V5.392/V5.400 dictionary update

wwpdb-dictionaries · Apr 29, 2024 · 244398e · 244398e
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commit 244398e
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Showing 9 changed files with 360,075 additions and 169 deletions.
diff --git a/archive/mmcif_pdbx_v50-v5.392.dic b/archive/mmcif_pdbx_v50-v5.392.dic
diff --git a/archive/mmcif_pdbx_v5_next-v5.400.dic b/archive/mmcif_pdbx_v5_next-v5.400.dic
diff --git a/base/mmcif_pdbx-base.dic b/base/mmcif_pdbx-base.dic
@@ -16,7 +16,7 @@ data_mmcif_pdbx-base.dic
 _pdbx_dictionary_component.datablock_id   mmcif_pdbx-base.dic
 _pdbx_dictionary_component.dictionary_component_id   mmcif_pdbx-base.dic
 _pdbx_dictionary_component.title          "mmCIF/PDBx base dictionary"
-_pdbx_dictionary_component.version        0.28
+_pdbx_dictionary_component.version        0.29
 
 loop_
 _pdbx_dictionary_component_history.dictionary_component_id
@@ -220,7 +220,12 @@ Changes (ep):
   + Extend enumeration of _pdbx_chem_comp_depositor_info.type based on use
   + Extend _diffrn_source.type enumeration with "PETRA III, DESY BEAMLINE P09 HiPhaX"
 ;
-
+mmcif_pdbx-base.dic  0.29  2024-04-29
+;
+Changes (ep):
+  + Change type of _pdbx_chem_comp_upload_depositor_info.upload_file_type
+    to uline to reflect usage. Add JPG and PDBX to enumeration.
+;
 ###############
 ## ATOM_SITE ##
 ###############
@@ -110090,11 +110095,13 @@ save__pdbx_chem_comp_upload_depositor_info.upload_file_type
     _item.name                  '_pdbx_chem_comp_upload_depositor_info.upload_file_type'
     _item.category_id             pdbx_chem_comp_upload_depositor_info
     _item.mandatory_code          yes
-    _item_type.code               line
+    _item_type.code               uline
     loop_
     _item_enumeration.value
     _item_enumeration.detail
+                                 'PDBX'   .
                                  'GIF'    .
+				 'JPG'    .
                                  'JPEG'   .
                                  'PNG'    .
                                  'SVG'    .

diff --git a/base/mmcif_pdbx-data.dic b/base/mmcif_pdbx-data.dic
@@ -577,7 +577,7 @@ data_mmcif_pdbx-data.dic
    boolean char 'YES|NO' 'Boolean type'
 
    # 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.*)|(Center for Structural Genomics of Infectious Diseases.*))" '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.*)|(Center for Structural Genomics of Infectious Diseases.*)|(Center for Structural Biology of Infectious Diseases.*))" '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'

diff --git a/base/mmcif_pdbx_v50-header.dic b/base/mmcif_pdbx_v50-header.dic
@@ -17,7 +17,7 @@ data_mmcif_pdbx.dic
 
     _dictionary.title           mmcif_pdbx.dic
     _dictionary.datablock_id    mmcif_pdbx.dic
-    _dictionary.version         5.391
+    _dictionary.version         5.392
 #
      loop_
     _dictionary_history.version
@@ -2909,3 +2909,11 @@ Changes (ep/mgb):
 Changes (ep):
   + Extend enumeration of _pdbx_chem_comp_depositor_info.type based on use
 ;
+5.392  2024-04-29
+;
+Changes (ep/mgb):
+  + Remove biological function information from pdbx_modification_feature
+  + Extend em_author_list to support Center for Structural Biology of Infectious Diseases (CSBID)
+  + Change type of _pdbx_chem_comp_upload_depositor_info.upload_file_type
+    to uline to reflect usage. Add JPG and PDBX to enumeration.
+;
diff --git a/base/mmcif_pdbx_v5_next-header.dic b/base/mmcif_pdbx_v5_next-header.dic
@@ -17,7 +17,7 @@ data_mmcif_pdbx.dic
 
     _dictionary.title           mmcif_pdbx.dic
     _dictionary.datablock_id    mmcif_pdbx.dic
-    _dictionary.version         5.399
+    _dictionary.version         5.400
 #
      loop_
     _dictionary_history.version
@@ -3049,3 +3049,11 @@ Changes (ep):
   + Extend enumeration of _pdbx_chem_comp_depositor_info.type based on use
   + Extend _diffrn_source.type enumeration with "PETRA III, DESY BEAMLINE P09 HiPhaX"
 ;
+5.400  2024-04-29
+;
+Changes (ep/mgb):
+  + Remove biological function information from pdbx_modification_feature
+  + Extend em_author_list to support Center for Structural Biology of Infectious Diseases (CSBID)
+  + Change type of _pdbx_chem_comp_upload_depositor_info.upload_file_type
+    to uline to reflect usage. Add JPG and PDBX to enumeration.
+;
diff --git a/dist/mmcif_pdbx_v50.dic b/dist/mmcif_pdbx_v50.dic
@@ -9,7 +9,7 @@ _datablock.description
 #
 _dictionary.title         mmcif_pdbx.dic
 _dictionary.datablock_id  mmcif_pdbx.dic
-_dictionary.version       5.391
+_dictionary.version       5.392
 #
 loop_
 _dictionary_history.version
@@ -3168,6 +3168,15 @@ Changes (ep):
   + Extend enumeration of _pdbx_chem_comp_depositor_info.type based on use
 ;
 
+5.392  2024-04-29  
+;
+Changes (ep/mgb):
+  + Remove biological function information from pdbx_modification_feature
+  + Extend em_author_list to support Center for Structural Biology of Infectious Diseases (CSBID)
+  + Change type of _pdbx_chem_comp_upload_depositor_info.upload_file_type
+    to uline to reflect usage. Add JPG and PDBX to enumeration.
+;
+
 #
 loop_
 _sub_category.id
@@ -3501,7 +3510,7 @@ 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_]+\.)*)|(Seattle Structural Genomics Center for Infectious Disease.*)|(Structural Genomics Consortium.*)|(QCRG Structural Biology Consortium.*)|(Center for Structural Genomics of Infectious Diseases.*))"  "Author name in PDB format: Taylor, C.A."  
+author                    char   "(([A-Za-z0-9_]+(( |-|'|\. )[A-Za-z0-9_]+)*( Jr.| III)?, [A-Za-z0-9_]\.(-?[A-Za-z0-9_]+\.)*)|(Seattle Structural Genomics Center for Infectious Disease.*)|(Structural Genomics Consortium.*)|(QCRG Structural Biology Consortium.*)|(Center for Structural Genomics of Infectious Diseases.*)|(Center for Structural Biology of Infectious Diseases.*))"  "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"  
@@ -3714,13 +3723,13 @@ _pdbx_dictionary_component.datablock_id
 _pdbx_dictionary_component.dictionary_component_id
 _pdbx_dictionary_component.title
 _pdbx_dictionary_component.version
-mmcif_pdbx-base.dic                     mmcif_pdbx-base.dic                     "mmCIF/PDBx base dictionary"                   0.28   
+mmcif_pdbx-base.dic                     mmcif_pdbx-base.dic                     "mmCIF/PDBx base dictionary"                   0.29   
 mmcif_xfel_extensions-v3.dic            mmcif_xfel_extensions-v3.dic            "PDBx/mmCIF XFELDictionary License Extension"  0.0.1  
 mmcif_pdbx_audit_support-extension.dic  mmcif_pdbx_audit_support-extension.dic  "mmCIF/PDBx Audit support extension"           0.24   
 mmcif_pdbx_sifts.dic                    mmcif_pdbx_sifts.dic                    "PDBx/mmCIF Dictionary Sifts Extension"        0.0.2  
 mmcif_pdbx_license.dic                  mmcif_pdbx_license.dic                  "PDBx/mmCIF Dictionary License Extension"      0.0.1  
 initial-model-extension.dic             initial-model-extension.dic             "PDBx/mmCIF Initial model extension"           0.10   
-ptm-extension.dic                       ptm-extension.dic                       "PDBx/mmCIF PTM extension"                     0.3    
+ptm-extension.dic                       ptm-extension.dic                       "PDBx/mmCIF PTM extension"                     0.5    
 #
 loop_
 _pdbx_dictionary_component_history.dictionary_component_id
@@ -3951,6 +3960,13 @@ Changes (ep):
   + Extend _diffrn_source.type enumeration with "PETRA III, DESY BEAMLINE P09 HiPhaX"
 ;
 
+mmcif_pdbx-base.dic                     0.29   2024-04-29  
+;
+Changes (ep):
+  + Change type of _pdbx_chem_comp_upload_depositor_info.upload_file_type
+    to uline to reflect usage. Add JPG and PDBX to enumeration.
+;
+
 mmcif_xfel_extensions-v3.dic            0.0.1  2023-05-31  
 ;
 Changes (EP):
@@ -4310,6 +4326,12 @@ ptm-extension.dic                       0.4    2024-03-25
       _pdbx_modification_feature.modified_residue_label_alt_id
 ;
 
+ptm-extension.dic                       0.5    2024-04-29  
+;
+  Changes (mgb)
+  + removed biological function items
+;
+
 #
 loop_
 _pdbx_item_linked_group.category_id
@@ -132554,12 +132576,14 @@ save__pdbx_chem_comp_upload_depositor_info.upload_file_type
    _item.category_id     pdbx_chem_comp_upload_depositor_info
    _item.mandatory_code  yes
    #
-   _item_type.code  line
+   _item_type.code  uline
    #
    loop_
    _item_enumeration.value
    _item_enumeration.detail
+     PDBX   .  
      GIF    .  
+     JPG    .  
      JPEG   .  
      PNG    .  
      SVG    .  
@@ -167597,11 +167621,9 @@ save_pdbx_modification_feature
     _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
-    1 SEP A 65 ? .   . .  . SEP A 65 ? 1_555 .   . .  . .     .  .  SER 1 SEP Phosphorylation 'Named protein modification' ? ?
-    2 SEP B 65 ? .   . .  . SEP B 65 ? 1_555 .   . .  . .     .  .  SER 1 SEP Phosphorylation 'Named protein modification' ? ?
-    3 CYS A 46 ? CYS B 46 ? CYS A 46 ? 1_555 CYS B 46 ? 1_555 SG SG .   . .   None            'Disulfide bridge'           ? ?
+    1 SEP A 65 ? .   . .  . SEP A 65 ? 1_555 .   . .  . .     .  .  SER 1 SEP Phosphorylation 'Named protein modification'
+    2 SEP B 65 ? .   . .  . SEP B 65 ? 1_555 .   . .  . .     .  .  SER 1 SEP Phosphorylation 'Named protein modification'
+    3 CYS A 46 ? CYS B 46 ? CYS A 46 ? 1_555 CYS B 46 ? 1_555 SG SG .   . .   None            'Disulfide bridge'
 ;
 
 
@@ -167638,12 +167660,10 @@ save_pdbx_modification_feature
     _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
-    1 CSO C 32 ? .   . .  . CSO C 32   ? 1_555 .   . .  . .     .  .  CYS 1 CSO Hydroxylation  'Named protein modification' ? ?
-    2 CSO D 32 ? .   . .  . CSO D 32   ? 1_555 .   . .  . .     .  .  CYS 1 CSO Hydroxylation  'Named protein modification' ? ?
-    3 PLM E .  ? CYS A 82 ? PLM A 1068 ? 1_555 CYS A 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like             ? ?
-    4 PLM F .  ? CYS B 82 ? PLM B 1068 ? 1_555 CYS B 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like             ? ?
+    1 CSO C 32 ? .   . .  . CSO C 32   ? 1_555 .   . .  . .     .  .  CYS 1 CSO Hydroxylation  'Named protein modification'
+    2 CSO D 32 ? .   . .  . CSO D 32   ? 1_555 .   . .  . .     .  .  CYS 1 CSO Hydroxylation  'Named protein modification'
+    3 PLM E .  ? CYS A 82 ? PLM A 1068 ? 1_555 CYS A 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like
+    4 PLM F .  ? CYS B 82 ? PLM B 1068 ? 1_555 CYS B 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like
 ;
 
    #
@@ -168349,46 +168369,6 @@ save__pdbx_modification_feature.category
    #
 save_
 #
-save__pdbx_modification_feature.biological_function
-   _item_description.description  
-;              A flag to indicate if the protein modification at this site can 
-               occur naturally and that it is expected to have a biological 
-               function.
-;
-
-   #
-   _item.name            "_pdbx_modification_feature.biological_function"
-   _item.category_id     pdbx_modification_feature
-   _item.mandatory_code  no
-   #
-   _item_type.code  code
-   #
-   _item_examples.case  Y
-   #
-   loop_
-   _item_enumeration.value
-   _item_enumeration.detail
-     Y  "Protein modification has a biological function"  
-     N  "Protein modification does not have a biological function"  
-   #
-save_
-#
-save__pdbx_modification_feature.biological_function_details
-   _item_description.description  "          Details of the biological function of the protein modification at this site."
-   #
-   _item.name            "_pdbx_modification_feature.biological_function_details"
-   _item.category_id     pdbx_modification_feature
-   _item.mandatory_code  no
-   #
-   _item_type.code  text
-   #
-   loop_
-   _item_examples.case
-     "Phosphorylation at this position is required for full activity of the enzyme"  
-     "Glycosylation of this region of the protein surface shields the protein from antibody recognition"  
-   #
-save_
-#
 save__diffrn_refln.frame_id
    _item_description.description  
 ;             Pointer to _diffrn_scan_frame.frame_id in the DIFFRN_SCAN_FRAME