3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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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 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><strong>To view selected structures, click the <strong>"View"</strong>
66 <li>Additional structure data will be downloaded with the
67 EMBL-EBI's dbfetch service</li>
68 <li><a href="siftsmapping.html">SIFTS</a> records will also
69 be downloaded for mapping UniProt protein sequence data to PDB
75 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
76 2.3. Jalview 2.8.2 included support for
77 <a href="chimera.html">Chimera</a>, provided it is installed and can
78 be launched by Jalview. The default viewer can be configured in the
79 <a href="preferences.html#structure">Structure tab</a> in the
80 <strong>Tools→Preferences</strong> dialog box.
82 Structure data imported into Jalview can also be processed to
83 display secondary structure and temperature factor annotation. See
84 the <a href="xsspannotation.html">Annotation from Structure</a> page
89 If a <strong>single</strong> PDB structure is selected, one of the
90 following will happen:
94 <li>If no structures are open, then an interactive display of
95 the structure will be opened in a new window.</li>
97 <li>If another structure is already shown for the current
98 alignment, then you will be asked if you want to add and <a
99 href="jmol.html#align">align this structure</a> to the structure
100 in the existing view. (<em>new feature in Jalview 2.6</em>).
103 <li>If the structure is already shown, then you will be
104 prompted to associate the sequence with an existing view of the
105 selected structure. This is useful when working with multi-domain
106 or multi-chain PDB files.</li>
108 <li style="list-style: none">See the <a href="jmol.html">Jmol
109 </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
110 more information about the display.
116 <strong>Retrieving sequences from the PDB</strong><br>You can
117 retrieve sequences from the PDB using the <a
118 href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
119 retrieved with this service are derived directly from the PDB 3D
120 structure data, which can be viewed in the same way above. Secondary
121 structure and temperature factor annotation can also be added. <br />
123 <br>Jalview will also read PDB files directly - either in PDB
124 format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
125 as you would an alignment file. The sequences of any protein or
126 nucleotide chains will be extracted from the file and viewed in the
131 <strong>Associating a large number of PDB files to
132 sequences in an alignment</strong><br /> It is often the case when working
133 with structure alignments that you will have a directory of PDB
134 files, and an alignment involving one or more of the structures. If
135 you drag a number of PDB files onto an alignment in the Jalview
136 desktop, Jalview will give you the option of associating PDB files
137 with sequences that have the same filename. This means, for example,
138 you can automatically associate PDB files with names like '1gaq.pdb'
139 with sequences that have an ID like '1gaq'. <br /> <em>Note:
140 This feature was added in Jalview 2.7</em>
143 <em>Note for Jalview applet users:<br> Due to the applet
144 security constraints, PDB Files can currently only be imported by
145 cut and paste of the PDB file text into the text box opened by the
146 'From File' entry of the structure menu.
151 <strong>Viewing the PDB Residue Numbering</strong><br>
152 Sequences which have PDB entry or PDB file associations are
153 annotated with sequence features from a group named with the
154 associated PDB accession number or file name. Each feature gives the
155 corresponding PDB Residue Number for each mapped residue in the
156 sequence. The display of these features is controlled through the <strong>"View→Sequence
157 Features"</strong> menu item and the <a href="featuresettings.html">Feature
158 Settings dialog box</a>.
163 <strong>Switching between mmCIF and PDB format for
164 downloading files from the PDB</strong><br /> Jalview now employs the <a
165 href="mmcif.html">mmCIF format</a> for importing 3D structure data
166 from flat file and EMBL-PDBe web-service, as recommended by the
167 wwwPDB. If you prefer (for any reason) to download data as PDB files
168 instead, then first close Jalview, and add the following line to
169 your .jalview_properties file:<br />
170 <code> PDB_DOWNLOAD_FORMAT=PDB </code>
171 <br /> When this setting is configured, Jalview will only request
172 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
173 file support was added in Jalview 2.10.</em>
177 <em><strong>Outstanding problem with cut'n'pasted
178 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
179 via the cut'n'paste dialog box will not be correctly highlighted
180 or coloured when they are displayed in structure views, especially
181 if they contain more than one PDB structure. See the bug report at
182 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>