X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fstructurechooser.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=2c77049d23515dd5cf07a0134281aaa58dfef65e;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=512b68ff3cdc10365d0b1015dcd5ffb7c25f8845;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html index 512b68f..2c77049 100644 --- a/help/help/html/features/structurechooser.html +++ b/help/help/html/features/structurechooser.html @@ -67,13 +67,10 @@ Automated discovery of structure data
- After selecting "3D Structure Data ..", Jalview queries the PDB via
+ After selecting "3D Structure Data ..", Jalview queries its available structure data providers. When Uniprot identifiers are available, it queries the 3D-Beacons network (since Jalview 2.11.2), otherwise it searches the PDB via
the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
associated with the sequence. It does this based on the sequence's
ID string, and any other associated database IDs.
-
- Since Jalview 2.11.2, you can also initiate a search
- of the 3D-Beacons Network.
Viewing existing @@ -116,29 +113,54 @@ 3D-Beacons Network Search
- To initiate a search of the 3D-Beacons Network—which searches
- across experimentally determined and predicted structure models from
- several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
- PDBe-KB—click on the 3D-Beacons Search button at the top of the
- Structure Chooser window.
-
-
-
- The 3D-Beacons Network search requires UniProt references and Jalview will ask
- to attempt to fetch these references for the selected sequences.
- If no UniProt references are found, Jalview will still search the PDB for potential matches for the sequence's ID string.
-
-
-
- Structures found through the 3D-Beacons network can be filtered using the drop-down filter at the top of the Structure Chooser window.
- You can view information about each related model, such as the resource providing
- each model, in the displayed columns, and models can be reordered by clicking on
- column headings.
-
- Select and view the structures in the usual way using the open structure options at
- the bottom of the Structure Chooser window.
+ 3D beacons searches across experimentally determined and predicted
+ structure models from several resources including PDBe, AlphaFold
+ DB, SWISS-MODEL, PED, SASDB, Genome3D and PDBe-KB.
If your
+ sequences have Uniprot identifiers, Jalview will query the
+ 3D-Beacons network to discover relevant 3D structures and models.
+ When no uniprot identifiers are available you can initiate Uniprot
+ identifier discovery and a subsequent search of the 3D-Beacons
+ Network by pressing the 3D-Beacons Search button at
+ the top of the Structure Chooser window.
When the search button is
+ pressed, Jalview will ask to attempt to fetch any additional uniprot
+ references for the selected sequences - we do this because fetching
+ large numbers of Uniprot references can take some time. For
+ sequences without Uniprot accessions, Jalview will still search the
+ PDB for potential matches for the sequence's ID string.
+
+ 3D Beacons provides some additional information for each model,
+ including what positions on the Uniprot sequence have structure
+ data. These metadata (described below) are shown in the columns of
+ the table and used to provide additional filter options.
Use
+ the drop-down filter menu and table to browse and select structures,
+ and finally view them using the
+ open structure
+ options at the bottom of the Structure Chooser window.
Exploration of meta-data for available structures