3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>The PDB Sequence Fetcher</title>
27 <strong>The PDB Sequence Fetcher</strong>
28 <p>Jalview provides a specialised interface that allows fast and efficient discovery and retrieval of data from the PDB
29 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,
30 or <em>via</em> manual cross-referencing with other bioinformatics websites.</p>
32 To open the PDB Sequence Fetcher, select PDB as the database from any <a
33 href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em> <strong>"File
34 →Fetch Sequences"</strong>).
36 <img src="pdbseqfetcher.png" align="left"
37 alt="PDB sequence fetcher (introduced in Jalview 2.9)"/>
39 <p><strong>Searching the PDB Database</strong></p>
41 To search the PDB, begin typing in the text box. The results of your
42 query are shown in the search results tab, which updates every time
43 you type in the search text box. You can sort results according to
44 the displayed columns, and select entries with the mouse and
45 keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
46 button to retrieve and view them in Jalview.
49 <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>
50 <li><strong>Retrieving a unique chain for a PDB entry</strong><br>To
51 retrieve a specific chain for a PDB entry, append the PDB ID with a
52 colon followed by the chain code in the search box.<br/> e.g 1xyz:A
55 <li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
56 IDs can be specified by separating them with a semi-colon.<br/> e.g.
57 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically fetch
58 those IDs, like the default Sequence Fetcher interface.</li>
60 <li><strong>Wild card searching</strong><br>The following
61 wild cards are supported by the EMBL-EBI PDBe query service:
63 <li><strong>?</strong> matches a single character<br />The
64 search string te?t would match both test and text.</li>
65 <li><strong>*</strong> matches multiple characters<br />The
66 search string: tes* - would match test, testing, and tester.</li>
68 <em>Note:</em> you can use wildcard characters anywhere in a query
69 string.<br />For example: te*t - would match test and text. *est -
70 would match pest and test.</li>
71 <li><strong>Structured queries</strong><br />The PDBe SOLR
72 interface supports boolean query syntax, allowing quoted search
73 strings to be combined with AND, OR, and NOT. Currently, no
74 special support for constructing these queries is provided in the
75 query dialog box.</li>
78 <strong>Customising The PDB Sequence Fetcher</strong></p><p>To change the
79 displayed meta-data in the search result, click the 'Configure
80 Displayed Columns' tab, and select the fields you'd like displayed.
81 These fields can also be configured
82 <em>via</em> the Structure tab of the <a
83 href="preferences.html#structure">Jalview Desktop Preferences</a>.
86 <em>The PDB Sequence Fetcher interface was introduced in