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V5.379/5.387
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Ezra Peisach committed Aug 28, 2023
1 parent a027c39 commit 2fe011e
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172,758 changes: 172,758 additions & 0 deletions archive/mmcif_pdbx_v50-v5.379.dic
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186,058 changes: 186,058 additions & 0 deletions archive/mmcif_pdbx_v5_next-v5.387.dic
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8 changes: 5 additions & 3 deletions base/mmcif_pdbx-base.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -13115,6 +13115,7 @@ save__diffrn_detector.type
"_diffrn_detector.type" "RIGAKU AFC9" .
"_diffrn_detector.type" "RIGAKU HyPix-3000" PIXEL
"_diffrn_detector.type" "RIGAKU HyPix-6000HE" PIXEL
"_diffrn_detector.type" "RIGAKU HyPix-Arc 150" PIXEL
"_diffrn_detector.type" "RIGAKU JUPITER 140" CCD
"_diffrn_detector.type" "RIGAKU JUPITER 210" CCD
"_diffrn_detector.type" "RIGAKU MERCURY" CCD
Expand Down Expand Up @@ -101798,8 +101799,8 @@ save_em_staining
_em_staining.material 'Uranyl Acetate'
_em_staining.type NEGATIVE
;
# _pdbx_category_context.type WWPDB_LOCAL #V4
# _pdbx_category_context.category_id em_staining #V4
_pdbx_category_context.type EMDB_PUBLIC
_pdbx_category_context.category_id em_staining

save_

Expand Down Expand Up @@ -103130,7 +103131,7 @@ save_em_final_classification
; _em_final_classification.id 1
_em_final_classification.image_processing_id 1
;
_pdbx_category_context.type WWPDB_LOCAL
_pdbx_category_context.type WWPDB_LOCAL,EMDB_PUBLIC
_pdbx_category_context.category_id em_final_classification
save_

Expand Down Expand Up @@ -103633,6 +103634,7 @@ save__em_software.name
'_em_software.name' HADDOCK .
'_em_software.name' HARUSPEX .
'_em_software.name' hsearch_lorentz .
'_em_software.name' I3 .
'_em_software.name' I-TASSER .
'_em_software.name' ICON .
'_em_software.name' IHRSR .
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5 changes: 3 additions & 2 deletions base/mmcif_pdbx-data.dic
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Expand Up @@ -575,8 +575,9 @@ data_mmcif_pdbx-data.dic
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'
boolean char 'YES|NO' 'Boolean type'
#author char "[A-Za-z '\-]+,\s+([A-Z\-]+\.)+$" 'Author name in PDB format: Taylor, C.A.'
author char "[A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*$" 'Author name in PDB format: Taylor, C.A.'

# EM uses this data type
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.*)$" 'Author name in PDB format: Taylor, C.A.'
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'
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'
sequence_dep char '[a-zA-Z0-9\t \r\n\v\f\(\)]+$' 'Deposition specific one letter code'
Expand Down
11 changes: 10 additions & 1 deletion base/mmcif_pdbx_v50-header.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ data_mmcif_pdbx.dic

_dictionary.title mmcif_pdbx.dic
_dictionary.datablock_id mmcif_pdbx.dic
_dictionary.version 5.378
_dictionary.version 5.379
#
loop_
_dictionary_history.version
Expand Down Expand Up @@ -2803,3 +2803,12 @@ Changes (ep):
+ Add em_admin.process_site and em_admin.composite_map
+ For many EM categories and EMDB_PUBLIC
;
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
;
11 changes: 10 additions & 1 deletion base/mmcif_pdbx_v5_next-header.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ data_mmcif_pdbx.dic

_dictionary.title mmcif_pdbx.dic
_dictionary.datablock_id mmcif_pdbx.dic
_dictionary.version 5.386
_dictionary.version 5.387
#
loop_
_dictionary_history.version
Expand Down Expand Up @@ -2941,3 +2941,12 @@ Changes (ep):
+ Add em_admin.process_site and em_admin.composite_map
+ For many EM categories and EMDB_PUBLIC
;
5.387 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
;
113 changes: 64 additions & 49 deletions dist/mmcif_pdbx_v50.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ _datablock.description
#
_dictionary.title mmcif_pdbx.dic
_dictionary.datablock_id mmcif_pdbx.dic
_dictionary.version 5.378
_dictionary.version 5.379
#
loop_
_dictionary_history.version
Expand Down Expand Up @@ -3049,52 +3049,14 @@ Changes (ep):
+ For many EM categories and EMDB_PUBLIC
;

0.1 2023-05-26
;
Changes (mgb)
+ added new item type for UniProt PTM Accession IDs (PTM-XXXX)
+ added new item for PTM project to flag if the CCD can be used to
represent a protein modification
_chem_comp.pdbx_pcm
+ added new category for PTM project list all protein modifications in the entry
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
+ added new item for PTM project to flag if an entry contains protein modifications
_pdbx_entry_details.has_protein_modification
+ added new category for PTM project list all protein modifications in the entry
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
_pdbx_modification_feature.biological_function
_pdbx_modification_feature.biological_function_details
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
;

#
Expand Down Expand Up @@ -3430,7 +3392,7 @@ pdb_id_u uchar ([1-9][A-Za-z0-9]{3}|[Pp][Dd][Bb]_[A-Za-z0-9]{8
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"
boolean char YES|NO "Boolean type"
author char "[A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*$" "Author name in PDB format: Taylor, C.A."
author char "([A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*)|(Seattle Structural Genomics Center for Infectious Disease.*)|(Structural Genomics Consortium.*)|(QCRG Structural Biology Consortium.*)$" "Author name in PDB format: Taylor, C.A."
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"
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"
sequence_dep char "[a-zA-Z0-9\t \r\n\v\f\(\)]+$" "Deposition specific one letter code"
Expand Down Expand Up @@ -3980,6 +3942,54 @@ Changes (EP):
+ Add EMDB_PUBLIC context to pdbx_initial_refinement_model
;

ptm-extension.dic 0.1 2023-05-26
;
Changes (mgb)
+ added new item type for UniProt PTM Accession IDs (PTM-XXXX)
+ added new item for PTM project to flag if the CCD can be used to
represent a protein modification
_chem_comp.pdbx_pcm
+ added new category for PTM project list all protein modifications in the entry
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
+ added new item for PTM project to flag if an entry contains protein modifications
_pdbx_entry_details.has_protein_modification
+ added new category for PTM project list all protein modifications in the entry
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
_pdbx_modification_feature.biological_function
_pdbx_modification_feature.biological_function_details
;

#
loop_
_pdbx_item_linked_group.category_id
Expand Down Expand Up @@ -21301,6 +21311,7 @@ save__diffrn_detector.type
"_diffrn_detector.type" "RIGAKU AFC9" .
"_diffrn_detector.type" "RIGAKU HyPix-3000" PIXEL
"_diffrn_detector.type" "RIGAKU HyPix-6000HE" PIXEL
"_diffrn_detector.type" "RIGAKU HyPix-Arc 150" PIXEL
"_diffrn_detector.type" "RIGAKU JUPITER 140" CCD
"_diffrn_detector.type" "RIGAKU JUPITER 210" CCD
"_diffrn_detector.type" "RIGAKU MERCURY" CCD
Expand Down Expand Up @@ -122994,6 +123005,9 @@ save_em_staining
;

#
_pdbx_category_context.type EMDB_PUBLIC
_pdbx_category_context.category_id em_staining
#
save_
#
save__em_staining.details
Expand Down Expand Up @@ -124487,7 +124501,7 @@ save_em_final_classification
;

#
_pdbx_category_context.type WWPDB_LOCAL
_pdbx_category_context.type WWPDB_LOCAL,EMDB_PUBLIC
_pdbx_category_context.category_id em_final_classification
#
save_
Expand Down Expand Up @@ -125033,6 +125047,7 @@ save__em_software.name
"_em_software.name" HADDOCK .
"_em_software.name" HARUSPEX .
"_em_software.name" hsearch_lorentz .
"_em_software.name" I3 .
"_em_software.name" I-TASSER .
"_em_software.name" ICON .
"_em_software.name" IHRSR .
Expand Down
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