- <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" />