Structure Chooser Dialog Box

The Structure Chooser allows you to select 3D structures to view for the currently selected set of sequences. It is opened by selecting the "3D Structure Data..." option from the Sequence ID panel's pop-up menu.

The dialog provides:

• Automatic discovery, retrieval and association of PDB entries for sequences
• Exploration of meta-data for available 3D structures
• Automatic selection of the 'best structure' to display for each sequence
• Manual association of PDB entries by entering a PDB Id
• Association of structure data from a local file (in mmCIF or PDB format)

Selecting and Viewing Structures

The drop-down menu offers different options for structure discovery; the 'Cached' view is shown automatically if existing structure data has been imported for the selected sequences, and if none is available, the import PDB/mmCIF file options are shown.

Once one or more structures have been selected, pressing the View or Add button will import them a new or existing structure view. When multiple views are available, use the drop-down menu to pick the target viewer for the structures.

Automated discovery of structure data

After selecting "3D Structure Data ..", Jalview queries 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 structures for your sequences

If you have already loaded 3D structure data for the selected sequences, the structure chooser will first open with the Cached Structures View. This view shows associations between each sequence, and chains for 3D structure files already in memory. If you want to download additional structures, select one of the other options from the drop down menu.

Selection of the best structure for each sequence

Jalview can automatically select the best structures according to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.

Clicking on the drop down menu allows other criteria to be chosen. For the PDBe, these include including Resolution (only defined for X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.

When 'Invert' is selected, structures are selected in reverse order for the current criteria (e.g. worst quality rather than best).

The screenshot above shows the Structure Chooser displayed after selecting all the sequences in the Jalview example project. If no structures were auto-discovered, options for manually associating PDB records will be shown (see below).

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.

Exploration of meta-data for available structures

Information on each structure available is displayed in columns in the dialog box. By default, only the title, resolution and PDB identifier are shown, but many more are provided by the PDBe. 3D-Beacons structures have different data, including a quality score (such as Qmeans_DISCO). To configure which ones are displayed, select the 'Configure Displayed Columns' tab and tick the columns which you want to see.

Manual selection/association of PDB files with Sequences

To manually associate PDB files with a sequence, select 'From File', or 'Enter PDB Id' from the drop-down menu:

• From File - allows you to load a PDB file from the local machine or network and associate it with the selected sequence. PDB files associated in this way will also be saved in the Jalview Archive file.
  
• Enter PDB Id - allows you specify a PDB ID for your sequence. The PDB Rest API, provided by EMBL-EBI, is used to validate and fetch structure data.
  

The Structure Chooser interface was introduced in Jalview 2.9.