X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;fp=help%2Fhelp%2FhelpTOC.xml;h=6d7c9482fd6abffc5fa2da3837bd4be8fb4896d1;hb=469dc5a0e6d06a2c8a27f27b712ccfdbe3314ee4;hp=d7ff3d43837fc5cbbf94dc1ce8a9debdb9dbfdf9;hpb=f32142e854e6eadb5c85c4379d596369bd7098c5;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index d7ff3d4..6d7c948 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,13 +23,10 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
-				<tocitem text="Latest Release Notes" target="release"/>
-        		<tocitem text="Support for ChimeraX" target="chimera"/>
-				<tocitem text="Support for Pymol" target="pymol"/>
-				<tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
-				<tocitem text="Startup Memory Settings" target="startupprefs" />
-		        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
-		        <tocitem text="Command line launch" target="jalviewcltool"/>
+			<tocitem text="Latest Release Notes" target="release"/>
+			<tocitem text="Next Generation Command Line Interface" target="clarguments" />
+			<tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
+			<tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />				
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />