3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>PDB Viewing</title>
27 <strong>Viewing PDB Structures</strong>
29 Jalview can be used to view protein structures by following the steps below:
31 <li>Select the <strong>"View Structure"</strong> option from a
32 sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.
34 <li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
35 dialogue is opened with a list of the found structures meta-data.</li>
36 <li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
39 <li>Choose the structure to view from the presented structures
40 summary list. This can be done either manually by clicking directly
41 on the desired structure from the list, or automatically by
42 using the filter combo-box which enables filtering on certain
43 criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </li>
44 <li>When the desired structure(s) have been selected, they can be
45 viewed by clicking the <strong>"View"</strong> button below the summary list.
51 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
52 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
53 installed and can be launched by Jalview. The default viewer can be
55 <a href="preferences.html#structure">Structure tab</a> in the
56 <strong>Tools→Preferences</strong> dialog box.
58 Structure data imported into Jalview can also be processed to display
59 secondary structure and temperature factor annotation. See the <a
60 href="xsspannotation.html">Annotation from Structure</a> page for
64 <p>The following menu entries are provided for viewing structure data
66 <li>The <strong>"Structure→View
67 Structure→</strong> submenu allows a single PDB structure to be chosen
68 for display from the available structures for a sequence.
70 <li>The <strong>"Structure→View all <em>N</em>
72 </strong> option will open a new window containing all structures associated
73 with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
74 capability was added in Jalview 2.7</em>
76 <li>The <strong>"Structure→View all <em>N</em>
77 representative structures
78 </strong> option will open a new window containing exactly one structure per
79 currently selected sequence.<br />
80 <em>The View representative structures option was introduced in
81 Jalview 2.8.1</em></li>
85 <p>If a <strong>single</strong> pdb
86 structure is selected, one of the following will happen:</p>
89 <li>If no structures are open, then an interactive display of the
90 structure will be opened in a new window.</li>
92 <li>If another structure is already shown for the current
93 alignment, then you will be asked if you want to add and <a
94 href="jmol.html#align">align this structure</a> to the structure in
95 the existing view. (<em>new feature in Jalview 2.6</em>).</li>
97 <li>If the structure is already shown, then you will be prompted
98 to associate the sequence with an existing view of the selected
99 structure. This is useful when working with multi-domain 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 more information about the display.</li>
104 <p><strong>Associating PDB files with Sequences</strong></p>
105 <p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
106 from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
107 EBI to discover PDB ids associated with the sequence. </p>
109 <p><strong>Manual association of PDB files with Sequences</strong> </p>
110 <p>To manually associate PDB files with a sequence, right click on a sequence
111 ID and select the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
114 <li><strong>From File</strong> - You can load a PDB file from the local machine or
115 network and associate it with the selected sequence. PDB files
116 associated in this way will also be saved in the <a
117 href="jalarchive.html">Jalview Archive file</a>.<br>
119 <li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest API, provided by the
120 EBI, to fetch the PDB file with the entered Id.<br>
124 <strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
126 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
127 You can retrieve sequences from the PDB using the <a
128 href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
129 this service are automatically associated with their source database
130 entry. For PDB sequences, simply select PDB as the database and enter
131 your known PDB id (appended with ':' and a chain code, if desired).<br>
132 Jalview will also read PDB files directly. Simply load in the file as
133 you would an alignment file. The sequences of any peptide chains will be
134 extracted from the file and viewed in the alignment window.</p>
137 <strong>Associating a large number of PDB files to sequences
138 in an alignment</strong><br /> It is often the case when working with
139 structure alignments that you will have a directory of PDB files, and
140 an alignment involving one or more of the structures. If you drag a
141 number of PDB files onto an alignment in the Jalview desktop, Jalview
142 will give you the option of associating PDB files with sequences that
143 have the same filename. This means, for example, you can automatically
144 associate PDB files with names like '1gaq.pdb' with sequences that
145 have an ID like '1gaq'.
146 <br/><em>Note: This feature was added in Jalview 2.7</em>
148 <p><em>Note for jalview applet users:<br>
149 Due to the applet security constraints, PDB Files can currently only be
150 imported by cut and paste of the PDB file text into the text box opened
151 by the 'From File' entry of the structure menu.</em></p>
153 <p><strong>Viewing the PDB Residue Numbering</strong><br>
154 Sequences which have PDB entry or PDB file associations are annotated
155 with sequence features from a group named with the associated PDB
156 accession number or file name. Each feature gives the corresponding PDB
157 Residue Number for each mapped residue in the sequence. The display of
158 these features is controlled through the <strong>"View→Sequence
159 Features"</strong> menu item and the <a href="featuresettings.html">Feature
160 Settings dialog box</a>.</p>
162 <p><em><strong>Outstanding problem with cut'n'pasted
163 files in Jalview 2.6 and Jalview 2.7</strong><br>
164 Structures imported via the cut'n'paste dialog box will not be correctly
165 highlighted or coloured when they are displayed in structure views,
166 especially if they contain more than one PDB structure. See the bug
167 report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>