- 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 <strong>3D-Beacons Search</strong> button at the top of the
- Structure Chooser window.
- <br/>
- <img src="3dbeacons_button.png"/>
- <br/>
- The 3D-Beacons Network search requires UniProt references and Jalview will ask
- to attempt to fetch these references for the selected sequences.
- UniProt references might not always be found in which case you can revert to the PDB
- search.
- <br/>
- <img src="3dbeacons_structurechooser.png"/>
- <br/>
- If structures are found through the 3D-Beacons network you can filter which structures
- are shown using the drop-down filter at the top of the Structure Chooser window.
- <br/>
- You can view information about each related model, such as the resource providing
- each model, in the columns displayed. You can sort the list of models by clicking on
- column headings.
- <br/>
- Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> 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.<br /> 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 <strong>3D-Beacons Search</strong> button at
+ the top of the Structure Chooser window. <br /> <img
+ src="3dbeacons_button.png" /> <br />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. <br />
+ <br /> <img src="3dbeacons_structurechooser.png" /> <br /> <br />
+ 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.<br />Use
+ the drop-down filter menu and table to browse and select structures,
+ and finally view them using the
+ <a href="viewingpdbs.html#afterviewbutton">open structure
+ options</a> at the bottom of the Structure Chooser window.