Merge: 497958b 68dcaa7

[jalview.git] / help / html / na / index.html

diff --git a/help/html/na/index.html b/help/html/na/index.html
index f3c4a56..844b6b7 100644 (file)
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -67,7 +67,7 @@ td {
                        as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
                        output consensus RNA secondary structure lines in the line normally
                        reserved for the Clustal consensus line in a clustal file.</li>
-               <!-- <li><em>RNAML</em> - (coming soon) - Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li> -->
+               <li><em>RNAML</em> Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li>
        </ul>
        <p>
                <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
@@ -85,6 +85,10 @@ td {
                                Visualization in VARNA</a> - allows linked viewing of the consensus or
                        an individual sequence's structure</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>
+         
        <p><strong>Limitations when working with RNA in Jalview</strong><br/>
        Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
        </br>