| Version |
Date |
Revision |
| 4.022 |
2012-02-03 |
Changes (jdw):
+ Remove parent link from '_struct_ref_seq_dif.db_mon_id' to '_chem_comp.id'.
+ Remove items:.
_pdbx_reference_entity_poly.nstd_chirality
_pdbx_reference_entity_poly.nstd_linkage
_pdbx_reference_entity_poly.nstd_monomer
_pdbx_reference_entity_poly.number_of_monomers
_pdbx_reference_entity_poly_seq.insert_code
_pdbx_reference_entity_poly_seq.modification_details
_pdbx_reference_entity_poly_seq.modified_mon_id
_pdbx_reference_entity_list.auth_asym_id
_pdbx_reference_molecule_features.citation_id
_pdbx_reference_entity_nonpoly.auth_asym_id
_pdbx_reference_entity_nonpoly.auth_seq_id
_pdbx_reference_entity_nonpoly.label_alt_id
_pdbx_reference_entity_nonpoly.PDB_ins_code
_pdbx_reference_entity_poly_link.insert_code_1
_pdbx_reference_entity_poly_link.insert_code_2
_pdbx_reference_entity_link.nonpoly_res_num_1
_pdbx_reference_entity_link.nonpoly_res_num_2
+ Remove category
_pdbx_reference_molecule_instances
+ Add new items
_pdb_reference_molecule.representative_PDB_id_code
_pdbx_reference_molecule.release_status
_pdbx_reference_molecule.replaces
_pdbx_reference_molecule.replaced_by
_pdbx_reference_molecule_family.release_status
_pdbx_reference_molecule_family.replaces
_pdbx_reference_molecule_family.replaced_by
_pdbx_reference_entity_src_nat.source_id
_pdbx_reference_molecule_details.source_id
+ Add new category PDBX_MOLECULE to entry files to identify PRD reference molecules:
_pdbx_molecule.instance_id
_pdbx_molecule.asym_id
_pdbx_molecule.prd_id
+ Rename category -
pdbx_reference_entity_poly_nstd_link to pdbx_reference_entity_poly_link
this category expanded to include both standard and non-standard linkages.
+ Update categories pdbx_item_linked_group and pdbx_item_linked_group_list.
|
| 4.021 |
2012-01-24 |
Changes (jdw):
+ Added _pdbx_database_PDB_obs_spr.details
+ The following changes have been made to the new PDBX_REFERENCE_ categories -
Renamed categories and items:
pdbx_reference_entity_details -> pdbx_reference_molecule_details
pdbx_reference_entity_feature -> pdbx_reference_molecule_features
pdbx_reference_entity_annotatoin -> pdbx_reference_molecule_annotation
pdbx_reference_entity_synonyms -> pdbx_reference_molecule_synonyms
pdbx_reference_entity_related_structures -> pdbx_reference_molecule_related_structures
pdbx_reference_entity_family -> pdbx_reference_molecule_family
pdbx_reference_entity_instance -> pdbx_reference_molecule_instances
_pdbx_reference_entity_list.component -> _pdbx_reference_entity_list.component_id
_pdbx_reference_entity_list.component renamed -> _pdbx_reference_entity_list.component_id
_pdbx_reference_entity_poly_nstd_link.component -> _pdbx_reference_entity_poly_nstd_link.component_id
Renamed three_letter_code -> chem_comp_id in items:
_pdbx_reference_molecule.chem_comp_id
_pdbx_reference_entity_nonpoly.chem_comp_id
_pdbx_reference_molecule_instancess.chem_comp_id
_pdbx_reference_molecule_synonyms.chem_comp_id
_pdbx_reference_entity_subcomponents.chem_comp_id
_pdbx_reference_molecule_annotation.chem_comp_id
_pdbx_reference_molecule_features.chem_comp_id
Added audit categories for molecule and family information:
pdbx_prd_audit and pdbx_family_prd_audit
Added items:
_pdbx_reference_molecule_list.family_prd_id
_pdbx_reference_molecule_list.prd_id
_pdbx_reference_entity_list.auth_asym_id
_pdbx_reference_entity_nonpoly.auth_asym_id
_pdbx_reference_entity_nonpoly.auth_seq_id
_pdbx_reference_entity_nonpoly.PDB_ins_code
_pdbx_reference_entity_nonpoly.label_auth_id
_pdbx_reference_molecule.type_evidence_code
_pdbx_reference_molecule.class_evidence_code
Removed provisional categories -
pdbx_reference_entity_group
pdbx_reference_entity_group_components
pdbx_reference_entity_group_components
pdbx_reference_entity_grouping
Removed provisional items -
_pdbx_reference_molecule.family_prd_id
_pdbx_reference_entity_list.family_prd_id
_pdbx_reference_entity_nonpoly.family_prd_id
_pdbx_reference_molecule_instancess.family_prd_id
_pdbx_reference_molecule_instancess.PDB_chain_id_list
_pdbx_reference_molecule_instancess.PDB_residue_number
_pdbx_reference_entity_subcomponents.family_prd_id
_pdbx_reference_entity_link.family_prd_id
_pdbx_reference_entity_poly.family_prd_id
_pdbx_reference_entity_poly_seq.family_prd_id
_pdbx_reference_entity_sequence.family_prd_id
_pdbx_reference_entity_src_nat.family_prd_id
_pdbx_reference_entity_poly_nstd_link.family_prd_id
|
| 4.020 |
2012-01-04 |
Changes (jdw):
+ Revise enumerations for category pdbx_sg_project.
|
| 4.019 |
2011-12-13 |
Changes (jdw):
+ Revise enumerations for item _pdbx_coordinate_model.type
+ Update enumerations for pdbx_sg_projects category.
+ Added item _pdbx_database_status.methods_development_category
+ Update examples for _pdbx_database_related.db_name
|
| 4.018 |
2011-11-29 |
Changes (jdw):
+ Restore provisional data data items:
_pdbx_reference_entity_instances.PDB_chain_id_list
_pdbx_reference_entity_instances.PDB_residue_number
_pdbx_reference_entity_list.component
_pdbx_reference_entity_link.component_1
_pdbx_reference_entity_link.component_2
_pdbx_reference_entity_link.nonpoly_res_num_1
_pdbx_reference_entity_link.nonpoly_res_num_2
_pdbx_reference_entity_link.link_class
_pdbx_reference_entity_poly_nstd_link.component
_pdbx_reference_entity_poly_nstd_link.insert_code_1
_pdbx_reference_entity_poly_nstd_link.insert_code_2
_pdbx_reference_entity_poly_seq.parent_mon_id
_pdbx_reference_entity_poly_seq.insert_code
_pdbx_reference_entity_poly_seq.modification_details
+ _pdbx_reference_entity_list.component made part of key
+ _pdbx_reference_entity_poly_nstd_link.component made part of key
+ _pdbx_reference_entity_sequence.family_prd_id added to key
+ _pdbx_reference_entity_sequence.prd_id added to key
+ _pdbx_reference_entity_sequence.ref_entity_id added to key
+ _pdbx_reference_entity_poly_seq.mon_id restored in key
+ _pdbx_reference_entity_poly_seq.num boundary remove boundary conditions.
|
| 4.017 |
2011-11-11 |
Changes (jdw):
+ update enumerations for _chem_comp.pdbx_processing_site
|
| 4.016 |
2011-10-21 |
Changes (jdw):
+ Added item _pdbx_reference_entity_poly_seq.observed
+ Added item _pdbx_reference_entity_poly_seq.hetero
+ Corrected typos in the defintions of _pdbx_reference_entity_annotation.source
and _pdbx_struct_group_components.PDB_model_num
+ correct data type and parent references for _pdbx_struct_group_components.auth_comp_id,
_pdbx_struct_group_component_range.beg_auth_comp_id, and _pdbx_struct_group_component_range.end_auth_comp_id
|
| 4.015 |
2011-09-14 |
Changes (jdw):
+ Update enumerations for pdbx_sg_projects category.
|
| 4.014 |
2011-08-29 |
Changes (jdw):
+ correct typo in enumerations for item _pdbx_struct_group_list.type.
|
| 4.013 |
2011-07-22 |
Changes (jdw):
+ Update enumerations for pdbx_sg_projects category.
|
| 4.012 |
2011-07-11 |
Changes (jdw):
+ removed trailing space in enumeration of value for _pdbx_version.revision_type
|
| 4.011 |
2011-06-14 |
Changes (jdw):
+ update enumeration for _database_2.database_id
|
| 4.010 |
2011-06-07 |
Changes (jdw):
+ data type relaxed from line to text for -_chem_comp.pdbx_synonym _chem_comp.pdbx_modification_details.
+ add FLUORESCENCE TRANSFER/'FLUORESCENCE TRANSFER only as a supporting method' to
_exptl.method enumeration list.
|
| 4.009 |
2011-06-01 |
Changes (jdw):
+ update enumerations for _pdbx_chem_comp_audit.action_type'
|
| 4.008 |
2011-05-27 |
Changes (jdw & ak):
+ correct typo in enumeration for _pdbx_struct_group_list.type
+ correct typo in example for _em_vitrification.time_resolved_state
+ correct typo in definition of _pdbx_struct_group_component_range.PDB_model_num
+ correct typo in example for _reflns.phase_calculation_details
+ remove redunant information in the following items _pdbx_atom_site_aniso_tls.auth_comp_id,
_pdbx_struct_conn_angle.ptnr1_label_alt_id, _pdbx_struct_conn_angle.ptnr2_label_alt_id, and
_pdbx_reference_entity_annotation.source
+ update enumerations for _pdbx_SG_project.project_name
+ update enumerations for _pdbx_SG_project.full_name_of_center
|
| 4.007 |
2011-05-13 |
Changes (jdw):
+ _exptl.method enumeration and details extended with
'THEORETICAL MODEL' 'THEORETICAL MODEL only as a supporting method'
+ added new items -_refln.pdbx_FWT,_refln.pdbx_DELFWT,_refln.pdbx_PHWT, and
_refln.pdbx_DELPHWT
+ updated examples for _symmetry.space_group_name_H-M
+ add _refine_ls_restr.pdbx_refine_id to category key
+ add item pdbx_version.revision_type as key item in this category
+ _pdbx_version.minor_version data type changed to code.
+ update aliases for _pdbx_database_status.status_code_cs
+ add enumerations for _pdbx_version.revision_type
+ update enumerations for PSI centers -
+ extended enumeratio for _refine.pdbx_TLS_residual_ADP_flag
+ _em_imaging.microscope_id made optional -
+ relax parent child relationship for _pdbx_remediation_atom_site_mapping.auth_alt_id
|
| 4.006 |
2011-04-21 |
Changes: (jdw):
+ updated enumeration list for _pdbx_SG_project items.
|
| 4.005 |
2011-04-19 |
Changes: (jdw):
+ Add item _pdbx_reference_entity_poly_seq.modification_details
|
| 4.004 |
2011-04-13 |
Changes: (jdw):
+ The roles of _pdbx_reference_entity_poly_seq.modified_mon_id and _pdbx_reference_entity_poly_seq.mon_id
swapped.
+ _pdbx_reference_entity_poly_seq.modified_mon_id removed
+ _pdbx_reference_entity_poly_seq.parent_mon_id added as an optional item for the
parent items in ribosomal proteins.
+ _pdbx_reference_entity_poly_seq.mon_id made mandatory and part of key
+ corrected examples link examples with bond orders = 'sing'
+ relax the comma separated item data type
+ add famil_prd_id and ref_entity_id to the category key of pdbx_entity_reference_sequence
|
| 4.003 |
2011-04-13 |
Changes: (jdw):
+ removed duplicate _pdbx_reference_entity_poly_seq.hetero definition
+ Changed the lower limit for _pdbx_reference_entity_poly_seq.num to include 0
|
| 4.002 |
2011-04-08 |
Changes: (jdw):
+ Added items -
_pdbx_reference_entity_link.component_1
_pdbx_reference_entity_link.component_2
_pdbx_reference_entity_poly_nstd_link.component
_pdbx_reference_entity_instances.PDB_residue_number
_pdbx_reference_entity_instances.PDB_chain_id_list
_pdbx_reference_entity_poly_seq.hetero
|
| 4.001 |
2011-04-07 |
Changes: (jdw):
+ Added items -
_pdbx_reference_entity_list.component
_pdbx_reference_entity_entity_link.link_class
_pdbx_reference_entity_entity_link.entity_seq_num_1
_pdbx_reference_entity_entity_link.nonpoly_res_num_1
_pdbx_reference_entity_entity_link.entity_seq_num_2
_pdbx_reference_entity_entity_link.nonpoly_res_num_2
|
| 4.000 |
2011-04-06 |
Changes (jdw):
+ Release as provision version 4.000
|
| 3.316 |
2011-04-05 |
Changes (jdw):
+ Added non-standard polymer linking details in category PDBX_REFERENCE_ENTITY_POLY_NSTD_LINK
+ Added _pdbx_reference_entity_list.nonpoly_residue_number
+ Changed the representative flag item name to _pdbx_reference_entity_instances.prd_representative_flag.
+ Added instance level nonpolymer residue preference, _pdbx_entity_group_components.nonpoly_residue_number
|
| 3.315 |
2011-03-31 |
Changes (jdw):
+ Add comma separated data type ucode-alphanum-csv
+ Revised with additional categories to capture entity level details.
PDBX_REFERENCE_ENTITY_LIST
PDBX_REFERENCE_ENTITY_NONPOLY
PDBX_REFERENCE_ENTITY_LINK
ref_entity_id incorporated as an additional key where appropriate.
_pdbx_reference_entity_list.ref_entity_id
_pdbx_reference_entity_nonpoly.ref_entity_id
_pdbx_reference_entity_link.ref_entity_id_1
_pdbx_reference_entity_poly.ref_entity_id
_pdbx_reference_entity_poly_seq.ref_entity_id
_pdbx_reference_entity_sequence.ref_entity_id
+ New categories to be included within PDB entries --
PDBX_ENTITY_GROUP_LIST and
PDBX_STRUCT_GROUP_LIST and related categories are provided to map
entity level information to the copies in the deposited coordinates.
PDBX_ENTITY_GROUP_INSTANCES is provided to map entity-level molecular definitions
to coordinate observations in the PDBX_STRUCT_GROUP_LIST.
|
| 3.314 |
2011-03-24 |
Changes (jdw):
+ updated enumeration list for _pdbx_SG_project.project_name.
|
| 3.313 |
2011-02-21 |
Changes (jdw):
+ Added categories pdbx_entity_group and pdbx_entity_group_components
|
| 3.312 |
2011-02-03 |
Changes (jdw):
+ Removed _chem_comp.type 'Iso-peptide linking' enumeration and replaced this
with - 'L-gamma-peptide, C-delta linking', 'D-gamma-peptide, C-delta linking',
'L-beta-peptide, C-gamma linking', and 'D-beta-peptide, C-gamma linking'.
|
| 3.311 |
2011-01-25 |
Changes (jdw):
+ Added new category pdbx_struct_comp_nstd_link.
+ Added _chem_comp.type 'Iso-peptide linking' enumeration.
|
| 3.310 |
2010-11-29 |
Changes (jdw):
Added new categories for PRD - pdbx_reference_entity_group, pdbx_reference_entity_group_components, and pdbx_reference_entity_grouping
|
| 3.309 |
2010-11-22 |
Changes (jdw):
+parent for _pdbx_remediation_atom_site_mapping.auth_alt_id removed.
|
| 3.308 |
2010-11-19 |
Changes (jdw):
+ Added __reflns.phase_calculation_details from the v3.2 dictionary
+ Replaced _refine.pdbx_adp_type with _refine.pdbx_TLS_residual_ADP_flag
|
| 3.307 |
2010-09-30 |
Changes (jdw):
+ change data type for _chem_comp.name from line to text.
+ add pdbx_entity_reference_family category and add pdbx_entity_reference_family.family_prd_id
as a part of key in pdbx_entity_reference* categories.
+ _pdbx_reference_entity_poly.db_code and _pdbx_reference_entity_poly.db_name
|
| 3.306 |
2010-09-24 |
Changes (jdw):
+ _chem_comp.pdbx_processing_site enumerations revised to 'PDBE' 'PDBJ' 'RCSB'
+ pdbx_chem_comp_atom_feature category
+ data type for _chem_comp.one_letter_code changed from uchar1 to ucode to handle components
derived from multiple parent components and chromophores.
+ standardized enumerations for _pdbx_database_status.process_site and deposit_site.
+ _chem_comp.pdbx_release_status enumeration extended with REF_ONLY to identify reference components.
|
| 3.305 |
2010-09-16 |
Changes (jdw):
+ Data type for _pdbx_chem_comp_audit.action_type changed from code to line.
+ Enumerations details corrected for _chem_comp_bond.pdbx_stereo_config
|
| 3.304 |
2010-08-02 |
Changes (jdw):
+ Updated enumerations for item _pdbx_chem_comp_audit.action_type and the example for this category.
|
| 3.303 |
2010-06-29 |
Changes (jdw):
+ Added items for fiber diffraction data collection -
_refln.pdbx_fiber_layer, _refln.pdbx_fiber_coordinate, _refln.pdbx_fiber_F_meas_au
|
| 3.302 |
2010-06-16 |
Changes (jdw):
+ _exptl.method - updated enumerations and details
'INFRARED SPECTROSCOPY' 'IR and FTIR only as supporting methods'
'EPR' 'EPR only as a supporting method'
|
| 3.301 |
2010-06-10 |
Changes (jdw):
+ Change to ordinal key in category REFLNS adding pdbx_ordinal.
+ Admit multiple comma separated values for child items of pdbx_diffrn_id.
+ added - _pdbx_database_status.date_hold_chemical_shifts
_pdbx_database_status.date_chemical_shifts
_pdbx_database_status.recvd_chemical_shifts
_pdbx_database_status.dep_release_code_chemical_shifts
_pdbx_database_status.date_of_cs_release
_pdbx_database_status.status_code_cs
|
| 3.300 |
2010-06-04 |
PRELIMINARY DICTIONARY SUPPORT V3.3 FORMAT (jdw):
+ added _refine.pdbx_adp_type - to differentiate entries containing mark residual or full
temperature factors
+ Modified _atom_site.B_iso_or_equiv definition modified to reflect new type information
in _refine.pdbx_adp_type
+ Change _refln.wavelength_id mandatory code to NO (optional)
+ Change _diffrn_refln.wavelength_id mandatory code to NO (optional)
+ Change _refln.crystal_id mandatory code to NO (optional)
+ Change _refln.scale_group_code mandatory code to NO (optional)
+ Change _diffrn_radiation.wavelength_id mandatory code to NO (optional)
+ Add _diffrn_radiation.pdbx_scattering_type
+ Add _refln.pdbx_diffrn_id as optional child item of _diffrn.id
+ Add _reflns.pdbx_diffrn_id as optional child of item _diffrn.id
+ Add _refine.pdbx_diffrn_id as optional child of item _diffrn.id
+ Add _reflns_shell.pdbx_ordinal as ordinal category key for reflns_shell category.
+ Add _reflns_shell.pdbx_diffrn_id as optional child of item _diffrn.id
+ Deprecate catetory PDBX_DIFFRN_REFLNS_SHELL
+ Change category key for REFLNS to _reflns.pdbx_diffrn_id
+ Change cateogry key for REFLNS_SHELL to _reflns_shell.pdbx_ordinal
|
| 1.0676 |
2010-06-03 |
Changes (jdw):
+ revisions for peptide reference dictionary in the pdbx_reference_entity_* category hierarchy.
+ added _pdbx_entity_src_syn.strain.
+ added _atom_site.pdbx_auth_asym_id,_atom_site.pdbx_auth_comp_id,
_atom_site.pdbx_auth_seq_id
+ updated examples for the pdbx_reference_entity_* categories -
+ added category pdbx_reference_entity_sequence
+ added item _pdbx_reference_entity_instances.published_name
+ removed unused item _pdbx_reference_entity_feature.support
+ added _pdbx_reference_entity_feature.source_ordinal
_pdbx_reference_entity_src_nat.source
_pdbx_reference_entity.class
_pdbx_reference_entity_related_structures.db_accession
+ renamed items in pdbx_reference_entity_related_structures category -
_pdbx_reference_entity_related_structures.db_name
_pdbx_reference_entity_related_structures.db_code
+ add category pdbx_bond_distance_limits
+ remove _pdbx_reference_entity_poly_seq.mon_id from category key
+ added items -
_pdbx_reference_entity_instances.auth_asym_id
_pdbx_reference_entity_instances.auth_seq_id
_pdbx_reference_entity_instances.label_alt_id
_pdbx_reference_entity_instances.PDB_ins_code
_pdbx_reference_entity_instances.published_subcomponent
+ Added REFI to enumerations for _pdbx_database_status.status_code and
_pdbx_database_status.release_status_code
|
| 1.0675 |
2010-02-04 |
Changes (jdw):
+ update aliases to local dictionaries
+ added _pdbx_soln_scatter_model.representative_conformer
+ added _pdbx_remediation_atom_site_mapping.occupancy
+ added _pdbx_remediation_atom_site_mapping.pre_occupancy
+ added enumeration 'tetartohedral' for _pdbx_reflns_twin.type
+ added _struct.pdbx_CASP_flag
+ added items for latest version of Buster.
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI
_refine.pdbx_overall_SU_R_Blow_DPI
_refine.pdbx_overall_SU_R_free_Blow_DPI
_refine_ls_restr.pdbx_restraint_function
|
| 1.0674 |
2009-10-28 |
Changes (jdw):
+ Add _pdbx_validate_planes.type enumerations for 'SIDE CHAIN' and
'MAIN CHAIN' and deprecate values that contained underscores
(e.g. MAIN_CHAIN). Update data type and category examples.
+ Added _pdbx_chem_comp_audit.processing_site and _pdbx_chem_comp_audit.details
+ Update enumerations for _pdbx_chem_comp_audit.action_type.
+ Added _pdbx_remediation_atom_site_mapping.auth_alt_id,_pdbx_remediation_atom_site_mapping.auth_asym_id,
_pdbx_remediation_atom_site_mapping.auth_atom_id,_pdbx_remediation_atom_site_mapping.auth_comp_id,
_pdbx_remediation_atom_site_mapping.auth_seq_id
|
| 1.0673 |
2009-07-23 |
Changes (jdw):
+ Complete missing definition elements for chem_comp_atom.type_symbol and
remove parent-child for this item which is not supported in the current
packaging of the chemical components dictionary.
+ Add _chem_comp.type's for 'L-RNA linking' 'L-DNA linking'
|
| 1.0672 |
2009-06-02 |
Changes (jdw):
+ Add category pdbx_remediation_atom_site_mapping
+ update internal tables of link relationships
+ minor typographical corrections in several examples.
|
| 1.0671 |
2009-05-12 |
Changes (jdw):
+ Add '_struct_conn.pdbx_value_order'
|
| 1.0670 |
2009-03-13 |
Changes (jdw):
+ Add '_refine_ls_restr_ncs.pdbx_ordinal' as new category key for this category.
+ Add '_refine_ls_restr_ncs.pdbx_auth_asym_id' as new category key for this category.
+ Add optional identifier _pdbx_refine_component.PDB_ins_code.
+ Make '_atom_sites_alt.id' child of '_atom_site.label_alt_id' to avoid
unspecified parent identifier issue with this item.
+ Update missing values in category examples accross the dictionary.
+ _pdbx_struct_assembly.oligomeric_details enumeration suppressed.
+ _pdbx_database_related.content_type - added enumeration 're-refinement'
+ Examples for _exptl.method promoted to an enumeratation.
+ added optional item _pdbx_struct_assembly_gen.auth_asym_id_list
+ _pdbx_refine_tls_group.selection enumerations changed to examples, type
changed to line.
|
| 1.0669 |
2009-01-16 |
Changes (jdw):
Add _struct_site.pdbx_evidence_code.
|
| 1.0668 |
2008-12-17 |
Changes (jdw):
+ update descriptions for _chem_comp.three_letter_code and _chem_comp.one_letter_code.
+ fix alias definiftion for _pdbx_nmr_exptl_sample.concentration_range.
|
| 1.0667 |
2008-12-11 |
Changes (jdw):
+ Add enumeration for InChIKey to _pdbx_chem_comp_descriptor.type
+ Add - 120-meric 180-meric 240-meric 62-meric 108-meric to oligomeric_details
+ Add viral symmetry descriptions to oligomeric_details:
cyclic tetrahedral dihedral octahedral icosahedral to oligomeric_details
+ Add pseudo-merohedral to _pdbx_reflns_twin.type enumeration
+ Add item _pdbx_struct_assembly.oligomeric_count which provides integer count
of the members of the assembly corresponding to the text description in
oligomeric_details.
+ Add item _pdbx_struct_oper_list.symmetry_operation to hold symop in (x,y,z) format.
+ _pdbx_entity_src_gen.ncbi_taxonomy_id, _pdbx_entity_src_gen.organism_scientific and
_pdbx_entity_src_gen.organism_common_name added to capture biological origin of
synthetic molecule.
Updates in EM data items: (cb,cl,jw):
+ Modified the data type code - change "line" to "text":
_em_assembly.composition
_em_assembly.name
_em_3d_fitting.software_name
_em_entity_assembly.ebi_expression_system
_em_vitrification.instrument
_em_imaging.specimen_holder_type
+ Inserted missing items.
_em_3d_reconstruction.euler_angles_details
_em_3d_reconstruction.num_class_averages
_em_3d_reconstruction.software
_em_entity_assembly.mutant_flag
_em_entity_assembly.number_of_copies
_em_entity_assembly.oligomeric_details
_em_imaging.astigmatism
_em_imaging.electron_beam_tilt_params
+ Added "NONE" to the enumeration list for _em_vitrification.cryogen_name
+ Added "OTHER" to the enumeration list for _em_virus_entity.virus_isolate
+ Updated enumeration list for _em_image_scans.scanner_model
'NIKON SUPER COOLSCAN 9000'
'NIKON COOLSCAN'
'PRIMESCAN'
'IMAGE SCIENCE PATCHWORK DENSITOMETER'
'EIKONIX IEEE 488'
+ Updated enumeration list for _em_imaging.specimen_holder_model
_item_enumeration.value
'JEM3200FSC CRYOHOLDER'
'PHILIPS ROTATION HOLDER'
'HOME BUILD'
'JEOL'
'SIDE ENTRY, EUCENTRIC'
+ Updated the enumeration list for _em_microscope.model:
_item_enumeration.value
'JEM2200FS'
'JEM3200FSC'
'PHILIPS EM400'
'PHILIPS EM420'
'JEOL 1200EX II'
'FEI TECNAI G20'
'ZEISS LEO 912'
'TECNAI G2'
+ Added the following items for the polymer reference dictionary.
These items will appear only in the polymer reference dictionary,
and not in any PDB entry data files.
+ Unused category _pdbx_entity_annotation renamed to _pdbx_reference_entity_annoation.
_pdbx_reference_entity.id
_pdbx_reference_entity.description
_pdbx_reference_entity.details
_pdbx_reference_entity.formula_weight
_pdbx_reference_entity.formula_weight
_pdbx_reference_entity.formula
_pdbx_reference_entity.type
_pdbx_reference_entity.name
_pdbx_reference_entity.represent_as
_pdbx_reference_entity.3-letter-code
_pdbx_reference_entity_synonyms.entity_id
_pdbx_reference_entity_synonyms.name
_pdbx_reference_entity_components.entity_id
_pdbx_reference_entity_components.names
_pdbx_reference_entity_poly.entity_id
_pdbx_reference_entity_poly.nstd_chirality
_pdbx_reference_entity_poly.nstd_linkage
_pdbx_reference_entity_poly.nstd_monomer
_pdbx_reference_entity_poly.number_of_monomers
_pdbx_reference_entity_poly.type
_pdbx_reference_entity_poly_seq.entity_id
_pdbx_reference_entity_poly_seq.mon_id
_pdbx_reference_entity_poly_seq.num
_pdbx_reference_entity_poly_seq.nstd_mon_parent_id
_pdbx_reference_entity_annotation.entity_id
_pdbx_reference_entity_annotation.text
_pdbx_reference_entity_annotation.type
_pdbx_reference_entity_annotation.support
_pdbx_reference_entity_annotation.source
_pdbx_reference_entity_feature.entity_id
_pdbx_reference_entity_feature.type
_pdbx_reference_entity_feature.support
_pdbx_reference_entity_feature.value
_pdbx_reference_entity_feature.source
_pdbx_reference_entity_src_nat.entity_id
_pdbx_reference_entity_src_nat.organism_scientific
_pdbx_reference_entity_src_nat.strain
|
| 1.0666 |
2008-11-25 |
+ make _struct_mon_prot_cis.pdbx_id ordinal key for this category.
|
| 1.0665 |
2008-11-21 |
+ change oligomeric_details enumerations from -mer to -meric
|
| 1.0664 |
2008-11-17 |
+ add additional enumerations for oligomeric_details
+ add _exptl.method to category key.
|
| 1.0663 |
2008-11-12 |
+ add enumeration for oligomeric_details
+ added items -
_exptl_crystal.pdbx_mosaicity
_exptl_crystal.pdbx_mosaicity_esd
_reflns_shell.pdbx_rejects
_diffrn_reflns.pdbx_d_res_low
_diffrn_reflns.pdbx_d_res_high
_diffrn_reflns.pdbx_percent_possible_obs
_diffrn_reflns.pdbx_Rmerge_I_obs
_diffrn_reflns.pdbx_Rsym_value
_diffrn_reflns.pdbx_chi_squared
_diffrn_reflns.pdbx_redundancy
_diffrn_reflns.pdbx_rejects
_diffrn_reflns.pdbx_observed_criterion
_diffrn_reflns.pdbx_number_obs
_pdbx_diffrn_reflns_shell.diffrn_id
_pdbx_diffrn_reflns_shell.d_res_low
_pdbx_diffrn_reflns_shell.d_res_high
_pdbx_diffrn_reflns_shell.percent_possible_obs
_pdbx_diffrn_reflns_shell.Rmerge_I_obs
_pdbx_diffrn_reflns_shell.Rsym_value
_pdbx_diffrn_reflns_shell.chi_squared
_pdbx_diffrn_reflns_shell.redundancy
_pdbx_diffrn_reflns_shell.rejects
_pdbx_diffrn_reflns_shell.number_obs
|
| 1.0662 |
2008-11-10 |
Changes (jdw):
+ remove spaces from enumerations in pdbx_reflns_twin.operator.
|
| 1.0661 |
2008-10-31 |
Changes (jdw):
Added enum 'Medical Structural Genomics of Pathogenic Protozoa' /MSGPP
|
| 1.0660 |
2008-10-30 |
Changes (jdw):
+ add _audit_author.pdbx_ordinal and make this category key for this audit_author category.
+ allow whitespace for all entity_src_gen.*taxonomy_id items.
+ add _pdbx_struct_assembly.oligomeric_details
|
| 1.0659 |
2008-10-23 |
Changes (jdw):
+ add _chem_comp.type 'peptide linking'
|
| 1.0658 |
2008-10-15 |
Changes (jdw):
+ added _reflns.pdbx_number_measured_all.
|
| 1.0657 |
2008-10-08 |
Changes (jdw):
+ add _atom_site.pdbx_formal_charge
|
| 1.0656 |
2008-10-04 |
Changes (jdw):
+add _pdbx_nmr_exptl_sample.concentration_range
|
| 1.0655 |
2008-10-03 |
Changes (jdw):
+ add _software.pdbx_ordinal and _pdbx_nmr_software.ordinal and make these
category keys in these categories.
+ set _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id type to line
|
| 1.0654 |
2008-09-18 |
Changes (jdw):
+ adjust enumeratiom for _pdbx_database_related.content_type
|
| 1.0653 |
2008-09-17 |
Changes (jdw):
+ Remove parent item for _refine_hist.pdbx_refine_id
|
| 1.0652 |
2008-09-12 |
Changes (jdw):
+ add _pdbx_reflns_twin.domain_id
+ add _pdbx_reflns_twin.operator to category key
+ adjust mandatory codes in pdbx_reflns_twin
|
| 1.0651 |
2008-09-04 |
Changes: (jdw)
+ Removed item_linked constraints on author identifiers and residue ranges
in pdbx_refine_tls_group. Residue ranges treated as author provided
parameters used for program input not necessarily corresponding to observed
residues in the deposited entry.
+ Added _pdbx_refine_tls_group.selection_details to capture text description
of TLS selection group.
+ Simplified category key for struct_ncs_dom_lim.
+ Added struct_ncs_dom_lim.selection_details
+ Updated examples for _exptl.method
+ Relax data type _refine.pdbx_refine_id and all of its children.
+ Make _struct_ncs_dom_lim.label_alt_id optional
+ Correct alias on _pdbx_refine.pdbx_refine_id
|
| 1.064 |
2008-09-03 |
Changes: (jdw)
+ Add category pdbx_atom_site_aniso_tls
+ Add category pdbx_struct_chem_comp_feature
|
| 1.063 |
2008-08-26 |
Changes: (jdw)
+ added pdbx_refine_id to the following category keys to distinguish
joint refinement methods:
refine
refine_analyze
refine_hist
refine_ls_restr
refine_ls_restr_ncs
refine_ls_shell
pdbx_refine_tls
pdbx_refine_tls_group
pdbx_refine
pdbx_xplor_file
pdbx_refine_aux_file
|
| 1.062 |
2008-08-19 |
Changes: (jdw)
+ Added _pdbx_poly_seq_scheme.hetero
|
| 1.061 |
2008-08-15 |
Changes: (jdw):
+ Add _pdbx_entity_annotation.source, _pdbx_chem_comp_feature.support
+ Make _pdbx_entity_annotation.text part of category key
+ Correct typo in enumeration in _pdbx_reflns_twin.type
+ Add enumerations for antibiotics to _entity.type and _entity_poly.type.
|
| 1.060 |
2008-07-30 |
Changes: (jdw):
+ update enumerations in _pdbx_database_related.content_type with 'split entry'
+ _pdbx_database_related.content_type added to key of this category.
|
| 1.059 |
2008-07-27 |
Changes: (jdw):
+ correct item_link for _pdbx_validate_chiral.auth_comp_id
|
| 1.058 |
2008-07-25 |
Changes: (jdw):
+ _pdbx_nmr_refine.method made optional:
+ adjust data type regular expression for ec-type
+ add _chem_comp_atom.pdbx_component_atom_id
+ add _chem_comp_atom.pdbx_component_comp_id
+ add _chem_comp_atom.pdbx_subcomponent_list
+ added _pdbx_chem_comp_feature.comp_id, _pdbx_chem_comp_feature.type,
_pdbx_chem_comp_feature.value and _pdbx_chem_comp_feature.source
+ _chem_comp.type added enumeration - 'peptide-like'
+ added _pdbx_coordinate_model.asym_id and _pdbx_coordinate_model.type
+ _reflns_shell.d_res_low _refine_ls_shell.d_res_low removed from key
+ _pdbx_nmr_software.authors made type text
+ _phasing_MAD_clust.id made type line
+ _phasing_MAD_expt.id made type line
+ add enumerations for sg projects
+ addjust parent child relationships for refine_ls_restr_ncs
|
| 1.057 |
2008-07-18 |
Changes: (jdw):
Added - _struct.pdbx_model_type_details
|
| 1.056 |
2008-07-16 |
Changes: (jdw/cl)
Added items:
_em_experiment.entry_id
_em_experiment.reconstruction_method
_em_experiment.specimen_type
_em_single_particle_entity.entry_id
_em_single_particle_entity.symmetry_type
Updated enumerations for: _em_assembly.aggregation_state
|
| 1.055 |
2008-06-20 |
Changes: (jdw)
Make the following items made optional -
_pdbx_struct_assembly_prop.details
_ndb_struct_na_base_pair.i_PDB_ins_code
_ndb_struct_na_base_pair.j_PDB_ins_code
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2
_struct_ref_seq_dif.db_mon_id
_struct_ncs_dom_lim.beg_label_alt_id
_struct_ncs_dom_lim.end_label_alt_id
_struct_site_gen.label_alt_id
_pdbx_struct_mod_residue.details
_refine.ls_d_res_low
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_label_atom_id
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.seq_num
Parent child corrections in categories
pdbx_poly_seq_scheme (entity_id exchange parent and child references)
struct_ref_seq_dif
Remove the following items from category key and make optional.
_entity_name_com.name
_entity_name_sys.name
_pdbx_nmr_software.version
_software.version
Add approximate regex for Enzyme Commission number.
|
| 1.054 |
2008-06-09 |
Changes: (jdw)
+ Removed parent child constraints from items -
_pdbx_refine_tls_group.beg_label_seq_id
_pdbx_refine_tls_group.beg_label_asym_id
_pdbx_refine_tls_group.end_label_seq_id
_pdbx_refine_tls_group.end_label_asym_id
|
| 1.053 |
2008-05-29 |
Changes: (jdw)
+ This dictionary is the first version supporting PDB V3.2
+ Added- _refine_ls_restr_ncs.pdbx_ens_id, _struct_ncs_dom.pdbx_ens_id,
_struct_ncs_dom_lim.pdbx_ens_id to category keys -
|
| 1.052 |
2008-05-29 |
Changes: (jdw)
+ Added- _refine_ls_restr_ncs.pdb_ens_id, _struct_ncs_dom.pdbx_ens_id,
_struct_ncs_dom_lim.pdbx_ens_id.
+ Removed parent-child references to the atom_site category from categories
pdbx_unobs_or_zero_occ_atoms/residues.
** Note this is the last version of the dictionary supporting version PDB 3.1 files.
|
| 1.051 |
2008-02-10 |
Changes: (jw):
+ Added contributed item from Acta Cryst. editors by way of Brian McMahon,
_reflns.pdbx_d_opt.
|
| 1.050 |
2008-01-24 |
Changes (jdw,zf):
+ make _pdbx_validate_close_contact.symm_as_xyz_1,2 optional
|
| 1.049 |
2008-01-09 |
+ Added _entity_poly.rcsb_build_self_reference, _refine.pdbx_overall_phase_error and
_refine_ls_shell.pdbx_phase_error
+ Added contributed items from Howard Einsphar and Manfred Weiss - _reflns.pdbx_Rpim_I_all
_reflns_shell.pdbx_Rpim_I_all
|
| 1.048 |
2007-11-18 |
Changes: (jdw/kh)
+ allow leading '+' for data type int
+ add '[]' to allowed characters for data types code and ucode -
+ make items other than the category key in ENTITY_SRC_NAT optional.
|
| 1.047 |
2007-08-24 |
Changes: (jdw/kh/zf)
+ Add categories pdbx_struct_ref_seq_insertion and pdbx_struct_ref_seq_deletion.
|
| 1.046 |
2007-08-14 |
Changes: (jdw/kh/zf)
+ Replace ebi_validate_* categories with pdbx_validate_* categories including
categories describing planar deviations. These categories provide placeholder
definitions for mapping PDB REMARK 500 validation data and other PDB remarks -
Added categories:
pdbx_validate_close_contact,pdbx_validate_symm_contact,pdbx_validate_rmsd_bond,
pdbx_validate_rmsd_angle,pdbx_validate_torsion,pdbx_validate_peptide_omega,
pdbx_validate_chiral,pdbx_validate_planes,pdbx_validate_planes_atom,
pdbx_validate_main_chain_plane, pdbx_struct_conn_angle, pdbx_unobs_or_zero_occ_residues
pdbx_unobs_or_zero_occ_atoms, pdbx_struct_mod_residue, and pdbx_entry_details
+ Add 'identity operation' to enums for _pdbx_struct_oper_list.type
+ _chem_comp.pdbx_processing_site added.
|
| 1.045 |
2007-06-23 |
Changes: (jdw)
+ change data type for _pdbx_database_PDB_obs_spr.replace_pdb_id to line
+ remove parent/child relationship for - _chem_comp.mon_nstd_parent_comp_id
+ extend enumerations for _pdbx_SG_project
+ data type _diffrn_detector.pdbx_collection_date made yyyy-mm-dd:hh:mm-flex
+ extend enumerations for _pdbx_nmr_exptl_sample.concentration_units
+ make pdbx_database_status - author_release_status and
recvd_initial_deposition_date items optional
+ adjust enumeration case for _pdbx_chem_comp_descriptor.type
+ supress parent relationship for _phasing_MIR_der_site.atom_type_symbol
+ uchar3 adjusted to accept all possible 3-letter-code values -
+ extended enumeration for _software.language
+ data type for _chem_comp.mon_nstd_parent_comp_id changed to uline
|
| 1.044 |
2007-05-30 |
Changes: (jdw/as)
+ added _citation_author.ordinal to category key
+ remove duplicate data item specifications in category entity_src_gen
+ miscellaneous corrections to data item references in definitions
+ make all 'replaces/replacedby' relationships reciprocal
+ make all key items mandatory.
+ add program and program_version to the key of category
pdbx_chem_comp_identifier
+ suppress aliases to the ebi_extension dictionary.
|
| 1.043 |
2007-05-28 |
Changes: (jdw)
+ adjust child data types for consistency with parent types.
+ removed aliases to local status items in pdbx_database_status.
|
| 1.042 |
2007-05-20 |
Changes: (jdw)
+ Add _software.classification to category key.
+ Change enumerations for _pdbx_chem_comp_descriptors.program and
_pdbx_chem_comp_identifiers.program to examples.
+ Make category keys in audit_conform mandatory
+ remove incorrect parent-child link to
_pdbx_struct_assembly_gen.oper_expression
+ Added _pdbx_struct_assembly_gen.asym_id_list and replaced
_pdbx_struct_assembly_gen.entity_inst_id with this item
in the key for this category. Suppressed parent child
relationships between _pdbx_struct_entity_inst.id and
categories outside the _pdbx_struct_* group.
+ Added _chem_comp.pdbx_model_coordinates_db_code, _chem_comp.pdbx_initial_date,
_chem_comp.pdbx_modified_date.
+ Data types changed to int for - _atom_site.pdbx_PDB_model_num,
_struct_conf.pdbx_PDB_helix_length, _pdbx_poly_seq_scheme.ndb_seq_num,
_pdbx_struct_sheet_hbond.range_1_label_seq_id,
_pdbx_struct_sheet_hbond.range_2_label_seq_id,
_atom_site_anisotrop.pdbx_label_seq_id, _struct_conn.pdbx_ptnr3_label_seq_id.
+ _em_vitrification.humidity data type changed to float.
+ category key for refine_ls_restr_ncs changed to
_refine_ls_restr_ncs.dom_id, _refine_ls_restr_ncs.pdbx_type,
_refine_ls_restr_ncs.pdbx_asym_id.
|
| 1.041 |
2007-04-04 |
Changes: (jdw)
Adjust category key for PDBX_VERSION category.
Update definition of _pdbx_struct_oper_list.id
|
| 1.040 |
2007-03-20 |
Changes: (jdw)
+ skip version 1.039 to sync with remediation dictionary version.
+ Updated enumerations and boundary values for _pdbx_database_status.deposit_site
*.isotopic_labeling, _citation.pdbx_database_id_PubMed.
|
| 1.038 |
2007-02-02 |
Changes: (jdw)
+ Added category PDBX_VERSION.
|
| 1.037 |
2006-12-15 |
Changes: (jdw)
+ corrected type in _chem_comp.pdbx_ideal_coordinates_details
_chem_comp.pdbx_model_coordinates_details definitions.
+ added _chem_comp.pdbx_ideal_coordinates_missing_flag
+ added _chem_comp.pdbx_model_coordinates_missing_flag
+ In chem_comp_atom /bond - added missing enumerations for atom/bond
stereo_config and aromatic flags.
+ added PUBCHEM_SID and PUBCHEM_CID to pdbx_chem_comp_identifier.type.
|
| 1.036 |
2006-11-14 |
Changes: (jdw)
+ revise category keys in pdbx_chem_comp_atom_edit
and pdbx_chem_comp_bond_edit.
+ removed unused category pdbx_chem_comp_protonation_site
+ added _chem_comp.pdbx_model_coordinates_details and
_chem_comp.pdbx_ideal_coordinates_details.
|
| 1.035 |
2006-11-05 |
Changes: (jdw)
+ missing data types in pdbx_struct_msym/asym_gen.
+ _citation.pdbx_unpublished enum typo
|
| 1.034 |
2006-11-01 |
Changes: (jdw)
+ Adjust mandatory codes for pdbx_entity_inst_id.
|
| 1.033 |
2006-10-16 |
Changes: (jdw)
+ Correct typos pdbx_chem_comp_descriptors/identifiers
+ add ordinal data items to these cateogories.
+ added _pdbx_refine.free_R_error_no_cutoff
|
| 1.032 |
2006-10-12 |
Changes: (jdw)
+Added Categories:
pdbx_helical_symmetry
pdbx_point_symmetry
pdbx_struct_entity_inst
pdbx_struct_oper_list
pdbx_struct_assembly
pdbx_struct_assembly_gen
pdbx_struct_asym_gen
pdbx_struct_msym_gen
pdbx_struct_legacy_oper_list
pdbx_reflns_twin
pdbx_struct_info
pdbx_re_refinement
pdbx_struct_assembly_prop
pdbx_struct_ref_seq_feature
pdbx_struct_ref_seq_feature_prop
pdbx_struct_chem_comp_diagnostics
+Added items:
_pdbx_helical_symmetry.entry_id
_pdbx_helical_symmetry.number_of_operations
_pdbx_helical_symmetry.rotation_per_n_subunits
_pdbx_helical_symmetry.rise_per_n_subunits
_pdbx_helical_symmetry.n_subunits_divisor
_pdbx_helical_symmetry.dyad_axis
_pdbx_helical_symmetry.circular_symmetry
_pdbx_point_symmetry.entry_id
_pdbx_point_symmetry.Schoenflies_symbol
_pdbx_point_symmetry.H-M_notation
_pdbx_point_symmetry.circular_symmetry
_pdbx_struct_entity_inst.details
_pdbx_struct_entity_inst.entity_id
_pdbx_struct_entity_inst.id
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
_pdbx_struct_assembly_gen.entity_inst_id
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_asym_gen.entity_inst_id
_pdbx_struct_asym_gen.asym_id
_pdbx_struct_asym_gen.oper_expression
_pdbx_struct_msym_gen.entity_inst_id
_pdbx_struct_msym_gen.msym_id
_pdbx_struct_msym_gen.oper_expression
_pdbx_struct_legacy_oper_list.id
_pdbx_struct_legacy_oper_list.name
_pdbx_struct_legacy_oper_list.matrix[1][1]
_pdbx_struct_legacy_oper_list.matrix[1][2]
_pdbx_struct_legacy_oper_list.matrix[1][3]
_pdbx_struct_legacy_oper_list.matrix[2][1]
_pdbx_struct_legacy_oper_list.matrix[2][2]
_pdbx_struct_legacy_oper_list.matrix[2][3]
_pdbx_struct_legacy_oper_list.matrix[3][1]
_pdbx_struct_legacy_oper_list.matrix[3][2]
_pdbx_struct_legacy_oper_list.matrix[3][3]
_pdbx_struct_legacy_oper_list.vector[1]
_pdbx_struct_legacy_oper_list.vector[2]
_pdbx_struct_legacy_oper_list.vector[3]
_pdbx_reflns_twin.diffrn_id
_pdbx_reflns_twin.crystal_id
_pdbx_reflns_twin.type
_pdbx_reflns_twin.operator
_pdbx_reflns_twin.fraction
_pdbx_reflns_twin.mean_I2_over_mean_I_square
_pdbx_reflns_twin.mean_F_square_over_mean_F2
_struct_conn.pdbx_dist_value
_pdbx_struct_info.type
_pdbx_struct_info.value
_pdbx_struct_assembly_prop.details
_pdbx_re_refinement.entry_id
_pdbx_re_refinement.citation_id
_pdbx_re_refinement.details
_pdbx_struct_assembly_prop.biol_id
_pdbx_struct_assembly_prop.type
_pdbx_struct_assembly_prop.value
_pdbx_struct_assembly_prop.details
_struct_biol.pdbx_aggregation_state
_struct_biol.pdbx_assembly_method
_entry.pdbx_DOI
_citation.unpublished_flag
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
_entity_src_nat.pdbx_ncbi_taxonomy_id
_pdbx_struct_ref_seq_feature.feature_id
_pdbx_struct_ref_seq_feature.align_id
_pdbx_struct_ref_seq_feature.type
_pdbx_struct_ref_seq_feature.details
_pdbx_struct_ref_seq_feature.pdb_strand_id
_pdbx_struct_ref_seq_feature.asym_id
_pdbx_struct_ref_seq_feature.beg_auth_seq_id
_pdbx_struct_ref_seq_feature.end_auth_seq_id
_pdbx_struct_ref_seq_feature.beg_seq_num
_pdbx_struct_ref_seq_feature.end_seq_num
_pdbx_struct_ref_seq_feature.beg_auth_mon_id
_pdbx_struct_ref_seq_feature.end_auth_mon_id
_pdbx_struct_ref_seq_feature.beg_pdb_ins_code
_pdbx_struct_ref_seq_feature.end_pdb_ins_code
_pdbx_struct_ref_seq_feature_prop.feature_id
_pdbx_struct_ref_seq_feature_prop.property_id
_pdbx_struct_ref_seq_feature_prop.type
_pdbx_struct_ref_seq_feature_prop.value
_pdbx_struct_ref_seq_feature_prop.details
_pdbx_struct_ref_seq_feature_prop.beg_db_mon_id
_pdbx_struct_ref_seq_feature_prop.end_db_mon_id
_pdbx_struct_ref_seq_feature_prop.beg_db_seq_id
_pdbx_struct_ref_seq_feature_prop.end_db_seq_id
|
| 1.031 |
2006-08-10 |
Changes: (jdw)
+ Correct typo in new definitions - change
_chem_comp_atom.pdbx_model_Cartn_[xyz]_2 to [xyz]_ideal
+ Add enum for NYSGXRC
+ Add enum for HOLD FOR 8 WEEKS.
|
| 1.030 |
2006-06-27 |
Changes: (zf)
+ fixed the alias for _pdbx_refine_tls_group.beg_auth_seq_id item
|
| 1.029 |
2006-06-12 |
Changes: (jdw)
+ More additions to enumerations for SG sites.
+ revise enumerations for status codes.
|
| 1.028 |
2006-05-11 |
Changes: (jdw)
+ Make _chemp_comp.pdbx_replaces a comma separated list.
+ Adjust enumerations for SG sites
|
| 1.027 |
2006-05-01 |
Changes: (jdw)
+ add _chemp_comp.pdbx_replaces/pdbx_replaced_by
|
| 1.026 |
2006-04-27 |
Changes: (jdw)
+ add 4 week enumeration/example for HOLD status items
+ add pdbx_ordinal items for chem_comp_atom/bond and pdbx_ambiguous_flag
to chem_comp.
|
| 1.025 |
2006-04-18 |
Changes: (jdw)
+ fix data type for _entity_poly.type
|
| 1.024 |
2006-04-13 |
Changes: (jdw)
+ Correct alias for _struct_site_gen.pdbx_auth_ins_code.
+ Add enum 'polydeoxyribonucleotide/polyribonucleotide hybrid' to entity_poly.type.
+ update enums in pdbx_SG_project.
|
| 1.023 |
2006-03-01 |
Changes: (jdw)
+ Add _pdbx_contact_author.continent
+ Remove enums for _pdbx_contact_author.country
+ Added EMDB, TARGETDB, PEPCDB to _pdbx_database_related.db_name examples and
associated EM volume, associated NMR restraints, associated
structure factors, and associated protein target sequence/protocol
data to _pdbx_database_related.content_type.
|
| 1.022 |
2006-02-24 |
Changes: (jdw)
+ Fixed syntax issues (ie. extra loop_) in items in _pdbx_construct.*
+ Added missing category groups in standard dictionary section 1.
+ Fixed category error for item _chem_comp_atom.pdbx_align
|
| 1.021 |
2005-10-12 |
Changes: (jdw)
+ added categories pdbx_refine_component, pdbx_chem_comp_descriptor,
pdbx_chem_comp_identifier, pdbx_chem_comp_import,pdbx_chem_comp_atom_edit,
pdbx_chem_comp_bond_edit, and pdbx_chem_comp_audit.
+ added stereochemistry and aromaticity flags to chem_comp_atom and
chem_comp_bond.
+ added alternate component and atom nomenclature to chem_comp_atom.
+ added alternate model coordinates to chem_comp_atom category
|
| 1.020 |
2005-08-23 |
Changes: (jdw)
+ Correct typos in pdbx_feature_monomer.
+ Correct typos in examples in categories refine and publ_manuscript_incl
|
| 1.019 |
2005-07-21 |
Changes: (jdw)
+ Added _struct.pdbx_formula_weight and _struct.pdbx_formula_weight_method
+ Added _refln.pdbx_HL_A_iso, _refln.pdbx_HL_B_iso, _refln.pdbx_HL_C_iso,
and _refln.pdbx_HL_D_iso
+ Added _phasing_set.pdbx_d_res_low/high _pdbx_phasing_MR.native_data_set_id
+ Added category pdbx_feature_monomer
|
| 1.018 |
2005-07-14 |
Changes: (jdw)
+ Added PDB_SOLN_SCATTER* definitions
+ Added _refln.pdbx_[F,I]_[minus,plus] and
_refln.pdbx_[F,I]_[minus,plus]_sigma
+ Extend enumeration for _pdbx_database_status.status_code_sf
|
| 1.017 |
2005-06-27 |
Changes: (BMcM)
+ added _reflns.threshold_expression and _publ_author.email
+ numerous minor changes to wordings of definitions to align with mmcif
version 2.0.09 as released on International Tables G CD-ROM
|
| 1.016 |
2005-06-24 |
Changes: (jdw)
+ aliases repointed for items in category pdbx_database_remark
+ Added the following items:
_diffrn_detector.pdbx_frames_total
_diffrn_detector.pdbx_collection_time_total
_refine.pdbx_ls_sigma_Fsqd
_reflns.pdbx_Rmerge_I_all
_reflns.pdbx_netI_over_sigmaI
_reflns.pdbx_res_netI_over_av_sigmaI_2
_reflns.pdbx_res_netI_over_sigmaI_2
_reflns_shell.pdbx_netI_over_sigmaI_all
_reflns_shell.pdbx_netI_over_sigmaI_obs
_struct_biol.pdbx_formula_weight
_struct_biol.pdbx_formula_weight_method
_struct_biol_gen.pdbx_PDB_order
_phasing_MAD.pdbx_number_data_sets
_phasing_MAD.pdbx_anom_scat_method
_phasing_MIR.pdbx_number_derivatives
_phasing_set.pdbx_temp_details
+ miscellaneous editorial changes in descriptions and enumerations.
|
| 1.015 |
2005-04-15 |
Changes: (jdw)
+ remove _entity_keywords.text from category key
|
| 1.014 |
2005-04-08 |
Changes: (jdw)
+ remove _struct_keywords.text from category key
|
| 1.013 |
2005-04-05 |
Changes: (jdw)
+ Temporarily remove definitions from Image CIF dictionary
+ Added mandatory code for _cell.reciprocal_angle_beta
+ Added mandatory code for _pdbx_entity_nonpoly.entity_id
+ Fixed category attribute for _reflns_shell.pdbx_chi_squared
+ Changed mandatory code for _software.citation_id
|
| 1.012 |
2005-03-29 |
Changes: (kh/jdw)
+ added preliminary set of extensions for macromolecular powder diffraction
experiments, including:
_pdbx_exptl_pd (category)
_pdbx_exptl_pd.entry.id
_pdbx_exptl_pd.spec_preparation_pH
_pdbx_exptl_pd.spec_preparation_pH_range
_pdbx_exptl_pd.spec_preparation
_diffrn_radiation.pdbx_analyzer
_refine.pdbx_pd_number_of_powder_patterns
_refine.pdbx_pd_number_of_points
_refine.pdbx_pd_meas_number_of_points
_refine.pdbx_pd_proc_ls_prof_R_factor
_refine.pdbx_pd_proc_ls_prof_wR_factor
_refine.pdbx_pd_Marquardt_correlation_coeff
_refine.pdbx_pd_Fsqrd_R_factor
_refine.pdbx_pd_ls_matrix_band_width
Changes: (fzk)
removed 'National Project on Protein Structural and Functional Analyses' from
_pdbx_SG_project.full_name_of_center,
added 'National Project on Protein Structural and Functional Analyses' to
_pdbx_SG_project.project_name
|
| 1.011 |
2005-03-08 |
Changes: (jdw)
+ Included extensions from mmCIF dictionary...
Changes: (fzk)
+ add _pdbx_refine_tls_group.beg_auth_asym_id
+ add _pdbx_refine_tls_group.end_auth_asym_id
+ add enumeration values 'SGC' and 'NPPSFA' for
_pdbx_SG_project.initial_of_center
+ add enumeration values 'Structural Genomics Consortium' and
'National Project on Protein Structural and Functional Analyses'
for _pdbx_SG_project.full_name_of_center
+ fix _item_description.description for _entity_poly.pdbx_target_identifier
|
| 1.010 |
2005-01-25 |
Changes: (jdw)
+ change mandatory doc for _pdbx_database_status.SG_entry
+ fix key in category pdbx_database_PDB_obs_spr
|
| 1.009 |
2005-01-13 |
Changes: (zkf)
+ add _pdbx_database_status.status_code_sf item
+ add _pdbx_database_status.date_of_sf_release item
+ add _pdbx_database_status.status_code_mr item
+ add _pdbx_database_status.date_of_mr_release item
+ add _pdbx_database_status.SG_entry item
+ add _entity_poly.pdbx_target_identifier item
+ add pdbx_SG_project category
+ fixed enumeration values for _software.language
|
| 1.008 |
2004-11-15 |
Changes: (jdw)
+ fix typo in category save frame name pdbx_exptl_crystal_grow_comp.
|
| 1.007 |
2004-11-02 |
Changes: (jdw)
+ added pdbx_entity_prod_protocol, pdbx_exptl_crystal_grow_sol,
pdbx_exptl_crystal_grow_comp, and pdbx_exptl_crystal_cryo_treatment
categories
+ relax enumerations in cryo-em dictionary.
+ remove upper-bound for refine.occupancy_max
|
| 1.006 |
2004-10-10 |
Changes: (jdw)
+ Update enumerations in cryo-em dictionary.
|
| 1.005 |
2004-09-28 |
Changes: (zkf,jdw)
+ Add missing pdbx_contact_author.postal_code item
+ Add missing pdbx_contact_author.city item
+ Add missing pdbx_contact_author.state_province item
+ Add enumerations in pdbx_contact_author.id
+ Modify enumerations in pdbx_contact_author.role
|
| 1.004 |
2004-08-04 |
Changes: (jdw)
+ Fix many data type errors in phasing section.
+ Add pdbx_contact_author
|
| 1.003 |
2004-06-16 |
Changes: (jdw)
+ Fix miscellaneous unresolved links.
|
| 1.002 |
2004-06-09 |
Changes: (jdw)
+ Added categories PDBX_DOMAIN, PDBX_SEQUENCE_RANGE,
PDBX_FEATURE_ENTRY, PDBX_FEATURE_ASSEMBLY, PDBX_FEATURE_DOMAIN,
and PDBX_FEATURE_SEQUENCE_RANGE.
|
| 1.001 |
2004-05-21 |
Changes: (jdw)
+ Fixed incorrect category in _pdbx_audit_author.address
+ Added _citation.pdbx_database_id_DOI
+ Fixed placement of _chem_comp.pdbx_align. Moved this item
to _chem_comp_atom.pdbx_align
|
| 1.000 |
2004-04-22 |
Changes: (jdw)
+ New packaging and naming
+ Integrate 3d em definitions
+ Relax enumerations to comply with existing legacy data.
+ Version to 1.000
|
| 0.020 |
2003-10-30 |
Changes: (jdw/zf)
+ Fix cases where category keys are not flagged as mandatory
+ Add category PDBX_AUDIT_AUTHOR
|
| 0.019 |
2003-09-21 |
Changes: (jdw/hy)
+ Added additional phasing items for PDB_EXTRACT.
|
| 0.018 |
2003-07-07 |
Changes: (jdw)
+ Integrated protein production data items.
|
| 0.017 |
2002-10-05 |
Changes: (jdw)
+ Final corrections of recommendations for NMR and X-ray deposition for
structural genomics.
|
| 0.016 |
2002-08-05 |
Changes: (jdw)
+ Add PDBX_AUDIT category.
|
| 0.015 |
2002-05-22 |
Changes: (jdw)
+ Add PDBX_ENTITY_NONPOLY and fix missing data type codes.
|
| 0.014 |
2002-02-28 |
Changes: (jdw)
+ Add items for NMR model and PDB insert code to GEOM_BOND, GEOM_ANGLE,
GEOM_CONTACT, and GEOM_TORSION categories.
|
| 0.013 |
2001-07-12 |
Changes: (jdw)
+ enumerations->examples for _pdbx_nmr_representative.selection_criteria and
_pdbx_database_related.db_name.
+ add regex for int and float ranges
|
| 0.012 |
2001-06-28 |
Changes: (jdw)
+ _atom_site_anisotrop.pdbx_auth_* aliases corrected.
+ adjust regex for date:time type
|
| 0.011 |
2001-06-14 |
Changes: (jdw)
+ Moved enumerations to examples for _pdbx_nmr_spectrometer.field_strength
+ _atom_site.pdb_auth_atom_name data type changed from code to atcode.
|
| 0.010 |
2001-04-18 |
Changes: (jdw)
+ Added missing _item_type.codes for
_refine_hist.number_atoms_solvent
_refine_hist.number_atoms_total
_refine.overall_SU_B
_refine.overall_SU_ML
_refine.pdbx_overall_ESU_R
+ Added CCP4 data items output from REFMAC V5.
|
| 0.009 |
2001-03-02 |
Changes: (jdw)
+ Added missing mandatory codes and reset aliases for
_diffrn_radiation.pdbx_wavelenth_list.
|
| 0.008 |
2001-01-22 |
Changes: (jdw)
+ Added item _pdbx_database_status.dep_release_code_sequence
|
| 0.007 |
2000-11-09 |
Changes: (jdw)
+ Added mandatory codes for _exptl_crystal_grow.pdbx_details and
_exptl_crystal_grow.pdbx_pH_range.
+ Added missing data types and category ids in category
pdbx_struct_sheet_hbond.
+ Updated data type for atom name references to atcode.
+ Updated aliases for _refine.overall_SU_B and _refine.overall_SU_ML.
+ Trimmed line lengths > 80 characters.
|
| 0.006 |
2000-10-26 |
Changes: (jdw)
+ Added _exptl_crystal_grow.rcsb_pH_range.
+ Added category PDBX_STRUCT_SHEET_HBOND to hold single hydrogen
bond registration between beta sheet strands.
|
| 0.005 |
2000-10-25 |
Changes: (jdw)
+ drop category PDBX_DATABASE_REMARK
|
| 0.004 |
2000-10-24 |
Changes: (jdw)
+ Added optional timestamps to data items.
+ Repositioned parent items in PDBX_POLY_SEQ_SCHEME.
|
| 0.003 |
2000-10-16 |
Changes: (jdw)
+ Move enumerations to examples for:
_pdbx_nmr_exptl.type
_pdbx_nmr_ensemble.conformer_selection_criteria
_pdbx_nmr_software.name
_struct_keywords.pdbx_keywords
+ Added _atom_site_anisotrop.pdbx_auth_* items
+ Added _struct_mon_prot_cis.pdbx_
+ Added _struct_conn.pdbx_ptnr3_auth_* items.
|
| 0.002 |
2000-06-06 |
Changes: (jdw)
+ Added items in refine_hist and exptl_crystal_grow
|
| 0.001 |
2000-05-23 |
Initial revision based on RCSB local dictionaries
and EBI database schema. J. Westbrook and J. Ionides
|
