V5.388/V5.396 dictionary update

wwpdb-dictionaries · Mar 4, 2024 · 9a5bf35 · 9a5bf35
1 parent 3af0783
commit 9a5bf35
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Showing 9 changed files with 360,059 additions and 90 deletions.
diff --git a/archive/mmcif_pdbx_v50-v5.388.dic b/archive/mmcif_pdbx_v50-v5.388.dic
diff --git a/archive/mmcif_pdbx_v5_next-v5.396.dic b/archive/mmcif_pdbx_v5_next-v5.396.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        0.25
+_pdbx_dictionary_component.version        0.26
 
 loop_
 _pdbx_dictionary_component_history.dictionary_component_id
@@ -170,7 +170,7 @@ Changes (ep):
   + Add PanthaRhei and PACEtomo to em_software.name enumeration
   + Add 'CEOS CEFID' to _em_imaging_optics.energyfilter_name enumeration
 ;
-mmcif_pdbx-base.dic  0.22  2023-01-16
+mmcif_pdbx-base.dic  0.22  2024-01-16
 ;
 Changes (ep):
   + em_software.name enumeration change "PanthaRhei" to "Panta Rhei"
@@ -180,23 +180,33 @@ Changes (ep):
   + Add IPCAS to _software.name enumeration
 ;
 
-mmcif_pdbx-base.dic  0.23  2023-01-22
+mmcif_pdbx-base.dic  0.23  2024-01-22
 ;
 Changes (ep):
   + Add new "DECTRIS PILATUS4 (R,X,XE) CdTe" detectors to _diffrn_detector.type enumeration
   + Add "GATAN ALPINE (2.3k x 3.2k)" to _em_image_recording.film_or_detector_model
 ;
-mmcif_pdbx-base.dic  0.24  2023-01-30
+mmcif_pdbx-base.dic  0.24  2024-01-30
 ;
 Changes (ep):
   + Add enumeration for _pdbx_database_related.db_name
   + Add "NMRtist" to pdbx_nmr_software.name enumeration
 ;
-mmcif_pdbx-base.dic  0.25  2023-02-04
+mmcif_pdbx-base.dic  0.25  2024-02-04
 ;
 Changes (ep):
   + Add "STFC Large Pixel Detector" to _diffrn_detector.type enumeration.
 ;
+mmcif_pdbx-base.dic  0.26  2024-03-04
+;
+Changes (ep):
+  + Example for _entity_poly.pdbx_seq_one_letter_code updted changing PTO -> TPO
+  + Enumeration for _software.name "MAIN" has roles added.
+  + Add CSearch to _software.name enumeration
+  + Add ASTRA-TOOLBOX to _em_software enumeration
+  + Add 4D-STEM to _em_iaging.mode enumeration
+  + Add PDB-Dev to _database_2.database_id
+;
 
 
 ###############
@@ -11609,6 +11619,9 @@ save__database_2.database_id
 ;
                                   PDB
 ;                                 Protein Data Bank
+;
+                                  PDB-Dev
+;                                 PDB-Dev integrative/hybrid methods
 ;
                                   PDF
 ;                                 Powder Diffraction File (JCPDS/ICDD)
@@ -33222,6 +33235,7 @@ save__software.name
        '_software.name' CrysalisPro       'data collection,data scaling,data reduction'
        '_software.name' CrystalClear      'data collection,data scaling,data reduction,phasing'
        '_software.name' CrystFEL          'data collection,data scaling,data reduction'
+       '_software.name' CSearch           phasing
        '_software.name' cxi.merge         'data scaling'
        '_software.name' d*TREK            'data scaling,data reduction'
        '_software.name' DENZO             'data reduction'
@@ -33269,7 +33283,7 @@ save__software.name
        '_software.name' LSCALE            .
        '_software.name' MADNESS           .
        '_software.name' MADSYS            phasing
-       '_software.name' MAIN              .
+       '_software.name' MAIN              'refinement,model building'
        '_software.name' Mantid            'data reduction'
        '_software.name' MAR345            'data collection'
        '_software.name' MAR345dtb         'data collection'
@@ -49976,7 +49990,7 @@ Y for Tyrosine
 (DT) for Thymidine-5'-monophosphate
 (MSE) for Selenomethionine
 (SEP) for Phosphoserine
-(PTO) for Phosphothreonine
+(TPO) for Phosphothreonine
 (PTR) for Phosphotyrosine
 (PCA) for Pyroglutamic acid
 (UNK) for Unknown amino acid
@@ -96984,6 +96998,7 @@ save__em_imaging.mode
     _item_enumeration.name  #V5
     _item_enumeration.value  #V5
     _item_enumeration.detail  #V5
+              '_em_imaging.mode' 4D-STEM .
               '_em_imaging.mode' 'BRIGHT FIELD'   .
               '_em_imaging.mode' 'DARK FIELD'    .
               '_em_imaging.mode' DIFFRACTION    .
@@ -102891,8 +102906,9 @@ save__em_image_recording.film_or_detector_model
   '_em_image_recording.film_or_detector_model'    "KODAK SO-163 FILM"   .
   '_em_image_recording.film_or_detector_model'    "GENERIC FILM"   .
   '_em_image_recording.film_or_detector_model'    "GENERIC IMAGE PLATES"   .
+#  '_em_image_recording.film_or_detector_model'    "DECTRIS ARINA (0.2k x 0.2k)" .
   '_em_image_recording.film_or_detector_model'    "DECTRIS ELA (1k x 0.5k)"   .  
-  '_em_image_recording.film_or_detector_model'    "DECTRIS SINGLA (1k x 1k)"   .  
+  '_em_image_recording.film_or_detector_model'    "DECTRIS SINGLA (1k x 1k)"   .
   '_em_image_recording.film_or_detector_model'    "DIRECT ELECTRON APOLLO (4k x 4k)"  .
   '_em_image_recording.film_or_detector_model'    "DIRECT ELECTRON DE-10 (5k x 4k)"   .
   '_em_image_recording.film_or_detector_model'    "DIRECT ELECTRON DE-12 (4k x 3k)"   .
@@ -103668,6 +103684,7 @@ save__em_software.name
         '_em_software.name'  AmiraFPM                           .
         '_em_software.name'  Appion                             .
 	'_em_software.name'  ARP/wARP                           .
+	'_em_software.name'  ASTRA-TOOLBOX                      .
         '_em_software.name'  Auto3DEM                           .
         '_em_software.name'  AV3                                .
         '_em_software.name'  Buccaneer                          .

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         5.387
+    _dictionary.version         5.388
 #
      loop_
     _dictionary_history.version
@@ -2877,3 +2877,15 @@ Changes (ep):
     Update description for pdbx_initial_refinement_model.entity_id_list.
   + Add "STFC Large Pixel Detector" to _diffrn_detector.type enumeration.
 ;
+5.388  2024-03-04
+;
+Changes (ep/mgb):
+  + Update ptm-extension
+  + Example for _entity_poly.pdbx_seq_one_letter_code updted changing PTO -> TPO
+  + Enumeration for _software.name "MAIN" has roles added.
+  + Add CSearch to _software.name enumeration
+  + Add ASTRA-TOOLBOX to _em_software enumeration
+  + Add 4D-STEM to _em_iaging.mode enumeration
+  + Add PDB-Dev to _database_2.database_id
+  + Update funding enumerations
+;
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         5.395
+    _dictionary.version         5.396
 #
      loop_
     _dictionary_history.version
@@ -3015,3 +3015,15 @@ Changes (ep):
     Update description for pdbx_initial_refinement_model.entity_id_list.
   + Add "STFC Large Pixel Detector" to _diffrn_detector.type enumeration.
 ;
+5.396  2024-03-04
+;
+Changes (ep/mgb):
+  + Update ptm-extension
+  + Example for _entity_poly.pdbx_seq_one_letter_code updted changing PTO -> TPO
+  + Enumeration for _software.name "MAIN" has roles added.
+  + Add CSearch to _software.name enumeration
+  + Add ASTRA-TOOLBOX to _em_software enumeration
+  + Add 4D-STEM to _em_iaging.mode enumeration
+  + Add PDB-Dev to _database_2.database_id
+  + Update funding enumerations
+;