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 that you want to open and view by selecting them
50 with 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
57 previously downloaded structures are available for your
58 sequences, the structure chooser will automatically offer them
59 via the <strong>Cached PDB Entries</strong> view. If you wish
60 to download new structures, select one of the PDBe selection
61 criteria from the drop-down menu.</li>
63 <li><strong>To view selected structures, click the <strong>"View"</strong>
67 <li>Additional structure data will be downloaded with the
68 EMBL-EBI's dbfetch service</li>
69 <li><a href="siftsmapping.html">SIFTS</a> records will also
70 be downloaded for mapping UniProt protein sequence data to PDB
72 <li>A new structure viewer will open, or you will be
73 prompted to add structures to existing viewers (see <a
74 href="#afterviewbutton">below</a> for details).
79 <strong>Structure Viewers in the Jalview Desktop</strong><br/>
81 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
82 2.3. Jalview 2.8.2 included support for
83 <a href="chimera.html">Chimera</a>, provided it is installed and can
84 be launched by Jalview. The default viewer can be configured in the
85 <a href="preferences.html#structure">Structure tab</a> in the
86 <strong>Tools→Preferences</strong> dialog box.
88 Structure data imported into Jalview can also be processed to
89 display secondary structure and temperature factor annotation. See
90 the <a href="xsspannotation.html">Annotation from Structure</a> page
94 <strong><a name="afterviewbutton">After pressing the
95 'View' button in the Structure Chooser</a></strong><br /> The behaviour of
96 the 'View' button depends on the number of structures selected, and
97 whether structure views already exist for the selected structures or
100 <p>If multiple structures are selected, then Jalview will always
101 create a new structure view. The selected structures will be
102 imported into this view, and superposed with the matched positions
103 from the aligned sequences. A message in the structure viewer's
104 status bar will be shown if not enough aligned columns were
105 available to perform a superposition.</p>
107 If a <strong>single</strong> PDB structure is selected, one of the
108 following will happen:
112 <li>If no structures are open, then an interactive display of
113 the structure will be opened in a new window.</li>
115 <li>If another structure is already shown for the current
116 alignment, then you will be asked if you want to add and <a
117 href="jmol.html#align"></a> to
118 the structure in the existing view. (<em>new feature in Jalview
122 <li>If the structure is already shown, then you will be
123 prompted to associate the sequence with an existing view of the
124 selected structure. This is useful when working with multi-domain
125 or multi-chain PDB files.</li>
127 <li style="list-style: none">See the <a href="jmol.html">Jmol
128 </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
129 more information about the display.
135 <strong>Retrieving sequences from the PDB</strong><br>You can
136 retrieve sequences from the PDB using the <a
137 href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
138 retrieved with this service are derived directly from the PDB 3D
139 structure data, which can be viewed in the same way above. Secondary
140 structure and temperature factor annotation can also be added. <br />
142 <br>Jalview will also read PDB files directly - either in PDB
143 format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
144 as you would an alignment file. The sequences of any protein or
145 nucleotide chains will be extracted from the file and viewed in the
150 <strong>Associating a large number of PDB files to
151 sequences in an alignment</strong><br /> It is often the case when working
152 with structure alignments that you will have a directory of PDB
153 files, and an alignment involving one or more of the structures. If
154 you drag a number of PDB files onto an alignment in the Jalview
155 desktop, Jalview will give you the option of associating PDB files
156 with sequences that have the same filename. This means, for example,
157 you can automatically associate PDB files with names like '1gaq.pdb'
158 with sequences that have an ID like '1gaq'. <br /> <em>Note:
159 This feature was added in Jalview 2.7</em>
162 <em>Note for Jalview applet users:<br> Due to the applet
163 security constraints, PDB Files can currently only be imported by
164 cut and paste of the PDB file text into the text box opened by the
165 'From File' entry of the structure menu.
170 <strong>Viewing the PDB Residue Numbering</strong><br>
171 Sequences which have PDB entry or PDB file associations are
172 annotated with sequence features from a group named with the
173 associated PDB accession number or file name. Each feature gives the
174 corresponding PDB Residue Number for each mapped residue in the
175 sequence. The display of these features is controlled through the <strong>"View→Sequence
176 Features"</strong> menu item and the <a href="featuresettings.html">Feature
177 Settings dialog box</a>.
182 <strong>Switching between mmCIF and PDB format for
183 downloading files from the PDB</strong><br /> Jalview now employs the <a
184 href="mmcif.html">mmCIF format</a> for importing 3D structure data
185 from flat file and EMBL-PDBe web-service, as recommended by the
186 wwwPDB. If you prefer (for any reason) to download data as PDB files
187 instead, then first close Jalview, and add the following line to
188 your .jalview_properties file:<br />
189 <code> PDB_DOWNLOAD_FORMAT=PDB </code>
190 <br /> When this setting is configured, Jalview will only request
191 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
192 file support was added in Jalview 2.10.</em>
196 <em><strong>Outstanding problem with cut'n'pasted
197 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
198 via the cut'n'paste dialog box will not be correctly highlighted
199 or coloured when they are displayed in structure views, especially
200 if they contain more than one PDB structure. See the bug report at
201 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>