X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=511b85f2e2b163e6687ad9c3ee46a850dbece35c;hb=bb49a7496f16118471764acae958b416e08c152c;hp=6ceccee2b945469e6c4a6db9639c6862a78dfdf3;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6ceccee..511b85f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,22 +1,24 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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>
@@ -29,14 +31,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
   <li><strong>Selection</strong> 
     <ul>
-      <li><a name="sqreport"><strong>Sequence Details ...<br>
+      <li><a name="sqreport"><strong>Sequence Details...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
-            and database cross references</a> normally shown in the sequence's
+            and database cross references</a>&nbsp;normally shown in the sequence's
             tooltip.</em></li>
+      <li><strong>Show Annotations...<br>
+          </strong><em>Choose to show (unhide) either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><strong>Hide Annotations...<br>
+          </strong><em>Choose to hide either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><strong>Add Reference Annotations...<br>
+          </strong><em>Add to the alignment window any annotations on the selected sequences
+          which have been read from reference sources or calculated (for example, 
+          secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
       <li><strong>Edit </strong> 
         <ul>
           <li><strong>Copy</strong><br>
-            <em>Copys the selected region. In the applet version, the copied sequences 
+            <em>Copies the selected region. In the applet version, the copied sequences 
             are not available to the system clipboard.</em></li>
           <li><strong>Cut<br>
             </strong><em>Cuts the selected region from the alignment. In the applet 
@@ -148,11 +160,11 @@ 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 
@@ -169,6 +181,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 			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> 
     </ul>
   </li>
   <li><strong>Hide Sequences</strong><br>
