Merge branch 'develop' into Release_2_9_Branch

[jalview.git] / help / html / menus / popupMenu.html

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9d6a0c6..abfd16d 100755 (executable)
--- 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
@@ -162,55 +166,17 @@
                                visible when you right-click on a sequence name. When this option is clicked, Jalview will open a <a href="../features/structurechooser.html">'Structure Chooser' </a>  
                                 dialogue with options to select the structure which will eventually be opened in
                                a 3D interactive view.<br> These entries will only be present if the sequence
-                               has <a href="../features/viewingpdbs.html">associated PDB structures</a>.
-                               <br /> If the sequence or alignment has RNA structure,
+                               has <a href="../features/viewingpdbs.html">associated PDB structures</a>.</em></li><li><strong>VARNA 2D Structure</strong><br/><em>
+                                If the sequence or alignment has RNA structure,
                                then <strong>VARNA 2D Structure</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>
                </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><a name="hideinserts"><strong>Hide Insertions</strong></a><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>