From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 25 Sep 2012 11:38:02 +0000 (+0100)
Subject: JAL-970 document interactive RNA secondary structure editing
X-Git-Tag: Jalview_2_9~293
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dbd3467478986ab9584aa39e2c9fe51ad606501b;p=jalview.git

JAL-970 document interactive RNA secondary structure editing
---

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 01353aa..eeed82e 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -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