X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=f6bb7c71309f947a5fdcd056d3492b3c759a5ad9;hb=590fbc1d8dd620511a02a77596631764219c370c;hp=5374e1a6b9627bad05b60f5d49469fa48a231799;hpb=076ec2ac8a7b1488476454c36b6a23255bed1529;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 5374e1a..f6bb7c7 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,9 +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="VCF Variant Attributes" target="importvcf.attribs"/>
-				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-				
+        		<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" />
@@ -62,6 +65,7 @@
 			<tocitem text="Feature Colourschemes" target="features.featureschemes" />
 			<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
 			<tocitem text="Editing Sequence Features" target="seqfeatedit" />
+			<tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
 			<tocitem text="HTML annotation report" target="io.seqreport" />
 		</tocitem>
 		
@@ -86,12 +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" />
@@ -129,9 +138,10 @@
 		</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">
@@ -154,16 +164,22 @@
 			</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: 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 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" />