Merge branch 'releases/Release_2_11_4_Branch'

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

diff --git a/help/help/html/menus/alwannotationpanel.html b/help/help/html/menus/alwannotationpanel.html
index cd09693..12f1242 100755 (executable)
--- a/help/help/html/menus/alwannotationpanel.html
+++ b/help/help/html/menus/alwannotationpanel.html
@@ -66,6 +66,20 @@
             (numerical or otherwise) at each position in the row. This
             is useful to export alignment quality measurements for
             further analysis.</em></li>
+        <li><strong>Colour by Annotation</strong> <br>
+          <em>Open's the <a href="../colourSchemes/annotationColouring.html">
+          Colour by Annotation</a> dialog, already configured 
+          for this annotation row.</em>
+          <br>
+          <strong>Colour by Annotation (Per-Sequence)</strong> may also be 
+          available for sequence associated annotations, such as secondary structure 
+          or AlphaFold PLDDT score annotation tracks.
+          </li>
+        <li><strong>Select/Hide columns by annotation...</strong> <br>
+          <em>Open's the <a href="../features/columnFilterByAnnotation.html">
+          select/hide by annotation</a> dialog, already configured 
+          for this annotation row.</em>
+          </li>
       </ul> <em>The following additional entries are available when the
         popup menu is opened on a consensus sequence annotation row:</em>
       <ul>
@@ -86,12 +100,31 @@
             highly variable regions.</em></li>
 
         <li>
+       </li>
         <li><strong>Copy Consensus Sequence</strong><br>
           Copies the consensus sequence to the clipboard in Fasta
           format, to allow the consensus sequence to be added to an
           alignment. Note the copied sequence is not accessible to other
           programs if Jalview is running as an applet in a web page.</li>
-      </ul></li>
+      </ul>
+      
+       <strong>Predicted Alignment Error</strong> annotation 
+       tracks have the following additional options (see 
+       <a href="../features/paematrices.html">working with 
+       PAE Matrices</a> for full details):
+       <ul>
+       <li><strong>Show Groups on Matrix</strong><br/><em>When ticked,
+       colour the columns of the matrix by the clusters on it tree.</em></li>
+       <li><strong>Cluster Matrix</strong><br/><em>Select this to calculate
+       a tree for the PAE matrix, allowing identification of reliably 
+       positioned regions of structure.</em></li>
+       <li><strong>Show Matrix</strong> or <strong>Show Tree for 
+       Matrix</strong><br/><em>Select this to either calculate
+       or show the tree calculated for the PAE matrix, allowing columns 
+       of the alignment to be clustered in order to identify reliably 
+       positioned regions of structure.</em></li>
+       </ul>
+      </li>
     <li><strong>Annotation Popup Menu<br>
     </strong><em>This menu is opened when right-clicking on the selected
         positions of an annotation.</em>