From 4497a70ab5bf22b6b6a16c723949625fcca4845b Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Oct 2016 15:52:49 +0100
Subject: [PATCH] JAL-2189 JAL-2152 Chimera 1.11.1 minimum version requirement

---
 help/html/features/chimera.html |   34 +++++++---------------------------
 help/html/whatsNew.html         |    4 ++++
 2 files changed, 11 insertions(+), 27 deletions(-)

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 0569513..98d8966 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -28,43 +28,23 @@
   </p>
   <p>
     Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
-    (http://www.cgl.ucsf.edu/chimera/) has been integrated into Jalview
-    for interactively viewing structures opened by entries in the <strong>&quot;Structure&quot;</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). Chimera is
-    available from the Jalview desktop, provided Chimera has been
-    separately installed.
+    (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
+    structures opened via the <a href="structurechooser.html"><strong>&quot;View
+        Structure Data..&quot;</strong> dialog</a>.
   </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).
+    differs from the standard paths searched by Jalview).<br />
+    <strong>Please make sure your version of Chimera is up to
+      date. Jalview requires at least Chimera version 1.11.1</strong>
+  </p>
   <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
-        Structure&#8594;</strong> submenu allows a single PDB structure to be chosen
-      for display from the available structures for a sequence.
-    </li>
-    <li>The <strong>&quot;Structure&#8594;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>&quot;Structure&#8594;View all <em>N</em>
-        representative structures
-    </strong> option will open a new window containing exactly one structure per
-      currently selected sequence.<br /></li>
-  </ul>
-  <br> 
-</p> -->
   <p>
     <a name="align"><strong>Superposing structures based on
         their aligned sequences</strong></a><br> If several structures are
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 1743f1c..545d55b 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -56,6 +56,10 @@
             to UniProt sequences</a>, even for structures containing
           multiple copies of a sequence.</li>
         <li><strong>Import structures as mmCIF</strong>. Jalview
+        <li><strong>Chimera users will need to upgrade to
+            1.11.1.</strong>If you use Chimera to view structures downloaded by
+          Jalview 2.10, you will need to make sure you are running the
+          latest version of <a href="features/chimera.html">Chimera</a>.</li>
           now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
           This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
       </ul></li>
-- 
1.7.10.2