X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=6d7c9482fd6abffc5fa2da3837bd4be8fb4896d1;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=3308456f6d04318efb4b1d89185629efa363f092;hpb=7283c5058e1ae501fe3ab99f6a6453afc6bf8240;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 3308456..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 scripts" 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" />
@@ -100,6 +97,7 @@
 			<tocitem text="Turn propensity" target="colours.turn" />
 			<tocitem text="Buried index" target="colours.buried" />
 			<tocitem text="Nucleotide colours" target="colours.nucleotide" />
+			<tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
 			<tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
 			<tocitem text="Blosum62" target="colours.blosum" />
 			<tocitem text="by Percentage Identity" target="colours.pid" />
@@ -168,12 +166,17 @@
 			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 		</tocitem>
 		<tocitem text="Command Line" target="commandline" expand="false">
-			<tocitem text="Command Line Arguments" target="clarguments" />
-    <tocitem text="Memory Settings" target="memory" expand="false"/>
-    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
-    </tocitem>
+			<tocitem text="Command Line: introduction and reference" target="clarguments" />
+			<tocitem text="Command Line: basic usage" target="clarguments-basic" />
+			<tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
+			<tocitem text="Command Line: argument files" target="clarguments-argfiles" />
+			<tocitem text="Command Line: reference" target="clarguments-reference" />
+			<tocitem text="Command Line: old command line arguments" target="clarguments-old" />
+		</tocitem>
+		<tocitem text="Memory Settings" target="memory" expand="false"/>
+		<tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
 		<tocitem text="Privacy" target="privacy" />
-	</tocitem>
+    </tocitem>
 	<tocitem text="Useful information" expand="true">
 		<tocitem text="Amino Acid Table" target="aminoAcids" />
 		<tocitem text="Amino Acid Properties" target="aaProperties" />