_shell.id _em_electron_crystallography_shell.res_low _em_electron_crystallography_shell.res_high _em_electron_crystallography_shell.phase_residual _em_electron_crystallography_shell.num_structure_factors _em_electron_crystallography_shell.num_meas_intensities _em_electron_crystallography_tilt.id _em_electron_crystallography_tilt.tilt_angle _em_electron_crystallography_tilt.num_diffraction_patterns _em_electron_crystallography_tilt.num_micrograph_images _em_tomography.id _em_tomography.entry_id _em_tomography.tilt_angle_incr _em_tomography.num_raw_images _em_tomography.details _em_3d_subvolume_selection.entry_id _em_3d_subvolume_selection.num_subvolumes _em_3d_subvolume_selection.num_tomograms _em_3d_subvolume_selection.method _em_3d_subvolume_selection.details _em_3d_subvolume_classification.id _em_3d_subvolume_classification.name _em_3d_subvolume_classification.method _em_3d_subvolume_classification.num_classes _em_3d_subvolume_classification.merit_function _em_3d_subvolume_classification.details _em_3d_fitting.id _em_3d_fitting.method _em_3d_fitting.target_criteria _em_3d_fitting.software_name _em_3d_fitting.details _em_3d_fitting.overall_b_value _em_3d_fitting.ref_space _em_3d_fitting.ref_protocol _em_3d_fitting_list.id _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.pdb_entry_id _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.details _emd.emd_entry_id _emd.title _emd_map.emd_entry_id _emd_map.annotation_details _emd_map.format _emd_map.sizeKb _emd_map.axisOrderFast _emd_map.axisOrderMedium _emd_map.axisOrderSlow _emd_map.cell_angle_alpha _emd_map.cell_angle_beta _emd_map.cell_angle_gamma _emd_map.cell_length_a _emd_map.cell_length_b _emd_map.cell_length_c _emd_map.data_type _emd_map.details _emd_map.num_columns _emd_map.num_rows _emd_map.num_sections _emd_map.origin_column _emd_map.origin_row _emd_map.origin_section _emd_map.pixel_x _emd_map.pixel_y _emd_map.pixel_z _emd_map.spaceGroupNumber _emd_map.spacing_x _emd_map.spacing_y _emd_map.spacing_z _emd_map.density_min _emd_map.density_max _emd_map.density_mean _emd_map.density_stddev _emd_map.contour_level _emd_map.contour_level_source _emd_files.id _emd_files.type _emd_files.file_name _emd_status.emd_entry_id _emd_status.current_status _emd_status.last_update _emd_status.deposition_date _emd_status.map_release_date _emd_status_history.id _emd_status_history.date _emd_status_history.code _emd_status_history.processing_site _emd_status_history.annotator_initials _emd_status_history.details _emd_obsolete_supersede.id _emd_obsolete_supersede.obsoleted_emd_entry_id _emd_obsolete_supersede.supersede_emd_entry_id _emd_obsolete_supersede.date _emd_obsolete_supersede.details _emd_auxiliary.id _emd_auxiliary.link _emd_auxiliary.link_data_type _emd_auxiliary.details _emd_database_related.db_name _emd_database_related.db_id _emd_database_related.details _emd_database_related.frame_relationship_flag _emd_database_related.fitted_coordinates_flag _emd_mask.id _emd_mask.annotation_details _emd_mask.format _emd_mask.sizeKb _emd_mask.axisOrderFast _emd_mask.axisOrderMedium _emd_mask.axisOrderSlow _emd_mask.cell_angle_alpha _emd_mask.cell_angle_beta _emd_mask.cell_angle_gamma _emd_mask.cell_length_a _emd_mask.cell_length_b _emd_mask.cell_length_c _emd_mask.data_type _emd_mask.details _emd_mask.num_columns _emd_mask.num_rows _emd_mask.num_sections _emd_mask.origin_column _emd_mask.origin_row _emd_mask.origin_section _emd_mask.pixel_x _emd_mask.pixel_y _emd_mask.pixel_z _emd_mask.spaceGroupNumber _emd_mask.spacing_x _emd_mask.spacing_y _emd_mask.spacing_z _emd_mask.density_min _emd_mask.density_max _emd_mask.density_mean _emd_mask.density_stddev _emd_mask.contour_level _emd_mask.contour_level_source + added various items to capture depositor information for the wwPDB deposition and annotation system. _pdbx_chem_comp_depositor_info.ordinal _pdbx_chem_comp_depositor_info.comp_id _pdbx_chem_comp_depositor_info.name _pdbx_chem_comp_depositor_info.upload_file_type _pdbx_chem_comp_depositor_info.upload_file_name _pdbx_chem_comp_depositor_info.formula _pdbx_chem_comp_depositor_info.type _pdbx_chem_comp_depositor_info.descriptor _pdbx_chem_comp_depositor_info.descriptor_type _pdbx_chem_comp_depositor_info.detailes _pdbx_struct_ref_depositor_info.biol_id _pdbx_struct_ref_depositor_info.db_code _pdbx_struct_ref_depositor_info.db_name _pdbx_struct_ref_depositor_info.entity_id _pdbx_struct_ref_depositor_info.id _pdbx_struct_ref_depositor_info.db_accession _pdbx_struct_ref_depositor_info.seq_one_letter_code _pdbx_struct_ref_depositor_info.align_begin _pdbx_struct_ref_seq_depositor_info.align_id _pdbx_struct_ref_seq_depositor_info.db_align_beg _pdbx_struct_ref_seq_depositor_info.db_align_end _pdbx_struct_ref_seq_depositor_info.details _pdbx_struct_ref_seq_depositor_info.ref_id _pdbx_struct_ref_seq_depositor_info.db_accession _pdbx_struct_ref_seq_depositor_info.db_code _pdbx_struct_ref_depositor_info.db_name _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code _pdbx_struct_ref_seq_dif_depositor_info.align_id _pdbx_struct_ref_seq_dif_depositor_info.db_mon_id _pdbx_struct_ref_seq_dif_depositor_info.db_seq_id _pdbx_struct_ref_seq_dif_depositor_info.details _pdbx_struct_ref_seq_dif_depositor_info.auth_mon_id _pdbx_struct_ref_seq_dif_depositor_info.auth_seq_id _pdbx_struct_ref_seq_dif_depositor_info.db_accession _pdbx_struct_ref_seq_dif_depositor_info.db_code _pdbx_struct_ref_dif_depositor_info.db_name _pdbx_struct_ref_dif_depositor_info.annotation _pdbx_struct_assembly_prop_depositor_info.biol_id _pdbx_struct_assembly_prop_depositor_info.type _pdbx_struct_assembly_prop_depositor_info.value _pdbx_struct_assembly_prop_depositor_info.details _pdbx_struct_assembly_depositor_info.details _pdbx_struct_assembly_depositor_info.id _pdbx_struct_assembly_depositor_info.method_details _pdbx_struct_assembly_depositor_info.oligomeric_details _pdbx_struct_assembly_depositor_info.oligomeric_count _pdbx_struct_assembly_depositor_info.matrix_flag _pdbx_struct_assembly_depositor_info.upload_file_name _pdbx_struct_assembly_gen_depositor_info.asym_id_list _pdbx_struct_assembly_gen_depositor_info.assembly_id _pdbx_struct_assembly_gen_depositor_info.oper_expression _pdbx_struct_oper_list_depositor_info.id _pdbx_struct_oper_list_depositor_info.type _pdbx_struct_oper_list_depositor_info.name _pdbx_struct_oper_list_depositor_info.symmetry_operation _pdbx_struct_oper_list_depositor_info.matrix[1][1] _pdbx_struct_oper_list_depositor_info.matrix[1][2] _pdbx_struct_oper_list_depositor_info.matrix[1][3] _pdbx_struct_oper_list_depositor_info.matrix[2][1] _pdbx_struct_oper_list_depositor_info.matrix[2][2] _pdbx_struct_oper_list_depositor_info.matrix[2][3] _pdbx_struct_oper_list_depositor_info.matrix[3][1] _pdbx_struct_oper_list_depositor_info.matrix[3][2] _pdbx_struct_oper_list_depositor_info.matrix[3][3] _pdbx_struct_oper_list_depositor_info.vector[1] _pdbx_struct_oper_list_depositor_info.vector[2] _pdbx_struct_oper_list_depositor_info.vector[3] _pdbx_point_symmetry_depositor_info.entry_id _pdbx_point_symmetry_depositor_info.Schoenflies_symbol _pdbx_point_symmetry_depositor_info.circular_symmetry _pdbx_point_symmetry_depositor_info.H-M_notation _pdbx_helical_symmetry_depositor_info.entry_id _pdbx_helical_symmetry_depositor_info.number_of_operations _pdbx_helical_symmetry_depositor_info.rotation_per_n_subunits _pdbx_helical_symmetry_depositor_info.rise_per_n_subunits _pdbx_helical_symmetry_depositor_info.n_subunits_divisor _pdbx_helical_symmetry_depositor_info.dyad_axis _pdbx_helical_symmetry_depositor_info.circular_symmetry _pdbx_solvent_atom_site_mapping.id _pdbx_solvent_atom_site_mapping.label_alt_id _pdbx_solvent_atom_site_mapping.label_asym_id _pdbx_solvent_atom_site_mapping.label_atom_id _pdbx_solvent_atom_site_mapping.label_comp_id _pdbx_solvent_atom_site_mapping.label_seq_id _pdbx_solvent_atom_site_mapping.pdbx_align _pdbx_solvent_atom_site_mapping.PDB_ins_code _pdbx_solvent_atom_site_mapping.pre_auth_asym_id _pdbx_solvent_atom_site_mapping.pre_auth_atom_id _pdbx_solvent_atom_site_mapping.pre_auth_comp_id _pdbx_solvent_atom_site_mapping.pre_auth_seq_id _pdbx_solvent_atom_site_mapping.pre_PDB_ins_code _pdbx_solvent_atom_site_mapping.pre_auth_alt_id _pdbx_solvent_atom_site_mapping.auth_asym_id _pdbx_solvent_atom_site_mapping.auth_atom_id _pdbx_solvent_atom_site_mapping.auth_comp_id _pdbx_solvent_atom_site_mapping.auth_seq_id _pdbx_solvent_atom_site_mapping.auth_alt_id _pdbx_solvent_atom_site_mapping.occupancy _pdbx_solvent_atom_site_mapping.Cartn_x _pdbx_solvent_atom_site_mapping.Cartn_y _pdbx_solvent_atom_site_mapping.Cartn_z _pdbx_solvent_atom_site_mapping.pre_Cartn_x _pdbx_solvent_atom_site_mapping.pre_Cartn_y _pdbx_solvent_atom_site_mapping.pre_Cartn_z _pdbx_entity_src_gen_depositor_info.alt_source_flag _pdbx_entity_src_gen_depositor_info.seq_type _pdbx_entity_src_gen_depositor_info.beg_seq_num _pdbx_entity_src_gen_depositor_info.end_seq_num _pdbx_molecule_features_depositor_info.entity_id _pdbx_molecule_features_depositor_info.class _pdbx_molecule_features_depositor_info.type _pdbx_molecule_features_depositor_info.name _pdbx_molecule_features_depositor_info.details + added flag for filtering STRUCT_CONN linkages relative to chemical component leaving atom assignments. _struct_conn.pdbx_leaving_atom_flag |
mmcif_pdbx.dic |
| 5.101 | 2012-08-22 | Changes (jdw): + added provisional extension for multi-source entities + added provisional extension for branched entities + added provisional extension for residues on special positions + added provisional extension for NMR data items for D&A deposition system + added provisional extension for identifying the ligand in a site |
mmcif_pdbx.dic |
| 5.100 | 2012-08-21 | Changes (jdw): + Release as provisional version 5.100 |
mmcif_pdbx.dic |
Data Type List
| Data Type Code | Primitive Type Code | Regular Expression | Description |
|---|---|---|---|
| 3x4_matrices | char | (((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})?(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n([\t ]*\n)*)){3})*((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})?(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n([\t ]*\n)*)){2}((([ \t]*-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? +){3})(-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? *\n?([\t ]*\n)*))[ \t]* | A set of 3x4 matrices separated by spaces and newlines on each line. Final newline optional. Optional spaces at start of lines. Blank lines accepted. |
| any | char | .* | A catch all for items that may take any form... |
| asym_id | char | [A-Za-z0-9]+ | A single chain or asym ids. |
| atcode | char | [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | Character data type for atom names ... |
| author | char | [A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*$ | Author name in PDB format: Taylor, C.A. |
| binary | char | \n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION---- |
binary items are presented as MIME-like ascii-encoded sections in an imgCIF. In a CBF, raw octet streams are used to convey the same information. |
| boolean | char | YES|NO | Boolean type |
| citation_doi | char | 10\..* | Citation DOI specification. |
| code | char | [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words ... |
| code30 | char | .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? | A string value, not allowed to exceed 30 characters. |
| date_dep | char | ([1-9][0-9](([02468][048])|([13579][26]))-02-29)|[1-9][0-9][0-9][0-9]-((((0[1-9])|(1[0-2]))-((0[1-9])|(1[0-9])|(2[0-8])))|((((0[13578])|(1[02]))-31)|(((0[1,3-9])|(1[0-2]))-(29|30)))) | Deposition specific date with better checking |
| deposition_email | uchar | [a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9.-]+ | code item types/single words (case insensitive) ... |
| ec-type | char | ([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-)))(([ ]*,[ ]*)([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-))))* | Approximate format of Enzyme Commission EC number. 1.2.3.4 with optional parts. |
| uchar | [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... | |
| emd_id | char | EMD-[0-9]{4,} | EMDB code |
| exp_data_doi | char | 10\.[0-9]{4,9}/[-._;()/:A-Za-z0-9]+ | Experimental dataset DOI |
| fax | uchar | [_,.;:"&<>/\{}'`~!@#$%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. |
| id_list | char | [A-Za-z0-9]+(,[A-Za-z0-9]+)* | A list of comma separated chain or asym ids. |
| id_list_spc | char | [ \t]*[A-Za-z0-9]+([ \t]*,[ \t]*[A-Za-z0-9]+)*[ \t]* | A list of comma separated chain or asym ids with optional spaces. |
| 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]+ | range of integer item types are the subset of numbers that are the negative or positive integers. |
| 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 |
| orcid_id | char | [0-9]{4}-[0-9]{4}-[0-9]{4}-([0-9]{3}X|[0-9]{4}) | ORCID pattern - dddd-dddd-dddd-dddd|dddX |
| pdb_id | char | [1-9][A-Z0-9][A-Z0-9][A-Z0-9] | PDB code (upper cases) |
| pdbx_PDB_obsoleted_db_id | char | [0-9][0-9a-zA-Z]{3}( [0-9][0-9a-zA-Z]{3})* | List of PDB ids for obsoletion - space separated |
| pdbx_related_db_id | char | [][_.:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words without semi-colon or comma ... |
| phone | uchar | [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... |
| point_group | char | (C[1-9][0-9]*|D[2-9]|D[1-9][0-9]+|O|T|I) | Point group symmetry in Schoenflies notation |
| point_group_helical | char | [CD][1-9][0-9]* | Point group symmetry for helices in Schoenflies notation |
| point_symmetry | char | [CD][1-9]|[CD][1-9][0-9]*|T|O|I | Encodes point symmetry as Cn, Dn, T, O, or I (case sensitive), where n is a positive integer. |
| positive_int | numb | [1-9][0-9]* | Positive integers (1,2,3,..) |
| seq-one-letter-code | char | (([\nUGPAVLIMCFYWHKRQNEDSTX]+)?|(\([0-9A-Z][0-9A-Z]?[0-9A-Z]?\))?)+ | One letter code sequence supporting parenthetical modified residues with 3-letter codes |
| sequence_dep | char | [a-zA-Z0-9\t \r\n\v\f\(\)]+$ | Deposition specific one letter code |
| symmetry_operation | char | [-+0-9XxYyZ/ ]+,[-+0-9XxYyZ/ ]+,[-+0-9XxYyZ/ ]+ | Allowed characters for use in symmetry operation such as 1/2-x,y,1/2-z |
| 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) ... |
| ucode-alphanum-csv | uchar | [A-Za-z0-9]+(,[A-Za-z0-9]+)? | comma separated alpha numeric codes (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)) |
| femtoseconds | femtoseconds (seconds * 10( -15)) |
| gigapascals | gigapascals |
| hertz | reciprocal seconds |
| hours | hours |
| ions_per_cm_squared_per_sec | ions per centimetre squared per second (ions/(meters * 10(-2))(-2)/second) |
| joules | Joules |
| kelvins | degrees (of temperature) Kelvin |
| kilodaltons | kilodaltons |
| kilodaltons/nanometer | kilodaltons/nanometer |
| kiloelectron_volts | KeV (electron volts * 10( 3)) |
| 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 |
| microjoules | joules * 10( -6) |
| microliters_per_min | microliters per minute |
| micrometres | micrometres (metres * 10( -6)) |
| micrometres_squared | micrometres squared (metres * 10( -6))2 |
| microns | micrometres (metres * 10( -6)) |
| microns_squared | micrometres squared (metres * 10( -6))2 |
| microseconds | microseconds (seconds * 10( -6)) |
| milliamperes | milliamperes |
| milligrams | grams / 1000 |
| milliliters | liter / 1000 |
| millimetres | millimetres (metres * 10( -3)) |
| millimolar | millimolar |
| milliradians | milliradians (of arc) |
| minutes | minutes |
| ml_per_min | milliliters per minute |
| nanometers | nanometers (metres * 10( -9)) |
| nanometres | nanometres (metres * 10( -9)) |
| nanometres_cubed | nanometres cubed (metres * 10( -9))3 |
| nanometres_squared | nanometres squared (metres * 10( -9))2 |
| pascals | pascals |
| 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 |
| teraphotons_per_pulse | (photons * 10( 12)) per pulse |
| volts | volts |
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 |