I've had this problem before. The root cause turned out to be that "/path/to/ChimeraX/python3.8 -m pip install --user" installed to the Python​ user directory rather than the ChimeraX user directory. Try running:

"C:\Program Files\ChimeraX\bin\ChimeraX-console.exe" -m pip install --user pandas
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 10 June 2021 09:27
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] using pandas
 

Hi Eric,

 

Thank you for the reply! Unfortunately, even though I followed your instructions and do have the bz2 module (I use Windows), I still get the same error. I can ‘import pandas’ in ChimeraX’s Python, but not from within the application itself. Do you have any idea what else might be going on?

 

Ilse

 

Van: Eric Pettersen <pett@cgl.ucsf.edu>
Verzonden: 09 June 2021 19:12
Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl>
CC: chimerax-users@cgl.ucsf.edu
Onderwerp: Re: [chimerax-users] using pandas

 

Hi Ilse,

                You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html .  The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on.  I will add you to the cc list for the ticket we have open for this problem, in case it matters to you.

 

--Eric

 

                Eric Pettersen

                UCSF Computer Graphics Lab

 



On Jun 9, 2021, at 3:09 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

 

Hello everyone,

 

Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line ‘import pandas’, but I get the error: ‘ModuleNotFoundError: No module named 'pandas'’.

 

Kind regards,

Ilse

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