Thanks for the help Eric. I am pretty close to everything working but I think this traj2nmr install approach might be a dead end. In my chimerax tool I have this at the beginning: if importlib.util.find_spec('traj2nmr') is None: app_dir = pathlib.Path(__file__).parent.resolve() subprocess.run(["python3", app_dir / 'Installable' / 'install_traj2nmr.py', sys.executable]) Then in my install_traj2nmr.py file that gets called by the above code I have this: this_files_dir = pathlib.Path(__file__).parent.resolve() chimerax = sys.argv[1] os.system(f"cd {this_files_dir}/traj2nmr; {chimerax} --nogui --script 'setup.py install' --exit") And it ALMOST works. Unfortunately it seems that I might need sudo access to run that command. This is the info Chimera gives back when it tries to run my code: /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. dist.fetch_build_eggs(dist.setup_requires) running install /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 13] Permission denied: '/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/test-easy-install-134656.write-test' There is a paragraph of explanation saying maybe I need root access. So, am I at a dead end? Or can you think of a workaround? Thanks for any insight. ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, August 15, 2023 6:18 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: BARRY E DEZONIA <barry.dezonia@wisc.edu> Subject: Re: [chimerax-users] Plugin development questions On Aug 15, 2023, at 4:11 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: the traj2nmr executable module is importable