Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into develop

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

diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html
index 3a057a8..fef5bb9 100755 (executable)
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -169,6 +169,16 @@
             paste the clipboard contents to a text editor, you will see
             the format of the copied residues FASTA.
         </em></li>
+        <li><strong>Copy Highlighted region (Control Shift
+            C)</strong><br> <em>Copies each stretch of highlighted
+            residues as a new sequence on the system clipboard - you can
+            also do this by pressing &lt;CTRL&gt; &lt;SHIFT&gt; and C
+            (&lt;APPLE&gt; &lt;SHIFT&gt; and C on MacOSX). <br>Use
+            this when you want to extract sequence regions highlighted
+            as a result of a Find operation, or due to mouseovers or
+            selections made in other views such as an assocated 3D
+            structure viewer.
+        </em></li>
         <li><strong>Paste </strong>
           <ul>
             <li><strong>To New Alignment (Control Shift V)<br>
@@ -477,8 +487,9 @@
           and the intensity threshold for transition between them. </em></li>
       <li>Colour Scheme options: <strong>None, ClustalX,
           Blosum62 Score, Percentage Identity, Zappo, Taylor,
+         gecos-flower, gecos-blossom, gecos-sunset, gecos-ocean,
           Hydrophobicity, Helix Propensity, Strand Propensity, Turn
-          Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+          Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
           Defined<br>
       </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
           for a description of all colour schemes.
@@ -547,7 +558,7 @@
     <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the 
     <a href="../calculations/calculations.html">calculations dialog</a> for
         for calculating <a href="../calculations/tree.html">trees</a> or
-         <a href="../calculations/pca.html">principle component analysis 
+         <a href="../calculations/pca.html">principal component analysis 
          plots</a> on the alignment or the currently selected
         region. 
       </em><br></li>