Supporting Data mmcif_pdbx.dic

Dictionary Revision History

Version Revision Date Revision Description
5.388 2024-03-04
Changes (ep/mgb):
+ Update ptm-extension
+ Example for _entity_poly.pdbx_seq_one_letter_code updted changing PTO -> TPO
+ Enumeration for _software.name "MAIN" has roles added.
+ Add CSearch to _software.name enumeration
+ Add ASTRA-TOOLBOX to _em_software enumeration
+ Add 4D-STEM to _em_iaging.mode enumeration
+ Add PDB-Dev to _database_2.database_id
+ Update funding enumerations
mmcif_pdbx.dic
5.387 2024-02-04
Changes (ep):
+ Add "int_list" data type for a comma separated list of positive integers.
Use for pdbx_item_type for -pdbx_initial_refinement_model.entity_id_list.
Update description for pdbx_initial_refinement_model.entity_id_list.
+ Add "STFC Large Pixel Detector" to _diffrn_detector.type enumeration.
mmcif_pdbx.dic
5.386 2024-01-29
Changes (ep):
+ Add enumeration for _pdbx_database_related.db_name
+ Add "NMRtist" to pdbx_nmr_software.name enumeration
mmcif_pdbx.dic
5.385 2024-01-22
Changes (ep):
+ Add pdbx_enumeration_enumeration for pdbx_initial_refinement_model.type removing "other"
+ Add new "DECTRIS PILATUS4 (R,X,XE) CdTe" detectors to _diffrn_detector.type enumeration
+ Add "GATAN ALPINE (2.3k x 3.2k)" to _em_image_recording.film_or_detector_model
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.384 2023-01-16
Changes (ep):
+ em_software.name enumeration change "PanthaRhei" to "Pantha Rhei"
+ Add "GATAN K3 BIOCONTINUUM (6k x 4k)" to _em_image_recording.film_or_detector_model
+ Add "RIGAKU HyPix-Arc 100" to _diffrn_detector.type enumeration
+ Add pdbx_item_description to _entity.details
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add IPCAS to _software.name enumeration
mmcif_pdbx.dic
5.383 2023-12-03
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add ARTINA to pdbx_nmr_software.name enumeration
+ Add "DECTRIS ELA (1k x 0.5k)" to em_image_recording.film_or_detector_model enumeration
+ Add PanthaRhei and PACEtomo to em_software.name enumeration
+ Add 'CEOS CEFID' to _em_imaging_optics.energyfilter_name enumeration
mmcif_pdbx.dic
5.382 2023-11-21
Changes (ep):
+ Remove NDB, BMCD, and BIOISIS from the pdbx_enumeration_list for pdbx_database_related.db_name
+ Add 'DECTRIS PILATUS4' detectors to _diffrn_detector.type
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.381 2023-10-23
Changes (ep):
+ author data type was corrected from 5.379 version so options properly checked
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "MAR CCD 300 mm" to _diffrn_detector.type
+ Add definitions for _pdbx_chem_comp_depositor.upload_file_name,
_pdbx_chem_comp_depositor.upload_file_type
+ Add example for _em_start_model.emdb_id
mmcif_pdbx.dic
5.380 2023-10-02
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ PTM extension updates to enumerations
+ Add Poky to _pdbx_nmr_softare.name enumeration
mmcif_pdbx.dic
5.379 2023-08-28
Changes (ep):
+ Add EMDB_PUBLIC context to em_staining and em_final_classification
categories
+ author data type extended to support structural genomics names
+ Add 'I3' to _em_software.name enumeration
+ Add "RIGAKU HyPix-Arc 150" to _diffrn_detector.type
mmcif_pdbx.dic
5.378 2023-08-22
Changes (ep):
+ Add em_admin.process_site and em_admin.composite_map
+ For many EM categories and EMDB_PUBLIC
mmcif_pdbx.dic
5.377 2023-08-15
Changes (ep):
+ Add PTM remediation categories and data
_chem_comp.pdbx_pcm, _chem_comp_atom.pdbx_backbone_atom_flag,
_chem_comp_atom.pdbx_n_terminal_atom_flag, _chem_comp_atom.pdbx_c_terminal_atom_flag,
category pdbx_chem_comp_pcm, _pdbx_entry_details.has_protein_modification,
category pdbx_modification_feature
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "CRYOSOL VITROJET" to em_vitrification.instrument
mmcif_pdbx.dic
5.376 2023-08-02
Changes (ep):
+ Correct pdbx_item_linked_group_list definitions for pdbx_entity_branch_link
+ Add PDB-Dev to pdbx_initial_refinement_model.source_name enumeration
+ Temporary removal atom_site.label_atom_id -> chem_comp_atom.atom_id parent/child relationship
mmcif_pdbx.dic
5.375 2023-07-24
Changes (ep):
+ Add _em_3d_fitting_list.initial_refinement_model_id
+ Add "PSI JUNGFRAU 8M" to _diffrn_detector.type enumeration
+ Add autoPX to _software.name enumeration
+ Add "SSRF BEAMLINE BL03HB" and "SSRF BEAMLINE BL17UM" to
_diffrn_source.type
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.374 2023-07-17
Changes (ep):
+ Add "JEOL 1400/HR + YPS FEG" to _em_imaginh.microscope_model enumeration
+ Add "DECTRIS SINGLA (1k x 1k)" to _em_image_recording.film_or_detector_model enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add 'consensus EM volume' and 'focused EM volume' to pdbx_database_related.content_type
+ Add 'Modify backbone' to _pdbx_chem_comp_audit.action_type enumeration
+ Add Servalcat to _em_softare.name, and _software.name enumerations
mmcif_pdbx.dic
5.373 2023-06-18
Changes (ep):
+ Add AUCO to enumeration of _pdbx_database_status.status_code_nmr_data
+ Correct pdb_id_u regular expression
mmcif_pdbx.dic
5.372 2023-06-12
Changes (ep):
+ Change type of _em_3d_fitting_list.pdb_entry_id to pdb_id_u
+ Add "MALVERN PANALYTICAL EMPYREAN TUBE" to _diffrn_source.type enumeration
+ Add _em_entity_assembly_naturalsource.details
+ Remove open enumeration from _pdbx_nmr_chem_shift_ref.mol_common_name
+ Make _pdbx_reference_entity_sequence.one_letter_codes non-mandatory
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.371 2023-06-01
Changes (ep/cl):
+ Add _ndb_struct_na_base_pair.hbond_type_leontis_westhof to eventually replace
_ndb_struct_na_base_pair.hbond_type_12
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Change "LNLS SIRUS" to "LNLS SIRIUS" in _diffrn_source.pdbx_synchrotron_site
and _diffrn_source.type enumerations
+ Change type of _em_obsolete.id to code
+ Make _diffrn.pdbx_serial_crystal_experiment mandatory for deposition
mmcif_pdbx.dic
5.370 2023-05-03
Changes (ep):
+ Correct "TFS FALCON 4i (4k x 4k)" to _em_image_recording.film_or_detector_model
+ Add 'Au-flat 1.2/1.3' to _em_sample_support.grid_type enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add IPLT to _em_software.name enumeration
+ Adjust entity_id_list data type to be alphanumeric entities which is more in line with
entity.id type.
+ Define pdb_id_u data type as case insensitive
+ Change data type for _em_3d_fitting_list.pdb_entry_id to pdb_id_u
mmcif_pdbx.dic
5.369 2023-04-12
+ Add 'HOLD FOR 6 WEEKS' to enumerations for _pdbx_database_status.dep_release_code_struct_fact
and _pdbx_database_status.dep_release_code_nmr_constraints
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add _reflns.pdbx_redundancy lower limit of 0.
+ Add 'Histidine' to _pdbx_nmr_chem_shift_ref.mol_common_name enumeration
+ Update pdbx_nmr_software.name list
mmcif_pdbx.dic
5.368 2023-03-14
Changes (ep):
+ Move 'EWALD SPHERE CORRECTION' to _em_software.category enumeration
+ Add _pdbx_depui_entry_details.validated_identifier_ORCID
+ Add "Malvern Panalytical PIXcel 1D" to _diffrn_detector.type enumeration
+ Add "TFS FALCON 4i (4k x 4x)" to _em_image_recording.film_or_detector_model
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.367 2023-03-07
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add 'Ewald Sphere Correction' to _em_software.name enumeration
mmcif_pdbx.dic
5.366 2023-01-28
Changes (ep):
+ Change _pdbx_sifts_xref_db.res_type enumeration to examples
+ Add pdbx_sifts_xref_db_segments.seq_id_start and
pdbx_sifts_xref_db_segments.seq_id_start as keys for category.
mmcif_pdbx.dic
5.365 2023-01-09
Changes (ep):
+ Add 'PDB-Dev' to _pdbx_database_related.db_name enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.364 2022-12-15
Changes (ep):
+ Mark _pdbx_initial_refinement_model.type as non-mandatory for deposition system
+ Attributes for _struct_ncs_oper changed to mandatory
+ Deposition type for _em_imaging.nominal_defocus_max and
_em_imaging.nominal_defocus_min to int
+ Add "RIGAKU PhotonJet-S" and "BRUKER IMUS DIAMOND MICROFOCUS"
to _diffrn_source.type
+ Add EMIRA to _em_software.name enumeration
+ Add CSBID to _pdbx_SG_project.full_name_of_center, _pdbx_SG_project.initial_of_center
enumerations
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.363 2022-12-01
Changes (ep/cv/ab):
+ Integrate unmerged data by bringing in minimal imgCIF dictionary and
define new categories _pdbx_diffrn_batch, _pdbx_diffrn_cell, _pdbx_diffrn_orientation
_pdbx_diffrn_batch_scan, _pdbx_diffrn_detector_panel_mapping. Add
_diffrn_refln.frame_id, _diffrn_refln.pdbx_batch_id, _diffrn_refln.pdbx_detector_obs_fast,
_diffrn_refln.pdbx_detector_obs_slow, _diffrn_refln.pdbx_detector_calc_fast,
_diffrn_refln.pdbx_detector_calc_slow, _diffrn_refln.pdbx_panel_mapping_id
+ Define uchar5 data type _chem_comp.three_letter_code
mmcif_pdbx.dic
5.362 2022-10-25
Changes (ep):
+ Add _em_3d_fitting_list.accession_code,
_em_3d_fitting_list.source_name,
_em_3d_fitting_list.type
+ Deprecate _em_3d_fitting.initiali_refinement_model_id
+ Extend em_software.name list to include CryoDRGN and CryoDRGN2
+ Add "DECTRIS EIGER2 X CdTe 9M" and "DECTRIS EIGER2 XE CdTe 9M"
to _diffrn_detector.type
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Mark _pdbx_nmr_chem_shift_ref.atom_group and
_pdbx_nmr_constraint_file.constraint_type as closed enumeration
mmcif_pdbx.dic
5.361 2022-08-31
Changes (ep/rp/cv):
+ Consolidate EMD/EM namespaces
+ Update _pdbx_audit_support
+ Correct _atom_type.scat_Cromer_Mann_* example
+ Add cctbx.xfel.merge and STARGazer to _software.name enumeration
+ Add "DECTRIS EIGER2 R 4M" to _diffrn_detector.type
+ Expand range of _em_image_scans.sampling_size to 100.0
mmcif_pdbx.dic
5.360 2022-07-19
Changes (ep/mw):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "DIRECT ELECTRON APOLLO (4k x 4k)" to _em_image_recording.film_or_detector_mode enumeration
+ Initial model extension added to dictionary (_pdbx_initial_refinement)
+ pdbx_investigation category added to the model
+ Add "CHESS BEAMLINE 7B2" to _diffrn_source.type enumeration
+ include 0 in the range for _reflns.pdbx_aniso_B_tensor_eigenvalue_*
+ Mark _struct.pdbx_structure_determination_methodology as internal to WWPDB
mmcif_pdbx.dic
5.359 2022-06-01
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "POSITION SENSITIVE DETECTOR" to _diffrn_detector.detector enumeration
+ Add Careless and Xtrapol8 to _software.name PDBX enumeration
+ Add "5ATM 3HE, CURVED 120X30 DEGREES" to _diffrn_detector.type enumeration
mmcif_pdbx.dic
5.358 2022-04-13
Changes (ep):
+ Add _em_depui.composite_map_deposition
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add pdbx_data_usage category
mmcif_pdbx.dic
5.357 2022-03-16
Changes (ep):
+ Add PRIME-X to _software.name enumeration
+ Enhance description of _entity_poly.pdbx_seq_one_letter_code_can
to describe chromophore handling
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.356 2022-02-23
Changes (ep/Aaron Brewster):
+ Enchanced descriptions and addition of attributes to better support
serial crystallography.
New definitions:
_pdbx_serial_crystallography_data_reduction.lattices_merged
_cell.pdbx_esd_method
_reflns.pdbx_CC_split_method,
_exptl_crystal.pdbx_mosaic_method
_exptl_crystal.pdbx_mosaic_block_size
_exptl_crystal.pdbx_mosaic_block_size_esd
_pdbx_crystal_alignment.overall_beam_divergence
_pdbx_crystal_alignment.overall_beam_divergence_esd
Updated definitions (description, ranges)
_pdbx_crystal_alignment.crossfire_x, _pdbx_crystal_alignment.crossfire_x_esd,
_pdbx_crystal_alignment.crossfire_y, _pdbx_crystal_alignment.crossfire_y_esd,
_exptl_crystal.pdbx_mosaicity
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Added 'ESRF BEAMLINE BM07' to _diffrn_source.type enumeration and 'BM07' to
diffrn_source.pdbx_synchrotron_beamline
mmcif_pdbx.dic
5.355 2022-02-02
Changes (ep):
+ Adjust enumerations in _database_2.database_id
+ Extend _pdbx_sudit_support.funding_organization enumeration
mmcif_pdbx.dic
5.354 2022-01-12
Changes (ep):
+ Introduce _pdbx_entity_remapping and _pdbx_chain_remapping categories
+ Extend _pdbx_sudit_support.funding_organization enumeration
+ Add "xia2.multiplex" to _software.name enumeration
+ Extend enumeration _database_2.database_id to include "AFDB", "SMR",
"MODBASE", "AFDB"
+ Add _struct.pdbx_structure_determination_methodology
+ Add "EMS Lacey Carbon" to _em_sample_support.grid_type enumeration.
mmcif_pdbx.dic
5.353 2021-12-07
Changes (ep/Antanas Vaitkus):
+ Correct capitalization of angstrom in descriptions
+ Correct capitalization of kelvins as a unit. Remove the word
"degrees" in context of it
+ Add "SCINTILLATION" to _diffrn_detector.detector enumeration
+ Add "Cyberstar LaBr3", "DECTRIS EIGER2 S 1M", "DECTRIS EIGER2 S 4M",
"DECTRIS EIGER2 S 9M", "DECTRIS EIGER2 S 16M" to
_diffrn_detector.type deposition enumeration
+ Add "ESRF BEAMLINE ID22" to _diffrn_source.type enumertion
+ Add "GSAS", "ISOLDE" and "PRODD" to _software.name enumeration
+ Extend _pdbx_sudit_support.funding_organization enumeration
+ Add "TFS Selectris" and "TFS Selectris X" to _em_imaging_optics.energyfilter_name
+ Add "FEI tomography" to _em_software.name enumeration
+ Add _pdbx_struct_oper_list.full_matrix
mmcif_pdbx.dic
5.352 2021-10-31
Changes (ep):
+ pdbx_prd_audit.processing_site enumeration change PDBe to PDBE to be consistent with rest of dictionary.
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ _refine.ls_R_factor_R_free and _refine.ls_R_factor_obs remove over broad advisory range
+ Add "RIGAKU PhotonJet-R" to _diffrn_source.type enumeration
+ Enhance pdb_id and support PDB extented codes
mmcif_pdbx.dic
5.351 2021-10-11
Changes (ep):
+ Update deposition help text for _diffrn.abient_temp
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add "BRUKER IMUS 3.0 MICROFOCUS" to _diffrn_source.type enumeration
+ Add IPET and TomoAlign to _em_software.name enumeration
+ Change pdx_item_tye for _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
mmcif_pdbx.dic
5.350 2021-09-09
Changes (ep):
+ Correct advisory limits for _em_image_recording.avg_electron_dose_per_subtomogram
+ Extend _pdbx_audit_support.funding_organization enumeration.
mmcif_pdbx.dic
5.349 2021-09-01
Changes (ep):
+ Using new conditional context for pdbx_contact_author, selectively all
principal investogator information out
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Extend _em_software.nameenumeration
+ Add _em_image_recording.avg_electron_dose_per_subtomogram
+ Extend _em_map.type enumerations
+ Add SIFTS extension - creating categories _pdbx_sifts_xref_db,
_pdbx_sifts_xref_db_segments, _pdbx_sifts_unp_segments and attributes
_atom_site.pdbx_label_index, _atom_site.pdbx_sifts_xref_db_name,
_atom_site.pdbx_sifts_xref_db_acc, _atom_site.pdbx_sifts_xref_db_num,
_atom_site.pdbx_sifts_xref_db_res
mmcif_pdbx.dic
5.348 2021-08-03
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add internal _struct.pdbx_center_of_mass_x, _struct.pdbx_center_of_mass_y,
_struct.pdbx_center_of_mass_z.
+ Add _em_entity_assembly.chimera
mmcif_pdbx.dic
5.347 2021-07-18
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Correct captilatization in description of _pdbx_nmr_spectrometer.field_strength
+ Add "SSRF BEAMLINE BL10U2" and "SSRF BEAMLINE BL02U1" to _diffrn_source.type enumeration
mmcif_pdbx.dic
5.346 2021-07-08
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Make _pdbx_contact_author.name_salutation non-mandatory
mmcif_pdbx.dic
5.345 2021-06-30
Changes (ep):
+ Add "GN" to _pdbx_nmr_spectrometer.model enumeration
+ Update examples for _database_2.pdbx_database_accession
and _database_2.pdbx_DOI
+ Update enumeration and details for _pdbx_nmr_spectrometer.field_strength
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Update description of _pdbx_molecule_features.prd_id
+ Add 'UCSF ChimeraX' to _em_software.name
+ Mark _struct.pdbx_descriptor as local context
+ Add limits for _refine.ls_percent_reflns_obs
+ Add _em_author_list.identifier_ORCID
mmcif_pdbx.dic
5.344 2021-06-08
Changes (ep):
+ Add _item_enumeration.pdbx_value_display for _exptl.method
mmcif_pdbx.dic
5.343 2021-06-02
Changes (ep):
+ Add 'NMR Distance Restraints' and 'electron microscopy' to enumerations for _pdbx_struct_assembly_auth_evidence.experimental_support
and pdbx_struct_assembly_auth_evidence_depositor_info.experimental_support
+ Create new attribute _pdbx_depui_status_flags.has_accepted_assemblies
+ Create new attribute _pdbx_database_status.date_accepted_terms_and_conditions
+ Update description of _reflns.pdbx_redundancy
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add 'TFS TUNDRA' to _em_imaging.microscope_model.
mmcif_pdbx.dic
5.342 2021-04-19
Changes (ep):
+ Add hard limits to _em_focused_ion_beam.initial_thickness
+ Update description of _struct_ref_seq_dif.pdbx_auth_seq_num
+ Add "ALS BREAMLINE 2.0.1" to _diffrn_source.type enumeration. "2.0.1" added to
enumeration for _diffrn_source.pdbx_synchrotron_beamline.
+ Update _pdbx_audit_support.funding_organization enumeration
+ Add 'subTOM' to _em_software.name enumeration and _emd_software.name
+ Change _em_map.symmetry_space_group type from line to int
+ Add acetonitrile to enumeration for _pdbx_nmr_chem_shift_ref.mol_common_name
mmcif_pdbx.dic
5.341 2021-03-15
Changes (ep/jw):
+ Add category pdbx_audit_conform
+ Update funding enumerations _pdbx_audit_support.funding_organization
+ Update descriptions for _entity_poly.pdbx_seq_one_letter_code_can and
_entity_poly.pdbx_seq_one_letter_code
+ Add "PSI JUNGFRAU 4M" to _diffrn_detector.type enumerations
mmcif_pdbx.dic
5.340 2021-03-10
Changes (jt):
+ Update funding enumerations _pdbx_audit_support.funding_organization
mmcif_pdbx.dic
5.339 2021-02-16
Changes (Global Phasing Ltd.):
+ Add items for anomalous diffraction statistics
_reflns.pdbx_redundancy_anomalous, _reflns.pdbx_CC_half_anomalous,
_reflns.pdbx_absDiff_over_sigma_anomalous, _reflns.pdbx_percent_possible_anomalous,
_reflns_shell.pdbx_redundancy_anomalous, _reflns_shell.pdbx_CC_half_anomalous,
_reflns_shell.pdbx_absDiff_over_sigma_anomalous,
_reflns_shell.pdbx_percent_possible_anomalous
+ Add items to cater for anistropic diffraction
Ellipsoid fit to the cut-off surface:
_reflns.pdbx_aniso_diffraction_limit_axis_?_ortho[?],
_reflns.pdbx_aniso_diffraction_limit_?
Anisotropic B tensor:
_reflns.pdbx_aniso_B_tensor_eigenvector_?_ortho[?],
_reflns.pdbx_aniso_B_tensor_eigenvalue_?
Statistics specific to anisotropic diffraction:
_reflns.pdbx_percent_possible_*,
_reflns_shell.pdbx_percent_possible_*
for ellipsoidal/spherical and anomalous/non-anomalous diffraction.

Also add _reflns.pdbx_orthogonalization_convention and new subcategories
unit_vector and eigendecomposition
+ Add items for a per-reflection signal and parameter-free definition of
the cut-off surface
_reflns.pdbx_observed_signal_threshold, _reflns.pdbx_signal_type,
_reflns.pdbx_signal_details, reflns.pdbx_signal_software_id,
_pdbx_refln_signal_binning.ordinal,
_pdbx_refln_signal_binning.upper_threshold,
_refln.pdbx_signal, _refln.pdbx_signal_status
+ Add and modify items to cater better for umerged reflection data
Add _diffrn_refln.pdbx_detector_x, _diffrn_refln.pdbx_detector_y,
_diffrn_refln.pdbx_scale_value
Modify _diffrn_refln.pdbx_image_id, _diffrn_refln.pdbx_scan_angle
mmcif_pdbx.dic
5.338 2021-01-20
Changes (ep):
+ Add LAUENORM to _software.name enumeration
+ Add 'JEOL 1000EES' to _em_imaging.microscope_model and _emd_microscopy.microscope
+ Add _citation.pdbx_database_id_patent to record patents
+ Update funding enumerations _pdbx_audit_support.funding_organization
mmcif_pdbx.dic
5.337 2021-01-05
Changes (ep/mw/cv):
+ Addition of _diffrn_refln.pdbx_image_id and _diffrn_refln.pdbx_scan_angle
+ Duplicate words cleanup in descriptions
+ Add enumerations for _pdbx_exptl_crystal_grow_sol.volume_units and
_pdbx_exptl_crystal_grow_comp.conc_units
+ Add usage information to description of _atom_site
+ Update funding enumerations _pdbx_audit_support.funding_organization
+ Add 'ARP/wARP' to _em_software.name
+ Add _database_2.pdbx_database_acceession and _database_2.pdbx_DOI
+ Add _em_imaging_optics.details
+ Change attributes to non-mandatory: _em_diffraction_stats.overall_phase_error,
_em_diffraction_stats.overall_phase_residual, and _em_diffraction_stats.r_sym,
+ Change type to float for _em_focused_ion_beam.duration and _emd_sectioning_focused_ion_beam.duration
mmcif_pdbx.dic
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
5.388 2024-03-04
Changes (ep/mgb):
+ Update ptm-extension
+ Example for _entity_poly.pdbx_seq_one_letter_code updted changing PTO -> TPO
+ Enumeration for _software.name "MAIN" has roles added.
+ Add CSearch to _software.name enumeration
+ Add ASTRA-TOOLBOX to _em_software enumeration
+ Add 4D-STEM to _em_iaging.mode enumeration
+ Add PDB-Dev to _database_2.database_id
+ Update funding enumerations
mmcif_pdbx.dic
5.387 2024-02-04
Changes (ep):
+ Add "int_list" data type for a comma separated list of positive integers.
Use for pdbx_item_type for -pdbx_initial_refinement_model.entity_id_list.
Update description for pdbx_initial_refinement_model.entity_id_list.
+ Add "STFC Large Pixel Detector" to _diffrn_detector.type enumeration.
mmcif_pdbx.dic
5.386 2024-01-29
Changes (ep):
+ Add enumeration for _pdbx_database_related.db_name
+ Add "NMRtist" to pdbx_nmr_software.name enumeration
mmcif_pdbx.dic
5.385 2024-01-22
Changes (ep):
+ Add pdbx_enumeration_enumeration for pdbx_initial_refinement_model.type removing "other"
+ Add new "DECTRIS PILATUS4 (R,X,XE) CdTe" detectors to _diffrn_detector.type enumeration
+ Add "GATAN ALPINE (2.3k x 3.2k)" to _em_image_recording.film_or_detector_model
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.384 2023-01-16
Changes (ep):
+ em_software.name enumeration change "PanthaRhei" to "Pantha Rhei"
+ Add "GATAN K3 BIOCONTINUUM (6k x 4k)" to _em_image_recording.film_or_detector_model
+ Add "RIGAKU HyPix-Arc 100" to _diffrn_detector.type enumeration
+ Add pdbx_item_description to _entity.details
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add IPCAS to _software.name enumeration
mmcif_pdbx.dic
5.383 2023-12-03
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add ARTINA to pdbx_nmr_software.name enumeration
+ Add "DECTRIS ELA (1k x 0.5k)" to em_image_recording.film_or_detector_model enumeration
+ Add PanthaRhei and PACEtomo to em_software.name enumeration
+ Add 'CEOS CEFID' to _em_imaging_optics.energyfilter_name enumeration
mmcif_pdbx.dic
5.382 2023-11-21
Changes (ep):
+ Remove NDB, BMCD, and BIOISIS from the pdbx_enumeration_list for pdbx_database_related.db_name
+ Add 'DECTRIS PILATUS4' detectors to _diffrn_detector.type
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.381 2023-10-23
Changes (ep):
+ author data type was corrected from 5.379 version so options properly checked
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "MAR CCD 300 mm" to _diffrn_detector.type
+ Add definitions for _pdbx_chem_comp_depositor.upload_file_name,
_pdbx_chem_comp_depositor.upload_file_type
+ Add example for _em_start_model.emdb_id
mmcif_pdbx.dic
5.380 2023-10-02
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ PTM extension updates to enumerations
+ Add Poky to _pdbx_nmr_softare.name enumeration
mmcif_pdbx.dic
5.379 2023-08-28
Changes (ep):
+ Add EMDB_PUBLIC context to em_staining and em_final_classification
categories
+ author data type extended to support structural genomics names
+ Add 'I3' to _em_software.name enumeration
+ Add "RIGAKU HyPix-Arc 150" to _diffrn_detector.type
mmcif_pdbx.dic
5.378 2023-08-22
Changes (ep):
+ Add em_admin.process_site and em_admin.composite_map
+ For many EM categories and EMDB_PUBLIC
mmcif_pdbx.dic
5.377 2023-08-15
Changes (ep):
+ Add PTM remediation categories and data
_chem_comp.pdbx_pcm, _chem_comp_atom.pdbx_backbone_atom_flag,
_chem_comp_atom.pdbx_n_terminal_atom_flag, _chem_comp_atom.pdbx_c_terminal_atom_flag,
category pdbx_chem_comp_pcm, _pdbx_entry_details.has_protein_modification,
category pdbx_modification_feature
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "CRYOSOL VITROJET" to em_vitrification.instrument
mmcif_pdbx.dic
5.376 2023-08-02
Changes (ep):
+ Correct pdbx_item_linked_group_list definitions for pdbx_entity_branch_link
+ Add PDB-Dev to pdbx_initial_refinement_model.source_name enumeration
+ Temporary removal atom_site.label_atom_id -> chem_comp_atom.atom_id parent/child relationship
mmcif_pdbx.dic
5.375 2023-07-24
Changes (ep):
+ Add _em_3d_fitting_list.initial_refinement_model_id
+ Add "PSI JUNGFRAU 8M" to _diffrn_detector.type enumeration
+ Add autoPX to _software.name enumeration
+ Add "SSRF BEAMLINE BL03HB" and "SSRF BEAMLINE BL17UM" to
_diffrn_source.type
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.374 2023-07-17
Changes (ep):
+ Add "JEOL 1400/HR + YPS FEG" to _em_imaginh.microscope_model enumeration
+ Add "DECTRIS SINGLA (1k x 1k)" to _em_image_recording.film_or_detector_model enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add 'consensus EM volume' and 'focused EM volume' to pdbx_database_related.content_type
+ Add 'Modify backbone' to _pdbx_chem_comp_audit.action_type enumeration
+ Add Servalcat to _em_softare.name, and _software.name enumerations
mmcif_pdbx.dic
5.373 2023-06-18
Changes (ep):
+ Add AUCO to enumeration of _pdbx_database_status.status_code_nmr_data
+ Correct pdb_id_u regular expression
mmcif_pdbx.dic
5.372 2023-06-12
Changes (ep):
+ Change type of _em_3d_fitting_list.pdb_entry_id to pdb_id_u
+ Add "MALVERN PANALYTICAL EMPYREAN TUBE" to _diffrn_source.type enumeration
+ Add _em_entity_assembly_naturalsource.details
+ Remove open enumeration from _pdbx_nmr_chem_shift_ref.mol_common_name
+ Make _pdbx_reference_entity_sequence.one_letter_codes non-mandatory
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.371 2023-06-01
Changes (ep/cl):
+ Add _ndb_struct_na_base_pair.hbond_type_leontis_westhof to eventually replace
_ndb_struct_na_base_pair.hbond_type_12
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Change "LNLS SIRUS" to "LNLS SIRIUS" in _diffrn_source.pdbx_synchrotron_site
and _diffrn_source.type enumerations
+ Change type of _em_obsolete.id to code
+ Make _diffrn.pdbx_serial_crystal_experiment mandatory for deposition
mmcif_pdbx.dic
5.370 2023-05-03
Changes (ep):
+ Correct "TFS FALCON 4i (4k x 4k)" to _em_image_recording.film_or_detector_model
+ Add 'Au-flat 1.2/1.3' to _em_sample_support.grid_type enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add IPLT to _em_software.name enumeration
+ Adjust entity_id_list data type to be alphanumeric entities which is more in line with
entity.id type.
+ Define pdb_id_u data type as case insensitive
+ Change data type for _em_3d_fitting_list.pdb_entry_id to pdb_id_u
mmcif_pdbx.dic
5.369 2023-04-12
+ Add 'HOLD FOR 6 WEEKS' to enumerations for _pdbx_database_status.dep_release_code_struct_fact
and _pdbx_database_status.dep_release_code_nmr_constraints
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add _reflns.pdbx_redundancy lower limit of 0.
+ Add 'Histidine' to _pdbx_nmr_chem_shift_ref.mol_common_name enumeration
+ Update pdbx_nmr_software.name list
mmcif_pdbx.dic
5.368 2023-03-14
Changes (ep):
+ Move 'EWALD SPHERE CORRECTION' to _em_software.category enumeration
+ Add _pdbx_depui_entry_details.validated_identifier_ORCID
+ Add "Malvern Panalytical PIXcel 1D" to _diffrn_detector.type enumeration
+ Add "TFS FALCON 4i (4k x 4x)" to _em_image_recording.film_or_detector_model
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.367 2023-03-07
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add 'Ewald Sphere Correction' to _em_software.name enumeration
mmcif_pdbx.dic
5.366 2023-01-28
Changes (ep):
+ Change _pdbx_sifts_xref_db.res_type enumeration to examples
+ Add pdbx_sifts_xref_db_segments.seq_id_start and
pdbx_sifts_xref_db_segments.seq_id_start as keys for category.
mmcif_pdbx.dic
5.365 2023-01-09
Changes (ep):
+ Add 'PDB-Dev' to _pdbx_database_related.db_name enumeration
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.364 2022-12-15
Changes (ep):
+ Mark _pdbx_initial_refinement_model.type as non-mandatory for deposition system
+ Attributes for _struct_ncs_oper changed to mandatory
+ Deposition type for _em_imaging.nominal_defocus_max and
_em_imaging.nominal_defocus_min to int
+ Add "RIGAKU PhotonJet-S" and "BRUKER IMUS DIAMOND MICROFOCUS"
to _diffrn_source.type
+ Add EMIRA to _em_software.name enumeration
+ Add CSBID to _pdbx_SG_project.full_name_of_center, _pdbx_SG_project.initial_of_center
enumerations
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.363 2022-12-01
Changes (ep/cv/ab):
+ Integrate unmerged data by bringing in minimal imgCIF dictionary and
define new categories _pdbx_diffrn_batch, _pdbx_diffrn_cell, _pdbx_diffrn_orientation
_pdbx_diffrn_batch_scan, _pdbx_diffrn_detector_panel_mapping. Add
_diffrn_refln.frame_id, _diffrn_refln.pdbx_batch_id, _diffrn_refln.pdbx_detector_obs_fast,
_diffrn_refln.pdbx_detector_obs_slow, _diffrn_refln.pdbx_detector_calc_fast,
_diffrn_refln.pdbx_detector_calc_slow, _diffrn_refln.pdbx_panel_mapping_id
+ Define uchar5 data type _chem_comp.three_letter_code
mmcif_pdbx.dic
5.362 2022-10-25
Changes (ep):
+ Add _em_3d_fitting_list.accession_code,
_em_3d_fitting_list.source_name,
_em_3d_fitting_list.type
+ Deprecate _em_3d_fitting.initiali_refinement_model_id
+ Extend em_software.name list to include CryoDRGN and CryoDRGN2
+ Add "DECTRIS EIGER2 X CdTe 9M" and "DECTRIS EIGER2 XE CdTe 9M"
to _diffrn_detector.type
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Mark _pdbx_nmr_chem_shift_ref.atom_group and
_pdbx_nmr_constraint_file.constraint_type as closed enumeration
mmcif_pdbx.dic
5.361 2022-08-31
Changes (ep/rp/cv):
+ Consolidate EMD/EM namespaces
+ Update _pdbx_audit_support
+ Correct _atom_type.scat_Cromer_Mann_* example
+ Add cctbx.xfel.merge and STARGazer to _software.name enumeration
+ Add "DECTRIS EIGER2 R 4M" to _diffrn_detector.type
+ Expand range of _em_image_scans.sampling_size to 100.0
mmcif_pdbx.dic
5.360 2022-07-19
Changes (ep/mw):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "DIRECT ELECTRON APOLLO (4k x 4k)" to _em_image_recording.film_or_detector_mode enumeration
+ Initial model extension added to dictionary (_pdbx_initial_refinement)
+ pdbx_investigation category added to the model
+ Add "CHESS BEAMLINE 7B2" to _diffrn_source.type enumeration
+ include 0 in the range for _reflns.pdbx_aniso_B_tensor_eigenvalue_*
+ Mark _struct.pdbx_structure_determination_methodology as internal to WWPDB
mmcif_pdbx.dic
5.359 2022-06-01
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add "POSITION SENSITIVE DETECTOR" to _diffrn_detector.detector enumeration
+ Add Careless and Xtrapol8 to _software.name PDBX enumeration
+ Add "5ATM 3HE, CURVED 120X30 DEGREES" to _diffrn_detector.type enumeration
mmcif_pdbx.dic
5.358 2022-04-13
Changes (ep):
+ Add _em_depui.composite_map_deposition
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Add pdbx_data_usage category
mmcif_pdbx.dic
5.357 2022-03-16
Changes (ep):
+ Add PRIME-X to _software.name enumeration
+ Enhance description of _entity_poly.pdbx_seq_one_letter_code_can
to describe chromophore handling
+ Extend _pdbx_audit_support.funding_organization enumeration
mmcif_pdbx.dic
5.356 2022-02-23
Changes (ep/Aaron Brewster):
+ Enchanced descriptions and addition of attributes to better support
serial crystallography.
New definitions:
_pdbx_serial_crystallography_data_reduction.lattices_merged
_cell.pdbx_esd_method
_reflns.pdbx_CC_split_method,
_exptl_crystal.pdbx_mosaic_method
_exptl_crystal.pdbx_mosaic_block_size
_exptl_crystal.pdbx_mosaic_block_size_esd
_pdbx_crystal_alignment.overall_beam_divergence
_pdbx_crystal_alignment.overall_beam_divergence_esd
Updated definitions (description, ranges)
_pdbx_crystal_alignment.crossfire_x, _pdbx_crystal_alignment.crossfire_x_esd,
_pdbx_crystal_alignment.crossfire_y, _pdbx_crystal_alignment.crossfire_y_esd,
_exptl_crystal.pdbx_mosaicity
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Added 'ESRF BEAMLINE BM07' to _diffrn_source.type enumeration and 'BM07' to
diffrn_source.pdbx_synchrotron_beamline
mmcif_pdbx.dic
5.355 2022-02-02
Changes (ep):
+ Adjust enumerations in _database_2.database_id
+ Extend _pdbx_sudit_support.funding_organization enumeration
mmcif_pdbx.dic
5.354 2022-01-12
Changes (ep):
+ Introduce _pdbx_entity_remapping and _pdbx_chain_remapping categories
+ Extend _pdbx_sudit_support.funding_organization enumeration
+ Add "xia2.multiplex" to _software.name enumeration
+ Extend enumeration _database_2.database_id to include "AFDB", "SMR",
"MODBASE", "AFDB"
+ Add _struct.pdbx_structure_determination_methodology
+ Add "EMS Lacey Carbon" to _em_sample_support.grid_type enumeration.
mmcif_pdbx.dic
5.353 2021-12-07
Changes (ep/Antanas Vaitkus):
+ Correct capitalization of angstrom in descriptions
+ Correct capitalization of kelvins as a unit. Remove the word
"degrees" in context of it
+ Add "SCINTILLATION" to _diffrn_detector.detector enumeration
+ Add "Cyberstar LaBr3", "DECTRIS EIGER2 S 1M", "DECTRIS EIGER2 S 4M",
"DECTRIS EIGER2 S 9M", "DECTRIS EIGER2 S 16M" to
_diffrn_detector.type deposition enumeration
+ Add "ESRF BEAMLINE ID22" to _diffrn_source.type enumertion
+ Add "GSAS", "ISOLDE" and "PRODD" to _software.name enumeration
+ Extend _pdbx_sudit_support.funding_organization enumeration
+ Add "TFS Selectris" and "TFS Selectris X" to _em_imaging_optics.energyfilter_name
+ Add "FEI tomography" to _em_software.name enumeration
+ Add _pdbx_struct_oper_list.full_matrix
mmcif_pdbx.dic
5.352 2021-10-31
Changes (ep):
+ pdbx_prd_audit.processing_site enumeration change PDBe to PDBE to be consistent with rest of dictionary.
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ _refine.ls_R_factor_R_free and _refine.ls_R_factor_obs remove over broad advisory range
+ Add "RIGAKU PhotonJet-R" to _diffrn_source.type enumeration
+ Enhance pdb_id and support PDB extented codes
mmcif_pdbx.dic
5.351 2021-10-11
Changes (ep):
+ Update deposition help text for _diffrn.abient_temp
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add "BRUKER IMUS 3.0 MICROFOCUS" to _diffrn_source.type enumeration
+ Add IPET and TomoAlign to _em_software.name enumeration
+ Change pdx_item_tye for _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
mmcif_pdbx.dic
5.350 2021-09-09
Changes (ep):
+ Correct advisory limits for _em_image_recording.avg_electron_dose_per_subtomogram
+ Extend _pdbx_audit_support.funding_organization enumeration.
mmcif_pdbx.dic
5.349 2021-09-01
Changes (ep):
+ Using new conditional context for pdbx_contact_author, selectively all
principal investogator information out
+ Extend _pdbx_audit_support.funding_organization enumeration
+ Extend _em_software.nameenumeration
+ Add _em_image_recording.avg_electron_dose_per_subtomogram
+ Extend _em_map.type enumerations
+ Add SIFTS extension - creating categories _pdbx_sifts_xref_db,
_pdbx_sifts_xref_db_segments, _pdbx_sifts_unp_segments and attributes
_atom_site.pdbx_label_index, _atom_site.pdbx_sifts_xref_db_name,
_atom_site.pdbx_sifts_xref_db_acc, _atom_site.pdbx_sifts_xref_db_num,
_atom_site.pdbx_sifts_xref_db_res
mmcif_pdbx.dic
5.348 2021-08-03
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add internal _struct.pdbx_center_of_mass_x, _struct.pdbx_center_of_mass_y,
_struct.pdbx_center_of_mass_z.
+ Add _em_entity_assembly.chimera
mmcif_pdbx.dic
5.347 2021-07-18
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Correct captilatization in description of _pdbx_nmr_spectrometer.field_strength
+ Add "SSRF BEAMLINE BL10U2" and "SSRF BEAMLINE BL02U1" to _diffrn_source.type enumeration
mmcif_pdbx.dic
5.346 2021-07-08
Changes (ep):
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Make _pdbx_contact_author.name_salutation non-mandatory
mmcif_pdbx.dic
5.345 2021-06-30
Changes (ep):
+ Add "GN" to _pdbx_nmr_spectrometer.model enumeration
+ Update examples for _database_2.pdbx_database_accession
and _database_2.pdbx_DOI
+ Update enumeration and details for _pdbx_nmr_spectrometer.field_strength
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Update description of _pdbx_molecule_features.prd_id
+ Add 'UCSF ChimeraX' to _em_software.name
+ Mark _struct.pdbx_descriptor as local context
+ Add limits for _refine.ls_percent_reflns_obs
+ Add _em_author_list.identifier_ORCID
mmcif_pdbx.dic
5.344 2021-06-08
Changes (ep):
+ Add _item_enumeration.pdbx_value_display for _exptl.method
mmcif_pdbx.dic
5.343 2021-06-02
Changes (ep):
+ Add 'NMR Distance Restraints' and 'electron microscopy' to enumerations for _pdbx_struct_assembly_auth_evidence.experimental_support
and pdbx_struct_assembly_auth_evidence_depositor_info.experimental_support
+ Create new attribute _pdbx_depui_status_flags.has_accepted_assemblies
+ Create new attribute _pdbx_database_status.date_accepted_terms_and_conditions
+ Update description of _reflns.pdbx_redundancy
+ Extend _pdbx_audit_support.funding_organization enumeration.
+ Add 'TFS TUNDRA' to _em_imaging.microscope_model.
mmcif_pdbx.dic
5.342 2021-04-19
Changes (ep):
+ Add hard limits to _em_focused_ion_beam.initial_thickness
+ Update description of _struct_ref_seq_dif.pdbx_auth_seq_num
+ Add "ALS BREAMLINE 2.0.1" to _diffrn_source.type enumeration. "2.0.1" added to
enumeration for _diffrn_source.pdbx_synchrotron_beamline.
+ Update _pdbx_audit_support.funding_organization enumeration
+ Add 'subTOM' to _em_software.name enumeration and _emd_software.name
+ Change _em_map.symmetry_space_group type from line to int
+ Add acetonitrile to enumeration for _pdbx_nmr_chem_shift_ref.mol_common_name
mmcif_pdbx.dic
5.341 2021-03-15
Changes (ep/jw):
+ Add category pdbx_audit_conform
+ Update funding enumerations _pdbx_audit_support.funding_organization
+ Update descriptions for _entity_poly.pdbx_seq_one_letter_code_can and
_entity_poly.pdbx_seq_one_letter_code
+ Add "PSI JUNGFRAU 4M" to _diffrn_detector.type enumerations
mmcif_pdbx.dic
5.340 2021-03-10
Changes (jt):
+ Update funding enumerations _pdbx_audit_support.funding_organization
mmcif_pdbx.dic
5.339 2021-02-16
Changes (Global Phasing Ltd.):
+ Add items for anomalous diffraction statistics
_reflns.pdbx_redundancy_anomalous, _reflns.pdbx_CC_half_anomalous,
_reflns.pdbx_absDiff_over_sigma_anomalous, _reflns.pdbx_percent_possible_anomalous,
_reflns_shell.pdbx_redundancy_anomalous, _reflns_shell.pdbx_CC_half_anomalous,
_reflns_shell.pdbx_absDiff_over_sigma_anomalous,
_reflns_shell.pdbx_percent_possible_anomalous
+ Add items to cater for anistropic diffraction
Ellipsoid fit to the cut-off surface:
_reflns.pdbx_aniso_diffraction_limit_axis_?_ortho[?],
_reflns.pdbx_aniso_diffraction_limit_?
Anisotropic B tensor:
_reflns.pdbx_aniso_B_tensor_eigenvector_?_ortho[?],
_reflns.pdbx_aniso_B_tensor_eigenvalue_?
Statistics specific to anisotropic diffraction:
_reflns.pdbx_percent_possible_*,
_reflns_shell.pdbx_percent_possible_*
for ellipsoidal/spherical and anomalous/non-anomalous diffraction.

Also add _reflns.pdbx_orthogonalization_convention and new subcategories
unit_vector and eigendecomposition
+ Add items for a per-reflection signal and parameter-free definition of
the cut-off surface
_reflns.pdbx_observed_signal_threshold, _reflns.pdbx_signal_type,
_reflns.pdbx_signal_details, reflns.pdbx_signal_software_id,
_pdbx_refln_signal_binning.ordinal,
_pdbx_refln_signal_binning.upper_threshold,
_refln.pdbx_signal, _refln.pdbx_signal_status
+ Add and modify items to cater better for umerged reflection data
Add _diffrn_refln.pdbx_detector_x, _diffrn_refln.pdbx_detector_y,
_diffrn_refln.pdbx_scale_value
Modify _diffrn_refln.pdbx_image_id, _diffrn_refln.pdbx_scan_angle
mmcif_pdbx.dic
5.338 2021-01-20
Changes (ep):
+ Add LAUENORM to _software.name enumeration
+ Add 'JEOL 1000EES' to _em_imaging.microscope_model and _emd_microscopy.microscope
+ Add _citation.pdbx_database_id_patent to record patents
+ Update funding enumerations _pdbx_audit_support.funding_organization
mmcif_pdbx.dic
5.337 2021-01-05
Changes (ep/mw/cv):
+ Addition of _diffrn_refln.pdbx_image_id and _diffrn_refln.pdbx_scan_angle
+ Duplicate words cleanup in descriptions
+ Add enumerations for _pdbx_exptl_crystal_grow_sol.volume_units and
_pdbx_exptl_crystal_grow_comp.conc_units
+ Add usage information to description of _atom_site
+ Update funding enumerations _pdbx_audit_support.funding_organization
+ Add 'ARP/wARP' to _em_software.name
+ Add _database_2.pdbx_database_acceession and _database_2.pdbx_DOI
+ Add _em_imaging_optics.details
+ Change attributes to non-mandatory: _em_diffraction_stats.overall_phase_error,
_em_diffraction_stats.overall_phase_residual, and _em_diffraction_stats.r_sym,
+ Change type to float for _em_focused_ion_beam.duration and _emd_sectioning_focused_ion_beam.duration
mmcif_pdbx.dic
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 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.
3x4_matrix 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)*)){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 3x4 matrix 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 [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* Character data type for atom names ...
author char (([A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*)|(Seattle Structural Genomics Center for Infectious Disease.*)|(Structural Genomics Consortium.*)|(QCRG Structural Biology Consortium.*)|(Center for Structural Genomics of Infectious Diseases.*)) Author name in PDB format: Taylor, C.A.
binary char \n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*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 [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
code30 char .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? A string value, not allowed to exceed 30 characters.
date_dep char ([1-9][0-9](([02468][048])|([13579][26]))-02-29)|[1-9][0-9][0-9][0-9]-((((0[1-9])|(1[0-2]))-((0[1-9])|(1[0-9])|(2[0-8])))|((((0[13578])|(1[02]))-31)|(((0[1,3-9])|(1[0-2]))-(29|30)))) Deposition specific date with better checking
deposition_email uchar [a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9.-]+ code item types/single words (case insensitive) ...
ec-type char ([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-)))(([ ]*,[ ]*)([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-))))*
Approximate format of Enzyme Commission EC number. 1.2.3.4 with
optional parts.
email uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
emd_id char EMD-[0-9]{4,} EMDB code
entity_id_list uchar [0-9A-Za-z]+(,[0-9A-Za-z]+)* comma separated alphanumeric codes (no spaces) ...
exp_data_doi char 10\.[0-9]{4,9}/[-._;()/:A-Za-z0-9]+ Experimental dataset DOI
fax uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? float item types are the subset of numbers that are the floating
numbers.
float-range numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)? int item types are the subset of numbers that are the floating
numbers.
id_list char [A-Za-z0-9]+(,[A-Za-z0-9]+)* A list of comma separated chain or asym ids.
id_list_spc char [ \t]*[A-Za-z0-9]+([ \t]*,[ \t]*[A-Za-z0-9]+)*[ \t]* A list of comma separated chain or asym ids with optional spaces.
idname uchar [_A-Za-z0-9]+ idname item types take the form...
int numb [+-]?[0-9]+ int item types are the subset of numbers that are the negative
or positive integers.
int-range numb [+-]?[0-9]+-[+-]?[0-9]+ range of integer item types are the subset of numbers that are the negative
or positive integers.
int_list uchar [1-9][0-9]*(,[1-9][0-9]*)* comma separated list of positive integers (no spaces) ...
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*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_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* sequence of parenthetical integer ranges and character codes
orcid_id char [0-9]{4}-[0-9]{4}-[0-9]{4}-([0-9]{3}X|[0-9]{4}) ORCID pattern - dddd-dddd-dddd-dddd|dddX
pdb_id char ([1-9][A-Z0-9]{3}|PDB_[A-Z0-9]{8}) PDB code (upper cases)
pdb_id_u uchar ([1-9][A-Za-z0-9]{3}|[Pp][Dd][Bb]_[A-Za-z0-9]{8}) PDB code (case insensitive)
pdbx_PDB_obsoleted_db_id char [0-9][0-9a-zA-Z]{3}( [0-9][0-9a-zA-Z]{3})* List of PDB ids for obsoletion - space separated
pdbx_related_db_id char [][_.:"&<>()/\{}'`~!@#$%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()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
uchar1 uchar [+]?[A-Za-z0-9]
data item for 1 character codes
uchar3 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?
data item for 3 character codes
uchar5 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?[A-Za-z0-9]?
data item for 5 character codes
ucode uchar [][_,.;:"&<>()/\{}'`~!@#$%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)...
uniprot_ptm_id char PTM-[0-9]{4} UniProt PTM List Accession ID Pattern - PTM-XXXX
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 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.
eigendecomposition The collection of items making up the Eigendecomposition of a
matrix. For an n x n matrix, instances of this subcategory will
consist of n Eigenvectors of dimension n, and n Eigenvalues.
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.
unit_vector The collection of elements of a vector whose norm equals 1.
vector The collection of elements of a vector.
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 temperature in 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_element (image) pixels per (array) element
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