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'Help files updated with RNA stuff' merge; JAL-580
[jalview.git] / help / html / menus / alignmentMenu.html
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ef2b989..5b6535d 100755 (executable)
--- 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>