From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 21 Sep 2016 15:49:43 +0000 (+0100)
Subject: JAL-1841 JAL-2214 updated RNA Structure Consensus documentation
X-Git-Tag: Release_2_10_0~39^2~14
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df5ad5c09e166650d21510105f9efc3d25055b08;p=jalview.git

JAL-1841 JAL-2214 updated RNA Structure Consensus documentation
---

diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 7325439..756e6e9 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -27,28 +27,35 @@
     <strong>Alignment RNA Structure Consensus Annotation</strong>
   </p>
 
-  <p>
-    The RNA structure consensus displayed below the alignment is the
-    percentage of valid base pairs per column. It is calculated in
-    relation to a secondary structure and just paired columns are
-    calculated. The canonical Watson-Crick base pairings (A-T/U, G-C)
-    and the wobble base pair (G-T/U) are regarded as valid pairings.<br>
-    The amount of valid base pairs is indicated by the profile in the
-    Alignment Annotation row.<br> By default this calculation
-    includes gaps in columns. You can choose to ignore gaps in the
-    calculation by right clicking on the label &quot;StrConsensus&quot;
-    to the left of the structure consensus bar chart.<br>
+  <p>The RNA structure consensus displayed below the alignment gives
+    the percentage of valid base pairs per column for the first
+    secondary structure annotation shown on the annotation panel. The
+    symbol below each histogram indicates whether the majority of base
+    pairs are:
+  <ul>
+    <li>'(' - Watson-Crick (A:C, G:T)</li>
+    <li>'[' - Canonical Pairs (A:C, G:U, A:U)</li>
+    <li>'{' - Invalid Pairs (the rest)</li>
+  </ul>
+  <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
+  
+<p>By default
+    this calculation includes gaps in columns. You can choose to ignore
+    gaps in the calculation by right clicking on the label
+    &quot;StrConsensus&quot; to the left of the structure consensus bar
+    chart.<br>
   <p>
     <strong>Structure logo</strong>
   </p>
-  By clicking on the label you can also activate the structure logo. It
-  is very similar to a sequence logo but counts the numbers of base
-  pairs. There are two residues per column, the actual column and the
-  interacting base. The opening bracket is always the one on the left
-  side.
-  <br> Like sequence logos the relative amount of a specific base
-  pair can be estimated by its size in the logo. The tool tip of a
-  column gives the exact numbers for all occurring valid base pairs.
+  Right-clicking on the label allows you to enable the structure logo.
+  It is very similar to a sequence logo but instead shows the
+  distribution of base pairs. There are two residues per column, the
+  actual column and the interacting base. The opening bracket is always
+  the one on the left side.
+  <br> Like sequence logos the relative amount of a specific base pair
+  can be estimated by its size in the logo. When the logo is displayed,
+  the tool tip of a column gives the exact numbers for all occurring
+  valid base pairs.
   </p>
 </body>
 </html>