X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;fp=help%2Fhelp%2FhelpTOC.xml;h=9f1942c7d9034112f1f1a10cc4ecee61aabfd30d;hb=3efc24bc7b7855ff135fa96e35ab1004eaeb4f5e;hp=a0c7fe6b066b870fcc9fb3028b2dfbae2f945af1;hpb=dae56c38c3f14e96308540c30f35ca8f1d917edf;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index a0c7fe6..9f1942c 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -27,7 +27,7 @@
         <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>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -131,9 +131,10 @@
 		</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 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">
@@ -156,6 +157,7 @@
 			</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>