From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 10 Sep 2015 02:39:03 +0000 (+0100)
Subject: JAL-1645 JAL-1595 sort by RNA helices docs
X-Git-Tag: Release_2_10_0~440
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=817fdd1ec02b7666659f96c5ddb34a7b13e8a0e7;p=jalview.git

JAL-1645 JAL-1595 sort by RNA helices docs
---

diff --git a/help/html/na/index.html b/help/html/na/index.html
index 11549fd..e860cf4 100644
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -77,14 +77,24 @@ 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>