JAL-2214 fix docs (consistent and correct base pair terminology) and link to ‘sequenc...

[jalview.git] / help / html / calculations / structureconsensus.html

diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 756e6e9..c194a53 100755 (executable)
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -27,35 +27,37 @@
     <strong>Alignment RNA Structure Consensus Annotation</strong>
   </p>
 
     <strong>Alignment RNA Structure Consensus Annotation</strong>
   </p>
 

-  <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>
+  <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. These values are
+    shown as a histogram labeled &quot;StrucConsensus&quot;, where a
+    symbol below each bar indicates whether the majority of base pairs
+    are:<ul>
+    <li>'(' - Watson-Crick (C:G, A:U/T)</li>
+    <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
+    <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>

   </ul>
   </ul>

-  <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
-  
-<p>By default
+  <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
     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
+    &quot;StrucConsensus&quot; to the left of the structure consensus bar

     chart.<br>
     chart.<br>

+  

   <p>
   <p>

-    <strong>Structure logo</strong>
-  </p>
-  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.
+    <strong>RNA Structure logo</strong><br /> 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 <a href="consensus.html#logo">sequence
+      logos</a>, the relative amount of a specific base pair can be
+    estimated by its size in the logo, and this can be made more obvious
+    by <em>normalising</em> the logo (enabled via the popup menu). When
+    the logo is displayed, the tool tip for a column gives the exact
+    percentages for all base pairs at that position.

   </p>
 </body>
 </html>
   </p>
 </body>
 </html>