From Jalview 2.9, a specialised interface was introduced for fast and efficient discovery/retrieval of sequence data from the PDB database. The introduced interface enables live querying of PDB data on-the-fly thereby eliminating the need to memorise database accession or to manually cross-reference other bioinformatics websites before retrieving sequence data in Jalview. The underlying infrastructure is provided by EBI and is based on Apache Solr which is a text based search engine.

The PDB Sequence Fetcher interface can be accessed from "File →Fetch Sequence(s) →Select Database →PDB" click the ok button after selecting PDB from the 'Select Database Retrieval Source' interface.

Searching the PDB Database

When the interface is opened, a live query to the PDB database is executed every time a character is typed into the search text box, and a result is displayed on-the-fly as seen in the screenshot above.

Use the drop-down menu to select a specific field to search by in the PDB database, the default option is 'ALL'.

Furthermore, the PDB search interface also provides the following functionalities:

• Retrieving a unique chain for a PDB entry:
  To retrieve a specific chain for a PDB entry, append the PDB ID with a colon followed by the chain code in the search box. eg: 1xyz:A
• Querying multiple PDB Id's in one operation:
  The PDB search interface supports querying of multiple PDB Ids in one operation by separating the list of PDB Ids with a semi-colon i.e: 1xyz;2xyz;3xyz
• Wild card searching:
  The PDB sequence fetcher also provides support for wild card querying of the PDB database.
  Single character (matches a single character) - ? The search string te?t would match both test and text.
  Multiple characters (matches zero or more sequential characters) - * The wildcard search: tes* - would match test, testing, and tester. You can also use wildcard characters in the middle of a term. For example: te*t - would match test and text. *est - would match pest and test.

Customising displayed meta-data
To change the displayed meta-data in the search result, click the 'Configure Displayed Columns' tab, then tick off the options wanted.

Importing Sequence
After querying the PDB database, to import the found data into Jalview, select the entries you wish to import then click the 'Ok' button at the bottom of the interface.

The PDB Sequence Fetcher interface was introduced in Jalview 2.9