X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;fp=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=e7017f0747f6f330ec836dc6e3ffcf11208bac7e;hb=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;hp=9d6a0c6b4f3bab5b07f34c6e4e428dc158c9d520;hpb=d924d4634167f98c9fd94df6714a6589c1368da3;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9d6a0c6..e7017f0 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -141,6 +141,10 @@
 							Annotations<br>
 					</strong><em>When enabled, copies any available alignment annotation
 							for this sequence to the current view.</em></li>
+              <li><strong>Set as Reference</strong> or <strong>Unmark as Reference</strong><br/>
+              Sets or unsets the reference sequence for the the alignment.
+              </li>
+              
 				<li><strong>Represent Group With (Sequence Id)</strong><br>
 					<em>All sequences in the current selection group will be
 						hidden, apart from (Sequence Id). Any edits performed on the
@@ -169,48 +173,10 @@
 				href="../features/varna.html">VARNA</a>.
 		</em>
 		</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>Associate Structure with Sequence</strong> 
-        <ul>
-          <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 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 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 
-            EBI, to retrieve all PDB ids associated with the sequences in the 
-            alignment if the sequences have valid Uniprot names or accession ids. 
-            </em></li>
-        </ul>
-      </li> 
-
-				<ul>
-					<li><strong>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>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><strong>Hide Sequences</strong><br> <em>Hides the
+    <li><strong>Hide Insertions</strong><br />
+    <em>Hides columns containing gaps in the current sequence or
+        selected region, and reveals columns not including gaps.</em>
+    <li><strong>Hide Sequences</strong><br> <em>Hides the
 				currently selected sequences in this alignment view.</em><strong><br>
 				</strong></li>
 	</ul>