From cbee3032010ef9a5b4b2ff43b47747b1e7f0389b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Aug 2006 14:20:27 +0000
Subject: [PATCH] 2.1 updates

---
 help/html/menus/popupMenu.html |  109 +++++++++++++++++++++++-----------------
 1 file changed, 63 insertions(+), 46 deletions(-)

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 940e3cf..734cdc5 100755
--- 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
   accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
-  <li><strong>Define</strong> 
+  <li><strong>Selection</strong> 
     <ul>
+      <li><strong>Edit </strong> 
+        <ul>
+          <li><strong>Copy</strong><br>
+            <em>Copys 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 
+            version, the copied sequences are not available to the system clipboard.</em> 
+          </li>
+          <li><strong>To Upper Case</strong><em><strong><br>
+            </strong><em>Changes the case of selected region to lower case.</em> 
+            </em></li>
+          <li><strong>To Lower Case<br>
+            </strong><em>Changes the case of selected region to upper case.</em><strong> 
+            </strong></li>
+          <li><strong>Toggle Case</strong><br>
+            <em>Switches the case of all residues within the selected region.</em> 
+          </li>
+        </ul>
+      </li>
+      <li><strong>Output to Textbox<br>
+        </strong><em>The selection area will be output to a a text window in the 
+        selected alignment format. </em></li>
       <li><strong>Group<br>
         </strong><em>This will display a window asking for the name of the currently 
         selected group. Click OK to set the name, cancel to use the default group 
-        name. </em><strong><br>
-        </strong></li>
+        name. </em></li>
       <li><strong>Remove Group<br>
-        </strong><em>This will undefine the selected group. </em><strong> <br>
-        </strong></li>
+        </strong><em>This will undefine the selected group. </em><strong> </strong></li>
       <li><strong>Group Colour<br>
         </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> 
-        of the group.</em><strong> <br>
-        </strong></li>
+        of the group.</em><strong> </strong></li>
       <li><strong>Boxes<br>
         </strong><em>If selected the background of a residue within the selected 
         group will be coloured according to the assigned colour scheme.</em><strong> 
-        <br>
         </strong></li>
       <li><strong> Text<br>
-        </strong><em>If selected the selected group will display text. </em><strong><br>
-        </strong></li>
+        </strong><em>If selected the selected group will display text. </em></li>
       <li><strong>Colour Text<br>
         </strong><em>If selected the selected group will display text in a colour 
-        slightly darker than the background colour of that residue.</em><strong><br>
-        </strong></li>
+        slightly darker than the background colour of that residue.</em></li>
       <li><strong>Border Colour <br>
         </strong><em>Selecting this will display a &quot;Colour Chooser&quot; 
-        window. Select a colour than press OK to set the border colour of a group.<br>
-        </em></li>
-    </ul>
-  </li>
-  <li><strong>Edit </strong> 
-    <ul>
-      <li><strong>Copy</strong><br>
-        <em>Copys the selected region. In the applet version, the copied sequences 
-        are not available to the system clipboard.</em> <br>
-      </li>
-      <li><strong>Cut<br>
-        </strong><em>Cuts the selected region from the alignment. In the applet 
-        version, the copied sequences are not available to the system clipboard.</em> 
-        <em><br>
-        </em></li>
-      <li><strong>To Lower Case<br>
-        </strong><em>Changes the case of selected region to upper case.</em><strong><br>
-        </strong></li>
-      <li><strong>To Upper Case<br>
-        </strong><em>Changes the case of selected region to lower case.</em><strong><br>
-        </strong></li>
-      <li><strong>Toggle Case</strong><br>
-        <em>Switches the case of all residues within the selected region.</em> 
-        <br>
-        <br>
+        window. Select a colour than press OK to set the border colour of a group.</em><br>
       </li>
     </ul>
   </li>
-  <li><strong>Sequence <br>
+  <li><strong>Sequence Id<br>
     </strong><em>This menu is only visible if you right-click on a sequence name. 
     </em> 
     <ul>
@@ -71,18 +64,42 @@
         </strong><em>You may edit the name and description of each sequence. A 
         window will be displayed asking for a new sequence name and sequence description 
         to be entered. Press OK to accept your edit. To save sequence descriptions, 
-        you must save in Fasta, PIR or Jalview File format.</em><strong><br>
-        </strong></li>
+        you must save in Fasta, PIR or Jalview File format.</em></li>
+      <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 PDB 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; 
+            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>
       <li><strong>View PDB Structure<br>
-        </strong><em> If the sequence has a PDB file associated with it Jalview 
-        will display a 3D interactive viewer of the file.<br>
+        </strong><em> If the sequence has an associated PDB file added by one 
+        of the methods described above, Jalview will display a 3D interactive 
+        viewer of the file.<br>
         This entry is only present if the sequence has an <a href="../features/viewingpdbs.html">associated 
-        PDB structure</a>. If you can't see this entry for your sequence, and 
-        the sequence name is a uniprot identifier, then try enabling the &quot;View 
-        -&gt; Sequence Features&quot; and opening the popup menu again.</em> </li>
+        PDB structure</a>. </em></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 visible representative 
+        sequence will be propagated to the hidden sequences. </em></li>
+      <li><strong>Link</strong><br>
+        <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> 
+        Connections tab.</em><strong><br>
+        </strong></li>
     </ul>
   </li>
-  <li><strong><em>Link</em></strong><br>
+  <li><strong>Hide Sequences</strong><br>
     <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> 
     Connections tab. It is only displayed when you right click (Apple click) on 
     a sequence id. </em><strong><br>
-- 
1.7.10.2