From Jalview 2.x.x a speciliased 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 cross-reference other bioinformatics websites before retrieving a sequence data in jalview. The underlying technology is provided by EBI and is based on Apache Solr which is a text based search engine.

The PDB Sequence Fetcher interface can be opened by selecting PDB as the choice database from the 'Select Database Retrieval Source' interface of Sequence Fetcher.

Searching the PDB Database
Once the interface is opened, typing in the search text box will execute a live query to the PDB database and display the results on-the-fly as seen in the screen-shot above. Use the drop-down menu to select a specific field to search by in the PDB database, the default option is 'ALL'.

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.x.x.