For the links to appear the documentation in your bundle needs to be organized the same way the user documentation is organized. See the section on Bundle Help Files in the documentation for writing bundles, https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html. And the linked to examples for commands, https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_command.html..., and tools, https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html.... Shown by example, but not explicitly stated, is that the bundle documentation needs to be included in your bundle. Usually by adding <DataFiles><DataDir>docs</DataDir></DataFiles> to bundle_info.xml.     HTH,     Greg On 5/2/2022 9:20 AM, William Hofsøy via ChimeraX-users wrote:

Hi, I am currently writing some help pages for my tools and noticed that on the Tool index page in the chimerax help pages my tools get listed but not hyperlinked to the pages I write. Is there a way I can fix this? I also noticed that my commands are not listed here.

--William

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