The PDB Sequence Fetcher

Jalview provides a specialised interface that allows fast and efficient discovery and retrieval of data from the PDB database, based on the EMBL-EBI's PDBe BioSOLR query interface. It allows interactive querying of PDB metadata with free text and structured queries, so structures can be located without prior knowledge of their database accessions, or via manual cross-referencing with other bioinformatics websites.

To open the PDB Sequence Fetcher, select PDB as the database from any Sequence Fetcher dialog (opened via "File →Fetch Sequences").

Searching the PDB Database

To search the PDB, begin typing in the text box. If the 'autosearch' checkbox is enabled, then the results of your query will be automatically updated and shown in the search results tab; otherwise, press return to update the results. To access previous searches, press the down-arrow or click the drop down menu icon at the side of the search box. If you just want to paste in a list of IDs, the 'Retrieve IDs' tab provides a batch-retrieval interface.

You can sort results according to the displayed columns, and select entries with the mouse and keyboard. Once you have selected one or more entries, hit the OK button to retrieve and view them in Jalview.

- Searching a specific PDB field
  If you want to find structures based on a specific PDB metadata field, you can select it from the drop-down menu.
- 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.
  e.g 1xyz:A
- Bulk PDB retrieval
  Multiple PDB IDs can be specified for retrieval via the Retrieve IDs tab.
- Wild card searching
  The following wild cards are supported by the EMBL-EBI PDBe query service:
  - ? matches a single character
    The search string te?t would match both test and text.
  - * matches multiple characters
    The search string: tes* - would match test, testing, and tester.
  Note: you can use wildcard characters anywhere in a query string.
  For example: te*t - would match test and text. *est - would match pest and test.
- Structured queries
  The PDBe SOLR interface supports boolean query syntax, allowing quoted search strings to be combined with AND, OR, and NOT. Currently, no special support for constructing these queries is provided in the query dialog box.

Customising The PDB Sequence Fetcher

To change the displayed meta-data in the search result, click the 'Configure Displayed Columns' tab, and select the fields you'd like displayed. These fields can also be configured via the Structure tab of the Jalview Desktop Preferences.

The PDB Sequence Fetcher interface was introduced in Jalview 2.9