X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=cbef39851b30124d51fb71a6f2b330ecb2a67cb9;hb=d08dd6439589ba0ed4b683301dffbd19d7d68c79;hp=f458cbc2228327c96a618b90694007861163be8b;hpb=88153d5bb04acd2b8e7fbc3e6789622b77b6cf58;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index f458cbc..cbef398 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,8 +24,11 @@
 	<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="Structure Chooser" target="pdbchooser"/>
-				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
+        <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>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -49,6 +52,7 @@
 		<tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 		
 		<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+		  <tocitem text="Annotating from VCF" target="importvcf" /> 
 			<tocitem text="Viewing RNA structure" target="varna" />
 			<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 			<tocitem text="RNA Helices coloring" target="colours.rnahelices" />
@@ -60,6 +64,7 @@
 			<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>
 		
@@ -127,9 +132,10 @@
 		</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">
@@ -152,13 +158,15 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
-		<tocitem text="Memory Settings" target="memory" expand="false"/>
+    <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>
+    <tocitem text="Memory Settings" target="memory" expand="false"/>
+    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
+    </tocitem>
 		<tocitem text="Privacy" target="privacy" />
 	</tocitem>
 	<tocitem text="Useful information" expand="true">