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mmcif_pdbx.dic辞書索引
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概要 
- 辞書名
- PDBアーカイブの現行データファイルに対応したPDB交換辞書（PDBx/mmCIF）バージョン5
- 辞書の説明
- PDB交換データ辞書の現行版
- 初期バージョンの開発者
- wwPDB
- 辞書管理者
- wwPDB
- 辞書ファイル名
- mmcif_pdbx.dic
- 辞書のバージョン
- 5.399
- 最終更新日
- 2024-11-06
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辞書の更新履歴
| バージョン | 更新日 | 更新内容 |
|---|---|---|
| 5.399 | 2024-11-06 |
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| 5.398 | 2024-10-22 |
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| 5.397 | 2024-09-23 |
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| 5.396 | 2024-08-26 |
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| 5.383 | 2023-12-03 |
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| 5.382 | 2023-11-21 |
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| 5.381 | 2023-10-23 |
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| 5.379 | 2023-08-28 |
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| 5.366 | 2023-01-28 |
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| 5.365 | 2023-01-09 |
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| 5.364 | 2022-12-15 |
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| 5.363 | 2022-12-01 |
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| 5.362 | 2022-10-25 |
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| 5.361 | 2022-08-31 |
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| 5.360 | 2022-07-19 |
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| 5.359 | 2022-06-01 |
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| 5.358 | 2022-04-13 |
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| 5.357 | 2022-03-16 |
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| 5.356 | 2022-02-23 |
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| 5.355 | 2022-02-02 |
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| 5.354 | 2022-01-11 |
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| 5.353 | 2021-12-07 |
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| 5.352 | 2021-10-31 |
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| 5.351 | 2021-10-11 |
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| 5.350 | 2021-09-09 |
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| 5.349 | 2021-09-01 |
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| 5.348 | 2021-08-03 |
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| 5.340 | 2021-03-10 |
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| 5.339 | 2021-02-16 |
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| 5.338 | 2021-01-20 |
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| 5.337 | 2021-01-05 |
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| 5.336 | 2020-11-10 |
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| 5.301 | 2018-11-08 |
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| 5.300 | 2018-10-15 |
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| 5.289 | 2018-01-11 |
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| 5.288 | 2017-11-27 |
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| 5.287 | 2017-10-18 |
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| 5.286 | 2017-09-10 |
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| 5.285 | 2017-08-30 |
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| 5.279 | 2017-04-20 |
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| 5.274 | 2017-03-20 |
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| 5.264 | 2017-01-05 |
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| 5.263 | 2017-01-03 |
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| 5.262 | 2016-12-19 |
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| 5.261 | 2016-12-06 |
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| 5.260 | 2016-11-30 |
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| 5.259 | 2016-11-30 |
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| 5.258 | 2016-11-29 |
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| 5.256 | 2016-10-18 |
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| 5.255 | 2016-09-28 |
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| 5.254 | 2016-09-19 |
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| 5.253 | 2016-09-19 |
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| 5.252 | 2016-07-27 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 5.247 | 2016-04-27 | Changes (ep): + deposition beamline enumeration updates + add extensions to support pdbx_struct_assembly evidence |
| 5.246 | 2016-04-11 | Changes (ep): + deposition beamline enumeration updates |
| 5.245 | 2016-04-02 | Changes (PDBj): + _diffrn_source.type/_diffrn_source.pdbx_synchrotron_beamline deposition enumeration update BL-21 -> PX-BL21 |
| 5.244 | 2016-03-31 | Changes (jw): + add extensions to capture results from ligand binding assays |
| 5.243 | 2016-03-25 | Changes (jy,zf): + add extensions for group depositions |
| 5.242 | 2016-03-21 | Changes (jw): + add regular expression for ORCID |
| 5.241 | 2016-03-08 | Changes (ep): + Update local context for selected em_* categories. + Update internal enumerations for detectors and secondary structure types. |
| 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 |
| 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 |
| 5.238 | 2016-02-03 | Changes (jy): + enumeration update for item _pdbx_database_status.methods_development_category |
| 5.237 | 2016-02-01 | Changes (es): + update enumerations and descriptions for EMD data items - |
| 5.236 | 2016-01-26 | Changes (cl,ep): + update enumerations and descriptions for EM data items - |
| 5.235 | 2016-01-21 | Changes (jw): + update context for EM data items - + add _em_admin.map_hold_date |
| 5.234 | 2016-01-06 | Changes (ep): + description text updates |
| 5.233 | 2015-12-08 | Changes (cl,ep): + EM extension update |
| 5.232 | 2015-12-07 | Changes (ep): + enumeration updates |
| 5.231 | 2015-12-04 | Changes (cl): + EM extension update |
| 5.230 | 2015-12-03 | Changes (es): + EMD extension update |
| 5.229 | 2015-12-03 | Changes (jdw): + Category context changed for pdbx_nmr_spectral_peak_list |
| 5.228 | 2015-11-28 | Changes (es): + EMD extension update |
| 5.227 | 2015-11-24 | Changes (ep): + DCC extension update |
| 5.226 | 2015-11-24 | Changes (cl): + EM extension update |
| 5.225 | 2015-11-24 | Changes (es): + EMD extension update |
| 5.224 | 2015-11-19 | Changes (es): + EMD extension update |
| 5.223 | 2015-11-11 | Changes (jw): + Adjust local context for selected NMR and EM data categories. |
| 5.222 | 2015-11-11 | Changes (es): + EMD extension update |
| 5.221 | 2015-11-02 | Changes (ep): + Enumeration updates |
| 5.220 | 2015-10-30 | Changes (ep): + Enumeration updates |
| 5.219 | 2015-10-22 | Changes (cl): + EM extension update |
| 5.218 | 2015-10-22 | Changes (es): + EMD extension update |
| 5.217 | 2015-10-15 | Changes (jw): + add item _pdbx_depui_entry_details.wwpdb_site_id |
| 5.216 | 2015-10-14 | Changes (cl): + Add _emd_admin.header_release_date, _emd_admin.obsoleted_date and _em_admin.header_release_date |
| 5.215 | 2015-10-13 | Changes (es): + EMD extension update |
| 5.214 | 2015-10-08 | Changes (ep): + Enumeration updates + regex update for type author |
| 5.213 | 2015-10-01 | Changes (jdw): + _pdbx_nmr_systematic_chem_shift_offset.ordinal replaces the natural category key for this category. + Enumeration updates |
| 5.212 | 2015-09-08 | Changes (cl): + EM extension update |
| 5.211 | 2015-09-08 | Changes (es): + EMD extension update |
| 5.210 | 2015-08-31 | Changes (cl,jw): + EM extension update |
| 5.209 | 2015-08-30 | Changes (ep,jw): + Enumeration updates |
| 5.208 | 2015-08-14 | Changes (cl,jw): + EM extension update |
| 5.207 | 2015-08-06 | Changes (ep,jw): + enumeration updates |
| 5.206 | 2015-07-20 | Changes (jw): + add new category pdbx_audit_conform_extension |
| 5.205 | 2015-07-17 | Changes (ep,jw): + enumeration updates |
| 5.204 | 2015-07-06 | Changes (es,cl): + EMD data type refinement |
| 5.203 | 2015-06-30 | Changes (es): + EMD data type refinement |
| 5.202 | 2015-06-26 | Changes (es): + EMD regular expression update |
| 5.201 | 2015-06-24 | Changes (es): + EMD extension update |
| 5.200 | 2015-06-19 | Changes (cl): + EMD extension update |
| 5.199 | 2015-06-09 | Changes (cl): + EMD extension update |
| 5.198 | 2015-06-03 | Changes (es,cl,jdw): + EMD extension update |
| 5.197 | 2015-05-06 | Changes (ep,ms,jdw): + enumeration updates |
| 5.196 | 2015-04-30 | Changes (ep,jdw): + enumeration updates |
| 5.195 | 2015-04-28 | Changes (es,jdw): + EMD extension dictionary update |
| 5.194 | 2015-04-22 | Changes (ep,jdw): + enumeration updates + add item _pdbx_contact_author.identifier_ORCID. + add chem_comp_model_group extensions. |
| 5.193 | 2015-03-31 | Changes (cs,jdw): + remove relationship between _pdbx_reference_entity_subcomponents.prd_id and _pdbx_reference_molecule_list.prd_id |
| 5.192 | 2015-03-18 | Changes (ep,jdw): + Add item _pdbx_depui_entry_details.replace_pdb_id + Enumeration updates |
| 5.191 | 2015-03-10 | Changes (es,jdw): + EMD extension dictionary update |
| 5.190 | 2015-02-28 | Changes (ep,jdw): + Enumeration updates - + removed _pdbx_poly_seq_scheme.hetero relationship with _entity_poly_seq.hetero |
| 5.189 | 2015-02-20 | Changes (es,ep,jdw): + EMD extension dictionary update + Enumeration updates |
| 5.188 | 2015-02-10 | Changes (es,jdw): + EMD extension dictionary update |
| 5.187 | 2015-02-03 | Changes (es,cl,jdw): + EMD extension dictionary update |
| 5.186 | 2015-02-01 | Changes (zf,jdw): + NMR updates for deposition system |
| 5.185 | 2014-12-17 | Changes (ag,ep,jdw): + NMR updates for deposition system |
| 5.184 | 2014-12-02 | Changes (es,jdw): + EMD extension dictionary update |
| 5.183 | 2014-11-21 | Changes (es,cl,jdw): + EMD extension dictionary update |
| 5.182 | 2014-11-07 | Changes (ag,ez,jdw): + NMR updates for deposition system - |
| 5.181 | 2014-10-28 | Changes (ag,ez,jdw): + NMR updates for deposition system - |
| 5.180 | 2014-10-21 | Changes (es,cl,jdw): + EMD dictionary update - make all categories optional -- |
| 5.179 | 2014-10-20 | Changes (es,cl,jdw): + EMD dictionary update |
| 5.178 | 2014-10-14 | Changes (ep,jdw): + update enumerations for deposition system. |
| 5.177 | 2014-09-25 | Changes (ep,jdw): + update detector enumerations for deposition system. |
| 5.176 | 2014-09-11 | Changes (to,jdw): + add _pdbx_depui_validation_status_flags.residual_B_factors_flag |
| 5.175 | 2014-09-10 | Changes (ep,jdw): + update of NMR alternative mandatory codes and examples |
| 5.174 | 2014-09-02 | Changes (cl,ep,jdw): + update of EM extensions definitions, examples and enumerations |
| 5.173 | 2014-08-28 | Changes (cl,jdw): + update of EM extensions definitions, examples and enumerations |
| 5.172 | 2014-07-30 | Changes (cl,jdw): + update of EM extensions definitions, examples and enumerations |
| 5.171 | 2014-07-21 | Changes (jdw): + _pdbx_depui_status_flags.has_viewed_validation_report made optional |
| 5.170 | 2014-07-17 | Changes (cl,ep,jdw): + update of enumerations for 3DEM and other deposition forms. |
| 5.169 | 2014-07-16 | Changes (ep,jdw): + update of enumerations for deposition forms. |
| 5.168 | 2014-07-10 | Changes (cl,ep,jdw): + update of EM extensions definitions, examples and enumerations + update of enumerations for deposition forms. |
| 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 |
| 5.166 | 2014-06-06 | Changes (jdw): + Add item _pdbx_struct_conn_angle.ptnr3_symmetry + Add category pdbx_database_status_history |
| 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 |
| 5.164 | 2014-06-03 | Changes (jdw): + Update mandatory codes in category pdbx_database_status |
| 5.163 | 2014-05-30 | Changes (jdw): + remove redundant mandatory code for _pdbx_database_status.data_hold_nmr_contraints |
| 5.162 | 2014-05-08 | Changes (ep/jdw): + update enumerations in category software |
| 5.161 | 2014-05-07 | Changes (jdw): + update enumerations in category pdbx_SG_project |
| 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. |
| 5.159 | 2014-04-10 | Changes (cl/jdw): + Update in EM extension dictionary in support of new deposition system. |
| 5.158 | 2014-04-03 | Changes (jdw): + Make context for _entity_poly.pdbx_explicit_linking_flag local. + extend enumeration for _pdbx_contact_author.id. |
| 5.157 | 2014-03-28 | Changes (ep/jdw): + Update internal enumerations and boundary values for deposition system - |
| 5.156 | 2014-03-24 | Changes (ep/jdw): + Update detector enumerations |
| 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. |
| 5.154 | 2014-03-10 | Changes (ag/eu/jdw): + Update deposition closed enumeration flags for NMR extension definitions. |
| 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 |
| 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 |
| 5.151 | 2014-03-01 | Changes (ep/jdw): + update deposition specific enumerations in category pdbx_database_related |
| 5.150 | 2014-02-25 | Changes (cl/ep/jdw): + update EM deposition specific metadata items. |
| 5.149 | 2014-02-20 | Changes (jdw): + update deposition mandatory codes and enumerations. |
| 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 |
| 5.147 | 2014-02-18 | Changes (jdw): + update diffraction detector enumerations/ |
| 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. |
| 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 |
| 5.144 | 2014-02-06 | Changes (cl/jdw): + Update of enumerations for save__em_experiment.reconstruction_method |
| 5.143 | 2014-01-24 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
| 5.142 | 2014-01-23 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
| 5.141 | 2014-01-21 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
| 5.140 | 2014-01-20 | Changes (ep/jdw): + Update of internal descriptions and enumerations for deposition system. |
| 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. |
| 5.138 | 2013-12-20 | Changes (jdw): + Update mandatory codes for category pdbx_contact_author. + Update enumerations for category software. |
| 5.137 | 2013-12-10 | Changes (jdw): + Update mandatory codes for category pdbx_contact_author. + Update enumerations for category software. |
| 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 |
| 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 |
| 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. |
| 5.133 | 2013-06-18 | Changes (jdw): + updated advisory limits for _reflns_shell.d_res_low and _refine_ls_shell.d_res_low |
| 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 |
| 5.131 | 2013-06-14 | Changes (jdw): + update enumerations for _pdbx_struct_ref_seq_depositor_info.db_name |
| 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. |
| 5.129 | 2013-05-29 | Changes (jdw): + _pdbx_database_status.pdbx_annotator replaces _pdbx_database_status.rcsb_annotator |
| 5.128 | 2013-05-23 | Changes (jdw): + add item _entity_poly.pdbx_sequence_evidence_code |
| 5.127 | 2013-04-27 | Changes (jdw): + Update alternate descriptions and enumerations for deposition system. |
| 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 + |
| 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 |
| 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 |
| 5.123 | 2013-03-12 | Changes (jdw): + add category pdbx_depui_entity_features |
| 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 |
| 5.121 | 2013-03-07 | Changes (jdw): + bulk import of RCSB local enumerations into internal pdbx_item_enumeration containers, |
| 5.120 | 2013-03-01 | Changes (jdw): + consolidated pdbx_struct_ref_depositor_info into pdbx_struct_ref_seq_depositor_info |
| 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 |
| 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. |
| 5.117 | 2013-02-13 | Changes (jdw): + Added internal categories -depui_validation_status_flags, pdbx_depui_upload, pdbx_depui_status_flags |
| 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 -- |
| 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 |
| 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 |
| 5.113 | 2012-12-04 | Changes (eu,ag): + Add _pdbx_nmr_exptl.sample_state |
| 5.112 | 2012-11-12 | Changes (cl,jdw): + Update to the 3DEM data categories - |
| 5.111 | 2012-11-08 | Changes (cl,jdw): + Update to the 3DEM data categories - |
| 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 |
| 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 |
| 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. |
| 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 |
| 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. |
| 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 |
| 5.104 | 2012-09-01 | Changes (jdw): + Added category pdbx_audit_support extension. + Incorporated D&A alternate descriptions and boundary values. |
| 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 |
| 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 |
| 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 |
| 5.100 | 2012-08-21 | Changes (jdw): + Release as provisional version 5.100 |