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:
- Automatic discovery, retrieval and association of PDB entries
for an alignment's sequences
- Visualisation of discovered structures' meta-data
- Ability to configure the meta-data entries to visualise
- Auto-selection of the best structure via filtering by the
available metric parameters in the meta-data (i.e. resolution,
quality etc).
- Selection of multiple structures in a single operation
Additionally, the Structure Chooser retains the following contemporary
features of Jalview:
- Manual association of PDB entries via entering the PDB Id or
From File
- Ability to view cached PDB entries
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.
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.
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.
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.
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:
- From File - You can 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 - Jalview will use the PDB Rest
API, provided by the EBI, to fetch the PDB file with the entered Id.
- Cached PDB Entries - You can view PDB structures which have previously been downloaded/viewed using this option. Jalview caches previously downloaded PDB entries in the computer memory. However, if the project is saved before exiting Jalview, Jalview will serialize the cached entries to the file system.
The Structure Chooser interface was introduced in Jalview 2.x.x.