Hi Garrett, You can’t remove numpy from Chimera — it needs numpy to start up. Once you remove it, you only option really is to reinstall Chimera from scratch. Chimera ships will numpy 1.7.2 preinstalled. You either need to install a version of pandas compatible with numpy 1.7.2, or you need to upgrade numpy to whatever version is compatible with the pandas you want to use. You install a specific version of pandas with: chimera --nogui --script `chimera --root`"/bin/pip install pandas=version_compatible_with_numpy” You might be able to upgrade the numpy inside Chimera similarly with: chimera --nogui --script `chimera --root`"/bin/pip install numpy=version_for_pandas” I’m not 100% certain the latter will work, or that Chimera will work smoothly with a different version of numpy. —Eric

On Apr 1, 2024, at 7:17 AM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Garrett Scapellato

Research Technician II Edwards Lab DHVI Duke University

<Outlook-xq1gx0pd.jpg> From: Garrett Scapellato <garrett.scapellato@duke.edu> Sent: Friday, March 29, 2024 2:24 PM To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu> Subject: Re: Chimera numpy error

Eric,

Apologies for sending so many emails. I was able to delete all numpy modules from Chimera. Now when I try to open Chimera I get this error.

Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy ImportError: No module named numpy

I tried reinstalling numpy the same way I installed pandas, but I get the same error as above. How can I fix this issue?

Thanks, Garrett Scapellato

Research Technician II Edwards Lab DHVI Duke University

<Outlook-t5tu01ez.jpg> From: Garrett Scapellato Sent: Friday, March 29, 2024 2:11 PM To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu> Subject: Chimera numpy error

Eric,

I get the following error whenever I try to open chimera. I tried uninstalling numpy with a pip installer, and that didn't work, I assume because it doesn't uninstall the module from chimera specifically.

DHVI-F5KJC04Q:~ edwardslab$ chimera Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import core File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/core/__init__.py", line 91, in <module> raise ImportError(msg.format(path)) ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version.

I also tried rm -rf ~/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/ repeatedly, but that didn't work. I couldn't use Finder to navigate to the python2.7 folder to delete the files manually, either. Any help would be appreciated.

Thanks, Garrett Scapellato

Research Technician II Edwards Lab DHVI Duke University

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