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<!--
- * 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.
*
sequence). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</p>
<p>You can set a default choice of Jmol or Chimera structure viewer in <a href="preferences.html#structure"> Preferences</a>.
You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview).
-<p>The following menu entries are provided for viewing structure data<br>
+<p>If you save your Jalview session as a project file, the state of any open Chimera windows will also be saved, and can be reopened by loading the project file on any machine with Chimera installed. <em>Since Jalview 2.9.</em>
+<!-- <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
currently selected sequence.<br /></li>
</ul>
<br>
-</p>
+</p> -->
<p><a name="align"><strong>Superposing structures based
on their aligned sequences</strong></a><br>
-<p>If several structures are available on the alignment, you may add
+If several structures are available on the alignment, you may add
additional structures to an existing Chimera view by selecting their entry
in the appropriate pop-up menu. Jalview will ask you if you wish to add
the structure to the existing alignment, and if you do, it will import
the updated alignment.<br>
</p>
<p><strong>Chimera Controls</strong><br>
-<p>The structure is by default rendered as a ribbon diagram. Moving the
+The structure is by default rendered as a ribbon diagram. Moving the
mouse over the structure brings up tooltips giving the residue name, PDB
residue number and chain code
([RES]Num:Chain). Moving the mouse over an
associated residue in an alignment window highlights the associated
-atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.</p>
+atoms in the displayed structures. When residues are selected in the Chimera window, they are highlighted on the alignment. For comprehensive details of Chimera's commands, refer to the tool's Help menu.
<p>Basic screen operations (see <a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a>
-(http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details).
+at http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html for full details).
<table border="1">
<tr>
<td><strong>Action</strong></td>
<td>alt + Click<br>
and drag</td>
</tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
</table>
</p>
<p><strong>Jalview Controls</strong>
-<p>The Jalview Chimera View window has up to five menus:
+<p>The Jalview Chimera View window has up to five menus:</p>
<ul>
<li><Strong>File<br>
</strong>
</ul>
</li>
</ul>
-</p>
+<p><strong>Chimera and Windows Firewall</strong></p>
+Jalview and Chimera communicate using Chimera's <a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST service</a> (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).<br>
+Technically this requires both Chimera and Jalview to open ports on the local network, and this may be blocked by Windows Firewall with a warning message such as<br/>
+"Windows Firewall has blocked some features of this program" (where the program may be jp2launcher.exe for Jalview Webstart, or java.exe or javaw.exe for the InstallAnywhere version).<br/>
+To allow Jalview and Chimera to interact, you may need to add permission for the program to communicate over the network. This can be done from the warning dialogue, or in Control Panel, Firewall settings.
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