<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>PDB Sequence Fetcher</title>
+<title>The PDB Sequence Fetcher</title>
</head>
<body>
- <strong>PDB Sequence Fetcher</strong>
- <p>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.</p>
- <p>
- The PDB Sequence Fetcher interface can be accessed from <b>"File →Fetch Sequence(s) →Select Database →PDB"</b> click the ok button after selecting PDB from the 'Select Database
- Retrieval Source' interface.
- </p>
- <p>
- <img src="pdbseqfetcher.png" align="left"
- alt="PDB sequence fetcher (introduced in Jalview 2.9)">
- </p>
+ <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><strong>Searching the PDB Database</strong></p>
- <p>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.</p>
-
- <p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
- option is 'ALL'.</p>
-
- <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
- <ul>
- <li>Retrieving a unique chain for a PDB entry: <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. eg: 1xyz:A
- </li>
+ <p>
+ <strong>Searching the PDB Database</strong>
+ </p>
+ <p>
+ To search the PDB, begin typing in the text box. The results of your
+ query are shown in the search results tab, which updates every time
+ you type in the search text box. 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>Querying multiple PDB Id's in one operation:<br>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
- </li>
+ <li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
+ IDs can be specified by separating them with a semi-colon.<br />
+ e.g. 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically
+ fetch those IDs, like the default Sequence Fetcher interface.</li>
- <li>Wild card searching: <br>The PDB sequence fetcher also
- provides support for wild card querying of the PDB database. <br>Single
- character (matches a single character) - ? The search string te?t
- would match both test and text. <br>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.
- </li>
- </ul>
- <p>
- <strong>Customising displayed meta-data</strong> <br>To change
- the displayed meta-data in the search result, click the 'Configure
- Displayed Columns' tab, then tick off the options wanted.
- </p>
- <p>
- <strong>Importing Sequence</strong><br> 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.
- </p>
- <p>
- <em>The PDB Sequence Fetcher interface was introduced in Jalview
- 2.9</em>
- </p>
+ <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>
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