X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fna%2Findex.html;h=e860cf4b05619a26bf8c80e5320b9bd798cf047e;hb=a49ce69b89678b3e6ba3c1a61b62d61cc9ee7342;hp=6bac556cceb9c47c7fa1920285d81c63cfcbc61e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/help/html/na/index.html b/help/html/na/index.html
index 6bac556..e860cf4 100644
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -1,22 +1,24 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
 <head>
 <title>Nucleic Acid Support</title>
 <style type="text/css">
@@ -65,7 +67,7 @@ td {
 			as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
 			output consensus RNA secondary structure lines in the line normally
 			reserved for the Clustal consensus line in a clustal file.</li>
-		<!-- <li><em>RNAML</em> - (coming soon) - Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li> -->
+		<li><em>RNAML</em> Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li>
 	</ul>
 	<p>
 		<strong>RNA Secondary Structure Visualization and Analysis</strong><br />
@@ -75,14 +77,28 @@ td {
 	<ul>
 		<li><a href="../colourschemes/rnaHelicesColouring.html">RNA
 				Helix colouring</a> - highlights columns of alignment involved in
-			particular RNA helices.</li>
-		<li><a href="../calculations/structureconsensus.html">Base Pair
+			particular RNA helices, Uses the first displayed secondary structure annotation.</li>
+      <li><a href="../calculations/structureconsensus.html">Base Pair
 				Conservation Analysis</a> - shown as a histogram and base-pair logo
-			below the alignment.</li>
+			below the alignment. Uses the first displayed secondary structure annotation row.</li>
 		<li><a href="../features/varna.html">2D Structure
 				Visualization in VARNA</a> - allows linked viewing of the consensus or
-			an individual sequence's structure</li>
-	</ul>
+			an individual sequence's structure. Accessed via the Sequence ID popup menu.</li>
+    <li><strong>per sequence secondary structure
+        annotation</strong><br /> Sequence associated secondary structure
+      annotation imported via stockholm, PDB files, or other sources can
+      be shown on the alignment with the <strong>Colours&#8594;By
+        Annotation</strong> dialog box. Colours are assigned according to RNA
+      helix topology number (number of distinct nested helices).
+      Alignments can also be sorted by RNA helix secondary structure
+      topology number, <em>via</em> the <strong>Calculations&#8594;Sort&#8594;By
+        Annotation&#8594;Secondary Structure</strong> option (only present when
+      per-sequence secondary structure is available).</li>
+  </ul>
+	<p><strong>Pseudo-knots</strong><br/>
+	  Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.<br/>
+  Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.</p>
+	  
 	<p><strong>Limitations when working with RNA in Jalview</strong><br/>
 	Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
 	</br>
