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
57 previously downloaded structures are available for your
58 sequences, the structure chooser will automatically offer them
59 via the <strong>Cached Structures</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 /> The
80 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
81 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
82 provided it is installed and can be launched by Jalview. The default
83 viewer can be configured in the <a href="preferences.html#structure">Structure
84 tab</a> in the <strong>Tools→Preferences</strong> dialog box.
87 Structure data imported into Jalview can also be processed to
88 display secondary structure and temperature factor annotation. See
89 the <a href="xsspannotation.html">Annotation from Structure</a> page
93 <img src="schooser_viewbutton.png"
94 style="width: 465px; height: 81px" /><br/> <strong><a
95 name="afterviewbutton">Controlling where the new structures
96 will be shown</a></strong>
97 <br />The Structure Chooser offers several options
98 for viewing a structure. <br/><strong>New View</strong> will open a new
99 structure viewer for the selected structures, but if there are views
100 already open, you can select which one to use, and press the <strong>Add</strong>
101 button. Jalview can automatically superimpose new structures based
102 on the linked alignments - but if this is not desirable, simple
103 un-tick the <strong>Superpose Structures</strong> checkbox.
107 <em>Superposing structures</em><br/>Jalview superposes structures using
108 the visible portions of any associated sequence alignments. A
109 message in the structure viewer's status bar will be shown if not
110 enough aligned columns were available to perform a superposition.
113 See the <a href="jmol.html">Jmol
114 </a> and <a href="chimera.html">Chimera</a> help pages for
115 more information about their capabilities.</p>
119 <strong>Retrieving sequences from the PDB</strong><br>You can
120 retrieve sequences from the PDB using the <a
121 href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
122 retrieved with this service are derived directly from the PDB 3D
123 structure data, which can be viewed in the same way above. Secondary
124 structure and temperature factor annotation can also be added. <br />
126 <br>Jalview will also read PDB files directly - either in PDB
127 format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
128 as you would an alignment file. The sequences of any protein or
129 nucleotide chains will be extracted from the file and viewed in the
134 <strong>Associating a large number of PDB files to
135 sequences in an alignment</strong><br /> It is often the case when working
136 with structure alignments that you will have a directory of PDB
137 files, and an alignment involving one or more of the structures. If
138 you drag a number of PDB files onto an alignment in the Jalview
139 desktop, Jalview will give you the option of associating PDB files
140 with sequences that have the same filename. This means, for example,
141 you can automatically associate PDB files with names like '1gaq.pdb'
142 with sequences that have an ID like '1gaq'. <br /> <em>Note:
143 This feature was added in Jalview 2.7</em>
146 <em>Note for Jalview applet users:<br> Due to the applet
147 security constraints, PDB Files can currently only be imported by
148 cut and paste of the PDB file text into the text box opened by the
149 'From File' entry of the structure menu.
154 <strong>Viewing the PDB Residue Numbering</strong><br>
155 Sequences which have PDB entry or PDB file associations are
156 annotated with sequence features from a group named with the
157 associated PDB accession number or file name. Each feature gives the
158 corresponding PDB Residue Number for each mapped residue in the
159 sequence. The display of these features is controlled through the <strong>"View→Sequence
160 Features"</strong> menu item and the <a href="featuresettings.html">Feature
161 Settings dialog box</a>.
166 <strong>Switching between mmCIF and PDB format for
167 downloading files from the PDB</strong><br /> Jalview now employs the <a
168 href="mmcif.html">mmCIF format</a> for importing 3D structure data
169 from flat file and EMBL-PDBe web-service, as recommended by the
170 wwwPDB. If you prefer (for any reason) to download data as PDB files
171 instead, then first close Jalview, and add the following line to
172 your .jalview_properties file:<br />
173 <code> PDB_DOWNLOAD_FORMAT=PDB </code>
174 <br /> When this setting is configured, Jalview will only request
175 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
176 file support was added in Jalview 2.10.</em>
180 <em><strong>Outstanding problem with cut'n'pasted
181 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
182 via the cut'n'paste dialog box will not be correctly highlighted
183 or coloured when they are displayed in structure views, especially
184 if they contain more than one PDB structure. See the bug report at
185 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>