From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Oct 2016 14:59:59 +0000 (+0100)
Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~10^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=23819c49b73c64e6c2bc45059d47919b7d49575b;hp=5326cbb4462396e84cdbbc178040f42b436c9146;p=jalview.git

Merge branch 'develop' of source.jalview.org/git/jalview into develop
---

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/releases.html b/help/html/releases.html
index 3a8c9f9..6eb42bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -90,11 +90,15 @@
               <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).  
             </li>
             <li>
-              <!-- -->   
+              <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10   
             </li>
             <li>
-              <!-- JAL- -->  
+              <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API   
+            </li>
+            <li>
+              <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)   
             </li>
+            <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
             <li>
               <!-- JAL- -->  
             </li>
@@ -113,7 +117,7 @@
           <ul>
             <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
             <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
-            <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+            <li><!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
             <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
             <li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
             <li><!-- JAL-2072  -->Feature based tree calculation not shown for DNA alignments</li>
@@ -154,7 +158,7 @@
             </li>
             <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
             <li>
-              <!-- JAL- -->
+              <!--  -->
             </li>
             <li>
               <!-- JAL- -->
@@ -186,7 +190,7 @@
             <li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
             <li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
             <li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
-            <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+            <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>            
             <li>
               <!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
             </li>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 1743f1c..21e6ffa 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,15 +24,13 @@
 </head>
 <body>
   <p>
-    <strong>What's new ?</strong>
+    <strong>What's new in Jalview 2.10 ?</strong>
   </p>
   <p>
     Jalview 2.10 is the next major release in the Jalview 2 series. Full
     details are in the <a href="releases.html#Jalview.2.10.0">Jalview
       2.10 Release Notes</a>, but the highlights are below.
   </p>
-  <p>
-    <strong>Highlights in Jalview 2.10</strong>
   <ul>
     <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
       transcripts and proteins can be retrieved via Jalview's new <a
@@ -58,6 +56,10 @@
         <li><strong>Import structures as mmCIF</strong>. Jalview
           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>
+        <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>
       </ul></li>
     <li><strong>UniProt Free Text Search.</strong> The new search
       dialog for UniProt allows you to browse and retrieve sequences
@@ -69,9 +71,10 @@
       sequence. The reference sequence for alignment views can also be
       saved and restored from Jalview projects.</li>
     <li><strong>Ensembl and ENA 'show cross-references'
-        support.</strong>The Calculations menu's 'Show cross-references' will now
+        support.</strong>The Calculations menu's <strong>'Show cross-references'</strong> will now
       offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
       mapping data is available for download or display.</li>
+      
   </ul>
 
 </body>