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<!--
- * 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.
*
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<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>
+ <strong>The PDB Sequence Fetcher</strong>
<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>).
+ 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>
- <img src="pdbseqfetcher.png" align="left"
- alt="PDB sequence fetcher (introduced in Jalview 2.9)"/>
+ <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>
+ <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
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>
+ <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 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>
+ 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><strong>Wild card searching</strong><br>The following
wild cards are supported by the EMBL-EBI PDBe query service:
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>
+ </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>
+ <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
git://source.jalview.org / jalview.git / blobdiff