<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>The Jmol PDB Viewer</title>
</head>
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>
+<!-- <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
Jalview 2.8.1</em></li>
</ul>
<br>
-</p>
+</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>
controls the behaviour of single and double mouse clicking on the
structure, and the 'Console' option opens the Jmol scripting console.</p>
<p>The state of each Jmol display is stored within <a
- href="jalarchive.html">jalview archives</a> as a Jmol state recovery
+ href="jalarchive.html">Jalview archives</a> as a Jmol state recovery
script file. This means that any Jmol visualization effects that you add
beyond those provided by Jalview will be able to be stored and recovered
along with the displayed alignments in Jalview.</p>
git://source.jalview.org / jalview.git / blobdiff