From b10940c1ac4f76bf27a91281e2afcdd2016ac73f Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 27 Aug 2015 11:51:30 +0100
Subject: [PATCH] JAL-1596 JAL-1725 JAL-1588 updates for selection in Chimera,
 save to Project, Windows Firewall

---
 help/html/features/chimera.html |   19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 11b43c8..713d6a8 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -32,6 +32,7 @@ id pop-up menu</a> (if you can't see this, then you need to <a
 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>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>&quot;Structure&#8594;View
@@ -68,9 +69,9 @@ 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.
+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>
@@ -97,10 +98,16 @@ atoms in the displayed structures. For comprehensive details of Chimera's comman
 		<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>
@@ -170,6 +177,10 @@ atoms in the displayed structures. For comprehensive details of Chimera's comman
 	</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. 
 </body>
 </html>
-- 
1.7.10.2