JAL-4090 what’s new and additional help docs for JAL-3858 JAL-3855

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

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index d7ff3d4..6d7c948 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,13 +23,10 @@
 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
        <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="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 text="Latest Release Notes" target="release"/>
+                       <tocitem text="Next Generation Command Line Interface" target="clarguments" />
+                       <tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
+                       <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />                            
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />