Merge branch 'develop' into merged_2_11_2_0_to_2_12

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 7a12745..00aa8b0 100755 (executable)
--- 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 scripts" target="jalviewcltool"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -88,6 +90,10 @@
                        <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" />
@@ -133,7 +139,8 @@
                        <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"/>
                <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">