id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9025	Issue with 'jax' module when opening .pkl files in ChimeraX	sritharan@…	Tom Goddard	"{{{
Dear ChimeraX Support,

I am currently experiencing an issue with ChimeraX that I am hoping you can help me with. When I attempt to open .pkl files using ChimeraX, I receive the following error message:

arduino

ModuleNotFoundError: No module named 'jax'
File ""/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/alphafold/pae.py"", line 887, in read_pickle_pae_matrix
p = pickle.load(f)

This error message suggests that the 'jax' module, which is a dependency for these .pkl files, is not found.

To try to resolve this issue, I have attempted to install 'jax' and 'jaxlib' using pip, specifically for Python 3.9 as indicated by the error message. Despite successfully installing 'jax' and 'jaxlib' in my Python 3.9 environment (as far as I can tell), I continue to encounter the same error message in ChimeraX.

Given that the error persists even after installing 'jax' and 'jaxlib', I suspect that ChimeraX might be using a different Python environment where these modules are not installed. However, I am not sure how to configure ChimeraX to use the correct Python environment, or if this is indeed the source of the problem.

I would greatly appreciate any guidance you could provide to help me resolve this issue. Thank you very much for your assistance.

Best regards,

}}}
"	defect	closed	normal		Structure Prediction		fixed						all	ChimeraX