From 01dd726fbb6c68bd834304e49eef1d72cc9586f4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 17 May 2017 15:39:17 +0100
Subject: [PATCH] JAL-2447 JAL-2295 JAL-2296 documenting as experimental
 features

---
 help/html/features/chimera.html  |   32 +++++++++++++++++++++++++++++---
 help/html/menus/desktopMenu.html |    1 +
 help/html/releases.html          |   25 ++++++++++++++-----------
 3 files changed, 44 insertions(+), 14 deletions(-)

diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 5ae00af..89a29c9 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -211,10 +211,36 @@
             structure in the alignment. The regions used to calculate
             the superposition will be highlighted using the 'Cartoon'
             rendering style, and the remaining data shown as a chain
-            trace.<br>
+            trace.<br/><br/>
         </em></li>
-      </ul></li>
-    <li><strong>Help<br>
+        <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
+          <em>
+            These are only available if the <strong>Tools&#8594;Enable
+            Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
+          <ul>
+            <li><strong>Write Jalview features</strong><br />
+              <em>Selecting this option will create new residue attributes
+              for any features currently visible in the associated
+              alignment views, allowing those positions to be selected
+              and analysed with via Chimera's 'Render by Attribute' tool
+              (found in the Tools submenu called Structure Analysis).<br />
+            <br />If you use this option, please remember to select the
+              <em>Refresh Menus</em> option in Chimera's Render by
+              Attribute dialog box in order to see the attributes
+              derived from Jalview sequence features.</em></li>
+            <li><strong>Fetch Chimera Attributes</strong><br />
+              <em>This submenu lists available Chimera residue attributes
+              that can be imported as Jalview features on associated
+              sequences.<br />This is particularly useful for
+              transferring quantitative positional annotation. For
+              example, structure similarity for an alignment can be
+              visualised by transferring the local RMSD attributes
+              generated by Chimera's Match->Align tool onto aligned
+              sequences and displayed with a <a
+              href="featureschemes.html">Graduated feature colour
+                scheme</a>.</em></li>
+          </ul></li>
+        <li><strong>Help<br>
     </strong>
       <ul>
         <li><strong>Chimera Help<br>
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 20e784b..a93ce4b 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -86,6 +86,7 @@
             the <a href="../features/groovy.html">Groovy Console</a> for
             interactive scripting.
         </em><strong><br></strong></li>
+        <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em>
 
       </ul></li>
     <li><strong>Vamsas</strong> <em>For more details, read the
diff --git a/help/html/releases.html b/help/html/releases.html
index 4406304..12b6706 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -82,21 +82,24 @@ li:before {
           </ul>
           <em>Application</em>
           <ul>
-          <li><!-- JAL-2447 --><em>Experimental Features</em>Checkbox in Desktop's Tools menu to hide or show untested features in the application<ul>
-                <li>
-                  <!-- JAL-2295 -->Entry in Chimera menu to create attributes on a structure in
-                  from its associated sequence's features in Jalview
-                </li>
-                <li>
-                  <!-- JAL-2296 -->Entry in Chimera menu to create sequence features in Jalview
-                  from structure attributes in Chimera
-                </li>
-              </ul></li>
-          <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
+            <li>
+              <!-- JAL-2447 -->
+              Experimental Features Checkbox in Desktop's Tools
+              menu to hide or show untested features in the application.
+            </li>
+            <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
           <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>  
           <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
           
           </ul>
+          <em>Experimental features</em>
+          <ul>
+            <li>
+              <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
+              to transfer Chimera's structure attributes as Jalview
+              features, and vice-versa.
+            </li>
+          </ul>
           <em>Applet</em>
           <ul>
           <li><!--  --></li>
-- 
1.7.10.2