<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
+ <p>
+ <strong>Viewing PDB Structures</strong>
+ </p>
+ Jalview can be used to view protein structures by following the steps below:
+ <ol>
+ <li>Select the <strong>"View Structure"</strong> option from a
+ sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
+ <ul>
+ <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
+ dialogue is opened with a list of the found structures meta-data.</li>
+ <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
+ </ul>
+ </li>
+ <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+ on the desired structure(s) in the list, or automatically by
+ using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+ criteria like quality, resolution, etc.</li>
+ <li>When the desired structure(s) have been selected, they can be
+ viewed by clicking the <strong>"View"</strong> button below the summary list.
+ </li>
-<p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure→"</strong> submenu from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
-A <a href="jmol.html">Jmol viewer</a> has been included since Jalview 2.3. Jalview 2.8.2 added support for <a href="https://www.cgl.ucsf.edu/chimera/">Chimera</a>,
-provided this has been separately installed. Choice of default viewer is configurable in the Preferences <a href="preferences.html#structure">Structure tab</a>.
-
-<p>The following menu entries are provided for viewing structure data<br>
+ </ol>
+
+ The
+ <a href="jmol.html">Jmol viewer</a> has been included since Jalview
+ 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
+ installed and can be launched by Jalview. The default viewer can be
+ configured in the
+ <a href="preferences.html#structure">Structure tab</a> in the
+ <strong>Tools→Preferences</strong> dialog box.
+ <p>
+ Structure data imported into Jalview can also be processed to display
+ secondary structure and temperature factor annotation. See the <a
+ href="xsspannotation.html">Annotation from Structure</a> page for
+ more information.
+ </p>
+ <!--
+ <p>The following menu entries are provided for viewing structure data
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
<em>The View representative structures option was introduced in
Jalview 2.8.1</em></li>
</ul>
-</p>
+</p> -->
-<p>If a single pdb
+<p>If a <strong>single</strong> pdb
structure is selected, one of the following will happen:</p>
<ul>
<li style="list-style: none">See the <a href="jmol.html">Jmol
</a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
- <p><strong>Associating PDB files with Sequences</strong></p>
- <p>To associate PDB files with a sequence, right click on a sequence
-ID and select "Structure<strong>→</strong> Associate Structure with
-Sequence", and one of the submenus:</p>
-
-<ul>
- <li>From File - You can load a PDB file from the local machine or
- network and associate it with the selected sequence. PDB files
- associated in this way will also be saved in the <a
- href="jalarchive.html">Jalview Archive file</a>.<br>
- </li>
-
- <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the
- EBI, to fetch the PDB file with the entered Id.<br>
- </li>
- <li>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
- EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</li>
-</ul>
<p><strong>Importing PDB Entries or files in PDB format</strong><br>
You can retrieve sequences from the PDB using the <a
have an ID like '1gaq'.
<br/><em>Note: This feature was added in Jalview 2.7</em>
</p>
-<p><em>Note for jalview applet users:<br>
+<p><em>Note for Jalview applet users:<br>
Due to the applet security constraints, PDB Files can currently only be
imported by cut and paste of the PDB file text into the text box opened
by the 'From File' entry of the structure menu.</em></p>
git://source.jalview.org / jalview.git / blobdiff