On Sep 11, 2023, at 7:19 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

One thing to keep in mind is that the installation has to be compatible with the version of Python ChimeraX is using, which is Python 3.9 for ChimeraX 1.6.1 and Python 3.11 for the daily build

What I should have say more explicitly here is that you need to build/install mdtraj with the same version of Python that the ChimeraX you're targeting uses.