I would discourage invoking pip from the ChimeraX executable. For plugin development, it’s best to add mdtraj as a dependency of your bundle. You can find documentation on how to do it here (XML)
or here (TOML)
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/pyproject.html
Dependencies go in a user packages folder, which helps us ensure ChimeraX has internal integrity. You can also type “pip install mdtraj” into ChimeraX’s command line (this did not work for me, and I’ll open a ticket on our bug tracker with you CC'd) or, if you really have to get something into ChimeraX’s internal site-packages folder, run (on a Mac) “/path/to/ChimeraX.app/Contents/bin/python3.9 -I -m pip install mdtraj”.
HTH,
Zach Pearson
Programmer, ChimeraX Team
UCSF RBVI
zjp@cgl.ucsf.edu
On Apr 24, 2023, at 14:33, BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am developing a chimerax plugin. My code will have some interaction with mdtraj. I need mdtraj to be installed in the python that ships with chimerax. I tried "chimerax -m pip install mdtraj" but I get all kinds of error dialogs popping up in the chimerax instance that gets launched during the installation. I terminate all the error dialogs and then exit chimerax (as the python install seems frozen) and then it indeed says installation has failed and gives unusual error messages (like setuptools was less than version 48.0.0 while chimerax reports it to be 65.x.y and even 66.x.y after upgrading).
Can someone tell me the correct syntax to use to install mdtraj in chimerax's python? Thank you.
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