2.1 updates

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 940e3cf..734cdc5 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -7,63 +7,56 @@
   on the alignment or on a selected sequence name. It may not be\r
   accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>\r
 <ul>\r
-  <li><strong>Define</strong> \r
+  <li><strong>Selection</strong> \r
     <ul>\r
+      <li><strong>Edit </strong> \r
+        <ul>\r
+          <li><strong>Copy</strong><br>\r
+            <em>Copys the selected region. In the applet version, the copied sequences \r
+            are not available to the system clipboard.</em> </li>\r
+          <li><strong>Cut<br>\r
+            </strong><em>Cuts the selected region from the alignment. In the applet \r
+            version, the copied sequences are not available to the system clipboard.</em> \r
+          </li>\r
+          <li><strong>To Upper Case</strong><em><strong><br>\r
+            </strong><em>Changes the case of selected region to lower case.</em> \r
+            </em></li>\r
+          <li><strong>To Lower Case<br>\r
+            </strong><em>Changes the case of selected region to upper case.</em><strong> \r
+            </strong></li>\r
+          <li><strong>Toggle Case</strong><br>\r
+            <em>Switches the case of all residues within the selected region.</em> \r
+          </li>\r
+        </ul>\r
+      </li>\r
+      <li><strong>Output to Textbox<br>\r
+        </strong><em>The selection area will be output to a a text window in the \r
+        selected alignment format. </em></li>\r
       <li><strong>Group<br>\r
         </strong><em>This will display a window asking for the name of the currently \r
         selected group. Click OK to set the name, cancel to use the default group \r
-        name. </em><strong><br>\r
-        </strong></li>\r
+        name. </em></li>\r
       <li><strong>Remove Group<br>\r
-        </strong><em>This will undefine the selected group. </em><strong> <br>\r
-        </strong></li>\r
+        </strong><em>This will undefine the selected group. </em><strong> </strong></li>\r
       <li><strong>Group Colour<br>\r
         </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
-        of the group.</em><strong> <br>\r
-        </strong></li>\r
+        of the group.</em><strong> </strong></li>\r
       <li><strong>Boxes<br>\r
         </strong><em>If selected the background of a residue within the selected \r
         group will be coloured according to the assigned colour scheme.</em><strong> \r
-        <br>\r
         </strong></li>\r
       <li><strong> Text<br>\r
-        </strong><em>If selected the selected group will display text. </em><strong><br>\r
-        </strong></li>\r
+        </strong><em>If selected the selected group will display text. </em></li>\r
       <li><strong>Colour Text<br>\r
         </strong><em>If selected the selected group will display text in a colour \r
-        slightly darker than the background colour of that residue.</em><strong><br>\r
-        </strong></li>\r
+        slightly darker than the background colour of that residue.</em></li>\r
       <li><strong>Border Colour <br>\r
         </strong><em>Selecting this will display a &quot;Colour Chooser&quot; \r
-        window. Select a colour than press OK to set the border colour of a group.<br>\r
-        </em></li>\r
-    </ul>\r
-  </li>\r
-  <li><strong>Edit </strong> \r
-    <ul>\r
-      <li><strong>Copy</strong><br>\r
-        <em>Copys the selected region. In the applet version, the copied sequences \r
-        are not available to the system clipboard.</em> <br>\r
-      </li>\r
-      <li><strong>Cut<br>\r
-        </strong><em>Cuts the selected region from the alignment. In the applet \r
-        version, the copied sequences are not available to the system clipboard.</em> \r
-        <em><br>\r
-        </em></li>\r
-      <li><strong>To Lower Case<br>\r
-        </strong><em>Changes the case of selected region to upper case.</em><strong><br>\r
-        </strong></li>\r
-      <li><strong>To Upper Case<br>\r
-        </strong><em>Changes the case of selected region to lower case.</em><strong><br>\r
-        </strong></li>\r
-      <li><strong>Toggle Case</strong><br>\r
-        <em>Switches the case of all residues within the selected region.</em> \r
-        <br>\r
-        <br>\r
+        window. Select a colour than press OK to set the border colour of a group.</em><br>\r
       </li>\r
     </ul>\r
   </li>\r
-  <li><strong>Sequence <br>\r
+  <li><strong>Sequence Id<br>\r
     </strong><em>This menu is only visible if you right-click on a sequence name. \r
     </em> \r
     <ul>\r
@@ -71,18 +64,42 @@
         </strong><em>You may edit the name and description of each sequence. A \r
         window will be displayed asking for a new sequence name and sequence description \r
         to be entered. Press OK to accept your edit. To save sequence descriptions, \r
-        you must save in Fasta, PIR or Jalview File format.</em><strong><br>\r
-        </strong></li>\r
+        you must save in Fasta, PIR or Jalview File format.</em></li>\r
+      <li><strong>Associate Structure with Sequence</strong> \r
+        <ul>\r
+          <li><strong>From File<br>\r
+            </strong><em>Load a PDB file from local disk which will be associated \r
+            with this sequence. This file will be used if the user subsequently \r
+            clicks on &quot;View PDB Structure&quot; menu item.</em></li>\r
+          <li><strong>Enter PDB id<br>\r
+            </strong><em>Enter the PDB id from an input window. This PDB id will \r
+            be used by the service WSDBFetch, provided by the EBI, to fetch the \r
+            PDB file if the user subsequently clicks on &quot;View PDB Structure&quot; \r
+            menu item. </em></li>\r
+          <li><strong>Discover PDB ids<br>\r
+            </strong><em>This will use the service WSDBFetch, provided by the \r
+            EBI, to retrieve all PDB ids associated with the sequences in the \r
+            alignment if the sequences have valid Uniprot names or accession ids. \r
+            </em></li>\r
+        </ul>\r
+      </li>\r
       <li><strong>View PDB Structure<br>\r
-        </strong><em> If the sequence has a PDB file associated with it Jalview \r
-        will display a 3D interactive viewer of the file.<br>\r
+        </strong><em> If the sequence has an associated PDB file added by one \r
+        of the methods described above, Jalview will display a 3D interactive \r
+        viewer of the file.<br>\r
         This entry is only present if the sequence has an <a href="../features/viewingpdbs.html">associated \r
-        PDB structure</a>. If you can't see this entry for your sequence, and \r
-        the sequence name is a uniprot identifier, then try enabling the &quot;View \r
-        -&gt; Sequence Features&quot; and opening the popup menu again.</em> </li>\r
+        PDB structure</a>. </em></li>\r
+      <li><strong>Represent Group With (Sequence Id)</strong><br>\r
+        <em>All sequences in the current selection group will be hidden, apart \r
+        from (Sequence Id). Any edits performed on the visible representative \r
+        sequence will be propagated to the hidden sequences. </em></li>\r
+      <li><strong>Link</strong><br>\r
+        <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
+        Connections tab.</em><strong><br>\r
+        </strong></li>\r
     </ul>\r
   </li>\r
-  <li><strong><em>Link</em></strong><br>\r
+  <li><strong>Hide Sequences</strong><br>\r
     <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
     Connections tab. It is only displayed when you right click (Apple click) on \r
     a sequence id. </em><strong><br>\r