X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=a6c62df18c93873e451dbb30dda9b2ddb30e4820;hb=59d682209891099d46b960509907c79e3fb276fe;hp=01353aa478d3fe77441008b9219ccf8894ffd1fc;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 01353aa..a6c62df 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -27,11 +27,15 @@
   Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up 
   menu obtained by right-clicking the label), or re-ordered by dragging the label to a new 
   position with the left mouse button.</p>
-<p>Web services can also add annotation to an alignment (see the
-  <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
-  annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations 
-  File</a> dragged into the alignment window or loaded from the
-  alignment's file menu.</p>
+<p>
+Web services can also add annotation to an alignment (see the <a
+href="../webServices/jnet.html">JNet</a> and <a
+href="../webServices/proteinDisorder.html">Disorder</a> protein
+structure prediction services), and as of Jalview 2.08 quantitative
+and symbolic annotations can be added to an alignment via an <a
+href="annotationsFormat.html">Annotations File</a> dragged into the
+alignment window or loaded from the alignment's file menu.
+</p>
 <p><strong>Interactive Alignment Annotation</strong></p>
 <p>
 Annotation rows are added using the <strong>Annotation Label</strong>
@@ -82,6 +86,16 @@ arrow oriented from left to right), and optional text label (see
 below). A dialog box will open for you to enter the text. Consecutive
 arrows will be joined together to form a single green arrow.</em>
 </li>
+<li><a name="rna">RNA Helix</a> (only shown when working with nucleotide sequences)<br>
+<em>Mark selected positions as participating in a base pair
+either upstream or downstream. When the dialog box opens, enter a
+'(' to indicate these bases pair with columns upstream (to right),
+and ')' to indicate this region pairs with bases to the left of the
+highlighted columns.<br />If any brackets do not match up, then an
+orange square will highlight the first position where a bracket was
+found not to match.
+</em>
+</li>
 <li>Label<br><em>Set the text label at the selected positions. A
 dialog box will open for you to enter the text.  If
 more that one consecutive position is marked with the same label, only
