X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=e28c7e1c88a87978bd7f4bc248ee9152801f534b;hb=c2214808f64b811a25cec10399dcff38db0c592c;hp=35377819f759fd0cb3bbaa0961cec33829d80fcc;hpb=111dd186e61e22f4145272494d14b038df528c17;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 3537781..e28c7e1 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,21 +1,24 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <head>
 <title>Popup Menu</title>
 </head>
@@ -59,18 +62,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
       <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
         <em>Opens the dialog box for creating sequence features over the currently 
         selected region on each selected sequence.</em></li>
-      <li><strong>Group</strong><br>
-        <em>Group Operations</em> 
-        <ul>
-          <li><strong>Group</strong><em>This is the first entry in the
-	  menu, and will display the currently selected group's
-	  name. Selecting it displays a window allowing the name and
-	  description for this group to be edited. Click OK to set the
-	  new name and decription, and cancel to leave the existing
-	  name and description unchanged.</em></li>
+      <li><strong>Create Group<br>
+            </strong><em>This will define a new group from the current selection.</em><strong> 
+            </strong></li>
           <li><strong>Remove Group<br>
             </strong><em>This will undefine the selected group. </em><strong> 
             </strong></li>
+          <li><strong>Edit (New) Group</strong><br>
+        <em>Group Editing Menu</em> <br />Options in this menu modify
+					the name and display properties of the currently selected group, or
+					a new group defined using the current selection.
+					<ul>
+          <li><strong>Name: &lt;Group&gt;</strong> or <strong>Edit name and description</strong><br><em>The first entry in the
+	  menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
+	  description for this group to be edited. Click OK to set the
+	  new name and decription, and cancel to leave the existing
+	  name and description unchanged.</em></li>
           <li><strong>Group Colour<br>
             </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> 
             of the group.</em><strong> </strong></li>
@@ -143,11 +150,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
           <li><strong>From File<br>
             </strong><em>Load a PDB file from local disk which will be associated 
             with this sequence. This file will be used if the user subsequently 
-            clicks on &quot;View PDB Structure&quot; menu item.</em></li>
+            clicks on &quot;View Structure&quot; menu item.</em></li>
           <li><strong>Enter PDB id<br>
             </strong><em>Enter the PDB id from an input window. This PDB id will 
             be used by the service WSDBFetch, provided by the EBI, to fetch the 
-            PDB file if the user subsequently clicks on &quot;View PDB Structure&quot; 
+            PDB file if the user subsequently clicks on its &quot;View Structure&quot; 
             menu item. </em></li>
           <li><strong>Discover PDB ids<br>
             </strong><em>This will use the service WSDBFetch, provided by the 
@@ -161,7 +168,26 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         of the methods described above, Jalview will open a 3D interactive 
         view of the file.<br>
         These entries will only be present if the sequence has <a
-			href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
+			href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
+			If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
+      </li>
+      <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
+  <ul>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        structures<br/>
+    </strong><em>Opens a new window containing all structures associated
+      with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
+      capability was added in Jalview 2.7)</em>
+    </li>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures<br/>
+    </strong><em>Open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    (The View representative structures option was introduced in
+        Jalview 2.8.1)</em></li>
+  </ul>
+  <br> <li>
+      
       </li>
     </ul>
   </li>
