X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5b6535d2567f145257e45f8a496ec9c0929e0991;hb=dfabc2facf04bc805f0b6001b94de3c62b3049b0;hp=ef2b98983413fce772f0c2f3a23ba981d641234d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ef2b989..5b6535d 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -15,7 +15,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
---!>
+-->
 <head>
 <title>Alignment Window Menus</title>
 </head>
@@ -26,7 +26,7 @@
 	<ul>
 		<li><strong>Fetch Sequence</strong><br>
 		<em>Shows a dialog window in which you can select known ids from
-		Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+		Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by
 		the European Bioinformatics Institute. See <a
 			href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
 		<li><strong>Add Sequences</strong><em><br>
@@ -361,7 +361,7 @@
 		<li>Colour Scheme options: <strong>None, ClustalX,
 		Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
 		Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
-		Nucleotide, User Defined<br>
+		Nucleotide, Purine/Pyrimidine, User Defined<br>
 		</strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a
 		description of all colour schemes.</em><br>
 		</li>
@@ -387,6 +387,11 @@
 		annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
 		Colouring</a>.</em><br>
 		</li>
+		<li><strong>By RNA Helices</strong><br>
+		<em>Colours the helices of an RNA alignment loaded from a Stockholm file. See 
+		<a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+		Colouring</a>.</em><br>
+		</li>
 	</ul>
 	</li>
 	<li><strong>Calculate</strong>
