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>PDB Viewing</title>
27 <strong>Discovering and Viewing PDB Structures</strong>
29 Jalview can be used to explore the 3D structures of sequences in an
30 alignment by following the steps below:
32 <li>Select the <strong>"3D Structure Data..."</strong> option
33 from a sequence's <a href="../menus/popupMenu.html">pop-up
34 menu</a> to open the <a href="structurechooser.html">Structure
35 Chooser</a> dialog box.
37 <li>If one or more structures exists for the given
38 sequence, the <a href="structurechooser.html">Structure
39 Chooser</a> dialog will open with them listed in the results
42 <li>However, if no structure was found, the <a
43 href="structurechooser.html">Structure Chooser</a> interface
44 will present options for manual association of PDB structures.
48 <li><strong>Selecting Structures</strong><br />You can select
49 the structures to you want to open and view by selecting them with
50 the mouse and keyboard.<br />By default, if structures were
51 discovered, then some will already be selected according to the
52 criteria shown in the drop-down menu. The default criteria is
53 'highest resolution', simply choose another to pick structures in
54 a different way.<br />
56 <li><strong>Viewing Cached Structures</strong><br />If you
57 have previously downloaded structures for your sequences, they
58 can be viewed by selecting the <strong>Cached PDB
59 Entries</strong> option from the drop down menu at the top of the
62 <li>To view selected structures, click the <strong>"View"</strong>
68 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
69 2.3. Jalview 2.8.2 included support for
70 <a href="chimera.html">Chimera</a>, provided it is installed and can
71 be launched by Jalview. The default viewer can be configured in the
72 <a href="preferences.html#structure">Structure tab</a> in the
73 <strong>Tools→Preferences</strong> dialog box.
75 Structure data imported into Jalview can also be processed to
76 display secondary structure and temperature factor annotation. See
77 the <a href="xsspannotation.html">Annotation from Structure</a> page
82 If a <strong>single</strong> PDB structure is selected, one of the
83 following will happen:
87 <li>If no structures are open, then an interactive display of
88 the structure will be opened in a new window.</li>
90 <li>If another structure is already shown for the current
91 alignment, then you will be asked if you want to add and <a
92 href="jmol.html#align">align this structure</a> to the structure
93 in the existing view. (<em>new feature in Jalview 2.6</em>).
96 <li>If the structure is already shown, then you will be
97 prompted to associate the sequence with an existing view of the
98 selected structure. This is useful when working with multi-domain
99 or multi-chain PDB files.</li>
101 <li style="list-style: none">See the <a href="jmol.html">Jmol
102 </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
103 more information about the display.
109 <strong>Retrieving sequences from the PDB</strong><br>You can
110 retrieve sequences from the PDB using the <a
111 href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
112 retrieved with this service are derived directly from the PDB 3D
113 structure data, which can be viewed in the same way above. Secondary
114 structure and temperature factor annotation can also be added. <br />
117 <strong>Retrieving sequences from the PDB</strong><br>Jalview
118 will also read PDB files directly - either in PDB format, or <a
119 href="mmcif.html">mmCIF</a>. Simply load in the file as you would
120 an alignment file. The sequences of any protein or nucleotide chains
121 will be extracted from the file and viewed in the alignment window.
125 <strong>Associating a large number of PDB files to
126 sequences in an alignment</strong><br /> It is often the case when working
127 with structure alignments that you will have a directory of PDB
128 files, and an alignment involving one or more of the structures. If
129 you drag a number of PDB files onto an alignment in the Jalview
130 desktop, Jalview will give you the option of associating PDB files
131 with sequences that have the same filename. This means, for example,
132 you can automatically associate PDB files with names like '1gaq.pdb'
133 with sequences that have an ID like '1gaq'. <br /> <em>Note:
134 This feature was added in Jalview 2.7</em>
137 <em>Note for Jalview applet users:<br> Due to the applet
138 security constraints, PDB Files can currently only be imported by
139 cut and paste of the PDB file text into the text box opened by the
140 'From File' entry of the structure menu.
145 <strong>Viewing the PDB Residue Numbering</strong><br>
146 Sequences which have PDB entry or PDB file associations are
147 annotated with sequence features from a group named with the
148 associated PDB accession number or file name. Each feature gives the
149 corresponding PDB Residue Number for each mapped residue in the
150 sequence. The display of these features is controlled through the <strong>"View→Sequence
151 Features"</strong> menu item and the <a href="featuresettings.html">Feature
152 Settings dialog box</a>.
157 <strong>Switching between mmCIF and PDB format for
158 downloading files from the PDB</strong><br /> Jalview now employs the <a
159 href="mmcif.html">mmCIF format</a> for importing 3D structure data
160 from flat file and EMBL-PDBe web-service, as recommended by the
161 wwwPDB. If you prefer (for any reason) to download data as PDB files
162 instead, then first close Jalview, and add the following line to
163 your .jalview_properties file:<br />
164 <code> DEFAULT_STRUCTURE_FORMAT=PDB </code>
165 <br /> When this setting is configured, Jalview will only request
166 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
167 file support was added in Jalview 2.10.</em>
171 <em><strong>Outstanding problem with cut'n'pasted
172 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
173 via the cut'n'paste dialog box will not be correctly highlighted
174 or coloured when they are displayed in structure views, especially
175 if they contain more than one PDB structure. See the bug report at
176 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>