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<head>
<title>The Jmol PDB Viewer</title>
</head>
<p><strong>The Jmol PDB Viewer</strong></p>
<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
has been integrated into Jalview for interactively viewing structures
-opened by selecting the <strong>"Structure→View PDB
-entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence
+opened by entries in the <strong>"Structure"</strong> submenu in the <a href="../menus/popupMenu.html">sequence
id pop-up menu</a> (if you can't see this, then you need to <a
href="viewingpdbs.html">associate a PDB structure</a> with the
sequence). Jmol is available from the Jalview desktop and should also
run in the JalviewLite applet, providing the browser supports Java 1.5.
If Jmol is not available, then the original <a href="pdbviewer.html">internal
pdb viewer</a> will be used as a fallback.</p>
+<p>The following menu entries are provided for viewing structure data<br>
+ <ul>
+ <li>The <strong>"Structure→View
+ Structure→</strong> submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+ <br>
+</p>
<p><a name="align"><strong>Superposing structures based
on their aligned sequences</strong></a><br>
If several structures are available on the alignment, you may add
and alpha carbon location. Double clicking an atom allows distances to
be measured from it to any other atom in the structure.</p>
<p>
-<table>
+<table border="1">
<tr>
<td><strong>Action</strong></td>
<td><strong>Windows</strong></td>
<li><strong>Select all views<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will add all associated views to the set used to colour the structure display.</em>
</li>
<li><strong>Invert selection<br></strong><em>This is only enabled when </em><strong>Select many views</strong><em> is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.</em>
- </li></ul></li>
+ </li></ul></li></ul>
<li><strong>Colours<br>
</strong>
<ul>
git://source.jalview.org / jalview.git / blobdiff