- Structure Chooser -
++ Structure Chooser +
- The Structure Chooser interface provides a smart technique for - selecting PDB structures to view in Jalview by querying readily - available meta-data of structures. The Interface can be invoked by selecting - the - "View Structure" option from a sequence's - pop-up menu. Some of the main - features it provides are listed below: -+ The Structure Chooser interface allows you to interactively select + which PDB 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: +
++ Selecting and Viewing Structures +
++ Once one or more structures have been selected, pressing the View + button will import them into a new or existing + structure view. +
++ 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.
+
+
+ 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 PDB. For alignments with no existing + structure data, the 'Best Quality' structure for each sequence will + by default be selected, but clicking on the drop down menu allows + other criteria to be chosen, including Resolution (only defined for + X-Ray structures), Highest Protein Chain etc. When 'Invert' is + selected, structures are selected in reverse order for the current + criteria (e.g. worst quality rather than best).
+
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- Associating PDB files with Sequences
- Discovery/Association of PDB entries to a sequence happens
- automatically during the initialisation of the Structure Chooser
- Interface. Jalview uses the sequence's ID to query the PDB Rest API,
- provided by the EBI to discover PDB Ids associated with the sequence.
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- Configuring displayed meta-data for Structures
- To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible.
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- Auto-selection of best Structures
-
Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data
- of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure
- Chooser interface: Best Uniprot coverage, Higest Resolution,
-
- Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.
- 
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-
The screenshot above shows the Structure Chooser interface
- along with the meta-data of auto-discovered structures for the sample
- alignment. Note however that if no structures were auto-discovered, a
- different interface for manual association will be invoked as seen in
- the screenshot below.
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- 
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- Manual selection/association of PDB files with Sequences -
-To manually associate PDB files with a sequence, select any of - the follwing options listed below from the drop-down menu in the - interface: -
+ 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. 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: +
- The Structure Chooser interface was introduced in Jalview 2.9. - -
++ The Structure Chooser interface was introduced in Jalview + 2.9. +