April 2024 - Chimera-users - RBVI Mailing Lists

Bug
by Anoop B S 09 Apr '24

09 Apr '24

Sometimes its not responsive.How to resolve that

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Opening chimera within MS powerpoint
by Prathvi Singh 08 Apr '24

08 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Fw: Chimera numpy error
by Garrett Scapellato 01 Apr '24

01 Apr '24

Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:133a3af9-3314-4e94-9c72-9d0bc6ffe6cc] ________________________________ From: Garrett Scapellato <garrett.scapellato(a)duke.edu> Sent: Friday, March 29, 2024 2:24 PM To: pett(a)cgl.ucsf.edu <pett(a)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 [cid:5a4e481b-169d-4789-87e0-4c616c5183fc] ________________________________ From: Garrett Scapellato Sent: Friday, March 29, 2024 2:11 PM To: pett(a)cgl.ucsf.edu <pett(a)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 [cid:570bb78a-e702-4643-995c-11d5cdaf82fd]

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