Hi Cui5, Thanks for reporting this problem, though the more appropriate address is chimerax-bugs, not chimerax-users. It has been fixed since about mid-August, though that’s after the 1.10.1 release that you have. So if you get the 1.11 release candidate then “pip list” will work. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Nov 21, 2025, at 6:23 AM, replacement2--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks.

Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf'

cui5 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Our implementation of the pip command doesn’t allow upgrading internal ChimeraX packages, and those packages take precedence over user installed packages, so additional copies of say certifi or numpy in the user site packages directory don’t break ChimeraX. I could be persuaded to add an option that does allow pip to upgrade internal packages, conditioned on disabling the bug reporter afterwards. — Zach

On 25 Nov 2025, at 07:59, G C via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Eric,

Thanks for getting back. Actually, I found this in release 1.10.1 accidentally when I was checking how to upgrade `certifi`. Glad to hear that it's been addressed. My organization flagged it as a potential security risk. When I tried to run `pip install certifi upgrade true` inside ChimeraX, it doesn't seem to do anything. I wonder I was doing it wrong. I also tried to run `%pip install --upgrade certifi` from the Jupyter console, but it gave an import error. What's the best way to do this on MacOS, since the application is locked down by Apple?

Best, cui5 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/