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 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 will also read PDB files directly - either in PDB format, or <a
118 href="mmcif.html">mmCIF</a>. Simply load in the file as you would
119 an alignment file. The sequences of any protein or nucleotide chains
120 will be extracted from the file and viewed in the alignment window.
124 <strong>Associating a large number of PDB files to
125 sequences in an alignment</strong><br /> It is often the case when working
126 with structure alignments that you will have a directory of PDB
127 files, and an alignment involving one or more of the structures. If
128 you drag a number of PDB files onto an alignment in the Jalview
129 desktop, Jalview will give you the option of associating PDB files
130 with sequences that have the same filename. This means, for example,
131 you can automatically associate PDB files with names like '1gaq.pdb'
132 with sequences that have an ID like '1gaq'. <br /> <em>Note:
133 This feature was added in Jalview 2.7</em>
136 <em>Note for Jalview applet users:<br> Due to the applet
137 security constraints, PDB Files can currently only be imported by
138 cut and paste of the PDB file text into the text box opened by the
139 'From File' entry of the structure menu.
144 <strong>Viewing the PDB Residue Numbering</strong><br>
145 Sequences which have PDB entry or PDB file associations are
146 annotated with sequence features from a group named with the
147 associated PDB accession number or file name. Each feature gives the
148 corresponding PDB Residue Number for each mapped residue in the
149 sequence. The display of these features is controlled through the <strong>"View→Sequence
150 Features"</strong> menu item and the <a href="featuresettings.html">Feature
151 Settings dialog box</a>.
156 <strong>Switching between mmCIF and PDB format for
157 downloading files from the PDB</strong><br /> Jalview now employs the <a
158 href="mmcif.html">mmCIF format</a> for importing 3D structure data
159 from flat file and EMBL-PDBe web-service, as recommended by the
160 wwwPDB. If you prefer (for any reason) to download data as PDB files
161 instead, then first close Jalview, and add the following line to
162 your .jalview_properties file:<br />
163 <code> PDB_DOWNLOAD_FORMAT=PDB </code>
164 <br /> When this setting is configured, Jalview will only request
165 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
166 file support was added in Jalview 2.10.</em>
170 <em><strong>Outstanding problem with cut'n'pasted
171 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
172 via the cut'n'paste dialog box will not be correctly highlighted
173 or coloured when they are displayed in structure views, especially
174 if they contain more than one PDB structure. See the bug report at
175 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>