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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ * Jalview is free software: you can redistribute it and/or
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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+<head>
+<title>The PDB Sequence Fetcher</title>
+</head>
+<body>
+
+ <strong>The PDB Sequence Fetcher</strong>
+ <p>
+ 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 <em>via</em> manual cross-referencing
+ with other bioinformatics websites.
+ </p>
+ <p>
+ To open the PDB Sequence Fetcher, select PDB as the database from
+ any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
+ <strong>"File →Fetch Sequences"</strong>).
+ </p>
+ <img src="pdbseqfetcher.png" align="left"
+ alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
+
+ <p>
+ <a name="pdbfts"><strong>Searching the PDB Database</strong></a>
+ </p>
+ <p>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.</p>
+ <p>
+ 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 <strong>OK</strong> button to retrieve and
+ view them in Jalview.
+ </p>
+ <p>
+ <ul>
+ <li><strong>Searching a specific PDB field</strong><br />If
+ you want to find structures based on a specific PDB metadata
+ field, you can select it from the drop-down menu.</li>
+ <li><strong>Retrieving a unique chain for a PDB entry</strong><br>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.<br /> e.g
+ 1xyz:A</li>
+
+ <li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
+ IDs can be specified for retrieval via the
+ <strong>Retrieve IDs</strong> tab.</li>
+
+ <li><strong>Wild card searching</strong><br>The following
+ wild cards are supported by the EMBL-EBI PDBe query service:
+ <ul>
+ <li><strong>?</strong> matches a single character<br />The
+ search string te?t would match both test and text.</li>
+ <li><strong>*</strong> matches multiple characters<br />The
+ search string: tes* - would match test, testing, and tester.</li>
+ </ul> <em>Note:</em> you can use wildcard characters anywhere in a
+ query string.<br />For example: te*t - would match test and text.
+ *est - would match pest and test.</li>
+ <li><strong>Structured queries</strong><br />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.</li>
+ </ul>
+ <p>
+ <strong>Customising The PDB Sequence Fetcher</strong>
+ </p>
+ <p>
+ 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 <em>via</em> the
+ Structure tab of the <a href="preferences.html#structure">Jalview
+ Desktop Preferences</a>.
+ </p>
+ <p>
+ <em>The PDB Sequence Fetcher interface was introduced in
+ Jalview 2.9</em>
+ </p>
+</body>
+</html>
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