Crystallographic Information Framework

[CIF logo]

Index

Protein Data Bank exchange dictionary (pdbx) version 1.0521

Revision history

========================================================================
Version 0.001 (2000-05-23)
------------------------------------------------------------------------

 Initial revision based on RCSB local dictionaries
 and EBI database schema.  J. Westbrook and J. Ionides

========================================================================
Version 0.002 (2000-06-06)
------------------------------------------------------------------------
 Changes: (jdw)
   + Added items in refine_hist and exptl_crystal_grow

========================================================================
Version 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.    

========================================================================
Version 0.004 (2000-10-24)
------------------------------------------------------------------------
 Changes: (jdw)
  + Added optional timestamps to data items.  
  + Repositioned parent items in PDBX_POLY_SEQ_SCHEME.

========================================================================
Version 0.005 (2000-10-25)
------------------------------------------------------------------------
 Changes: (jdw)
  + drop category PDBX_DATABASE_REMARK

========================================================================
Version 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.

========================================================================
Version 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. 

========================================================================
Version 0.008 (2001-01-22)
------------------------------------------------------------------------

 Changes: (jdw)
 + Added item _pdbx_database_status.dep_release_code_sequence

========================================================================
Version 0.009 (2001-03-02)
------------------------------------------------------------------------

 Changes: (jdw)
 +  Added missing mandatory codes and reset aliases for
    _diffrn_radiation.pdbx_wavelenth_list.

========================================================================
Version 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.

========================================================================
Version 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.

========================================================================
Version 0.012 (2001-06-28)
------------------------------------------------------------------------

 Changes: (jdw)
 +  _atom_site_anisotrop.pdbx_auth_* aliases corrected.
 +  adjust regex for date:time type

========================================================================
Version 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

========================================================================
Version 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.

========================================================================
Version 0.015 (2002-05-22)
------------------------------------------------------------------------

 Changes: (jdw)
 +  Add PDBX_ENTITY_NONPOLY and fix missing data type codes.

========================================================================
Version 0.016 (2002-08-05)
------------------------------------------------------------------------

 Changes: (jdw)
 +  Add PDBX_AUDIT category.

========================================================================
Version 0.017 (2002-10-05)
------------------------------------------------------------------------

 Changes: (jdw)
 + Final corrections of recommendations for  NMR and X-ray deposition for
   structural genomics.  

========================================================================
Version 0.018 (2003-07-07)
------------------------------------------------------------------------

 Changes: (jdw)
 +  Integrated protein production data items. 

========================================================================
Version 0.019 (2003-09-21)
------------------------------------------------------------------------

 Changes: (jdw/hy)
 + Added additional phasing items for PDB_EXTRACT.   

========================================================================
Version 0.020 (2003-10-30)
------------------------------------------------------------------------

 Changes: (jdw/zf)
 + Fix cases where category keys are not flagged as mandatory
 + Add category PDBX_AUDIT_AUTHOR

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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.

========================================================================
Version 1.003 (2004-06-16)
------------------------------------------------------------------------

 Changes:  (jdw)
 + Fix miscellaneous unresolved links. 

========================================================================
Version 1.004 (2004-08-04)
------------------------------------------------------------------------

 Changes:  (jdw)
 + Fix many data type errors in phasing section.
 + Add pdbx_contact_author 

========================================================================
Version 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

========================================================================
Version 1.006 (2004-10-10)
------------------------------------------------------------------------

 Changes: (jdw)
 + Update enumerations in cryo-em dictionary. 

========================================================================
Version 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

========================================================================
Version 1.008 (2004-11-15)
------------------------------------------------------------------------

 Changes: (jdw)
 + fix typo in category save frame name pdbx_exptl_crystal_grow_comp.

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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 

========================================================================
Version 1.014 (2005-04-08)
------------------------------------------------------------------------

 Changes: (jdw)
 + remove _struct_keywords.text from category key

========================================================================
Version 1.015 (2005-04-15)
------------------------------------------------------------------------

 Changes: (jdw)
 + remove _entity_keywords.text from category key

========================================================================
Version 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.

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 1.020 (2005-08-23)
------------------------------------------------------------------------

 Changes: (jdw)
 + Correct typos in pdbx_feature_monomer.
 + Correct typos in examples in categories refine and publ_manuscript_incl

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 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.

========================================================================
Version 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.

========================================================================
Version 1.025 (2006-04-18)
------------------------------------------------------------------------

 Changes: (jdw)
 + fix data type for _entity_poly.type

========================================================================
Version 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.

========================================================================
Version 1.027 (2006-05-01)
------------------------------------------------------------------------

 Changes: (jdw)
 + add _chemp_comp.pdbx_replaces/pdbx_replaced_by

========================================================================
Version 1.028 (2006-05-11)
------------------------------------------------------------------------

 Changes: (jdw)
 + Make _chemp_comp.pdbx_replaces a comma separated list.
 + Adjust enumerations for SG sites

========================================================================
Version 1.029 (2006-06-12)
------------------------------------------------------------------------

 Changes: (jdw)
 + More additions to enumerations for SG sites.
 + revise enumerations for status codes.

========================================================================
Version 1.030 (2006-06-27)
------------------------------------------------------------------------

 Changes: (zf)
 + fixed the alias for _pdbx_refine_tls_group.beg_auth_seq_id item

========================================================================
Version 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.

========================================================================
Version 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

========================================================================
Version 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

========================================================================
Version 1.034 (2006-11-01)
------------------------------------------------------------------------

 Changes: (jdw)
 + Adjust mandatory codes for pdbx_entity_inst_id.

========================================================================
Version 1.035 (2006-11-05)
------------------------------------------------------------------------

 Changes: (jdw)
 + missing data types in pdbx_struct_msym/asym_gen.
 + _citation.pdbx_unpublished enum typo

========================================================================
Version 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.

========================================================================
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.

========================================================================
Version 1.038 (2007-02-02)
------------------------------------------------------------------------

 Changes: (jdw)
 + Added category PDBX_VERSION.

========================================================================
Version 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.  

========================================================================
Version 1.041 (2007-04-04)
------------------------------------------------------------------------

 Changes: (jdw)
  Adjust category key for PDBX_VERSION category.
  Update definition of _pdbx_struct_oper_list.id

========================================================================
Version 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.  

========================================================================
Version 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.

========================================================================
Version 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.

========================================================================
Version 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

========================================================================
Version 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.

========================================================================
Version 1.047 (2007-08-24)
------------------------------------------------------------------------

  Changes: (jdw/kh/zf)
  + Add categories pdbx_struct_ref_seq_insertion and pdbx_struct_ref_seq_deletion.

========================================================================
Version 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.

========================================================================
Version 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

========================================================================
Version 1.050 (2008-01-24)
------------------------------------------------------------------------
 
 Changes (jdw,zf):

 + make _pdbx_validate_close_contact.symm_as_xyz_1,2 optional

========================================================================
Version 1.051 (2008-02-10)
------------------------------------------------------------------------

  Changes: (jw):
  + Added contributed item from Acta Cryst. editors by way of Brian McMahon,
     _reflns.pdbx_d_opt.

========================================================================
Version 1.052 (2008-05-29)
------------------------------------------------------------------------

  Changes: (jdw)
  + Added- _refine_ls_restr_ncs.pdb_ens_id, _struct_ncs_dom.pdbx_ens_id,
           _struct_ncs_dom_lim.pdbx_ens_id.
  + Removed parent-child references to the atom_site category from categories 
    pdbx_unobs_or_zero_occ_atoms/residues.
  ** Note this is the last main version of the dictionary supporting version PDB 3.1 files.

========================================================================
Version 1.0521 (2008-08-08)
------------------------------------------------------------------------

  Changes: (jdw)  BRANCH REVISION 
  + update enumeration for _pdbx_database_related.content_type
  + add _chem_comp_atom.pdbx_component_atom_id
  + add _chem_comp_atom.pdbx_component_comp_id
  + add _chem_comp_atom.pdbx_subcomponent_list
  + added _pdbx_chem_comp_feature.comp_id, _pdbx_chem_comp_feature.type, 
          _pdbx_chem_comp_feature.value and _pdbx_chem_comp_feature.source
  + _chem_comp.type added enumeration - 'peptide-like'

========================================================================