X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=6d7c9482fd6abffc5fa2da3837bd4be8fb4896d1;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=a0c7fe6b066b870fcc9fb3028b2dfbae2f945af1;hpb=2720003e4d3537f99f6c1643561cbdb3d0120d2d;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a0c7fe6..6d7c948 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,11 +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="Virtual Features in CDS/Protein Views" target="splitframe.virtualfeats"/>
-				<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
-				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-				
+			<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" />
@@ -88,12 +87,17 @@
 			<tocitem text="ClustalX" target="colours.clustal" />
 			<tocitem text="Zappo" target="colours.zappo" />
 			<tocitem text="Taylor" target="colours.taylor" />
+			<tocitem text="gecos Flower" target="colours.gecos-flower" />
+			<tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+			<tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+			<tocitem text="gecos Ocean" target="colours.gecos-ocean" />
 			<tocitem text="Hydrophobicity" target="colours.hydro" />
 			<tocitem text="Helix propensity" target="colours.helix" />
 			<tocitem text="Strand propensity" target="colours.strand" />
 			<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" />
@@ -131,9 +135,10 @@
 		</tocitem>
 		<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
 			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-			<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+			<tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
 			<tocitem text="Jmol Viewer" target="pdbjmol" />
-			<tocitem text="Chimera Viewer" target="chimera" />			
+			<tocitem text="Chimera/X Viewer" target="chimera" />
+			<tocitem text="Pymol Viewer" target="pymol" />			
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
@@ -156,16 +161,22 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		<tocitem text="Scripting with Groovy" target="groovy">
 			<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" />