X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=433139d1812dd460b196cb8c455f27dc330b86a5;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=9f1942c7d9034112f1f1a10cc4ecee61aabfd30d;hpb=cc7e689bec78376ed404e42ec8f425496bb435c0;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 9f1942c..433139d 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,10 +24,12 @@
 	<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="The Java Console, Logging and Reporting Bugs" target="logging" />
+        		<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>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -88,12 +90,17 @@
 			<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" />
@@ -133,7 +140,7 @@
 			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
 			<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"/>
@@ -162,12 +169,16 @@
 			<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: summary" target="clarguments" />
+			<tocitem text="Command Line: introduction" target="clarguments-intro" />
+			<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>
+		<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" />