Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2

[JJensen@…]

Thank you, Tristan. I am still obtaining a similar error in ChimeraX when trying to install ISOLDE manually:


toolshed install<help:user/commands/toolshed.html#install> /Users/JJensen/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/JJensen/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.5) (8.0.3) Requirement already satisfied: ChimeraX-Atomic~=1.36 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.5) (1.41.5) Requirement already satisfied: ChimeraX-Core<1.6,>=1.5rc202211032258 in /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from ChimeraX-ISOLDE==1.5) (1.5) ERROR: Could not install packages due to an OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/pki/ca-trust/source/anchors/ZscalerRootCertificate-2048-SHA256.crt WARNING: There was an error checking the latest version of pip.

Any ideas for fixes?

Thank you,


Jaime


From: Tristan Croll <tcroll@altoslabs.com>
Date: Thursday, December 29, 2022 at 12:31 PM
To: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>, Jaime Jensen <JJensen@eidresearch.org>
Cc: Bobby Singh <bsingh@hjf.org>
Subject: Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2
Hi Jaime,

In that case, this looks like an issue for the ChimeraX team (copied in). Probably a problem with the ToolShed server configuration.

In the meantime you could try installing ISOLDE manually… go to
https://cxtoolshed.rbvi.ucsf.edu/<https://urldefense.com/v3/__https:/cxtoolshed.rbvi.ucsf.edu/__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKw1yWrdBc$> in your web browser, navigate to and download the Clipper and ISOLDE bundles. Then in ChimeraX, type “toolshed install “ into the command line, drag-and-drop the ChimeraX_Clipper…whl file from your file browser and press return, then repeat for the ISOLDE file. Restart ChimeraX and you should be good to go.

Best,
Tristan

On Thu, 29 Dec 2022 at 17:25, Jaime Jensen <JJensen@eidresearch.org<mailto:JJensen@eidresearch.org>> wrote:
Hi Tristan,

Thanks for your reply. I obtain nearly the same error when trying to install 1.5:

Looking in indexes: https://pypi.org/simple<https://urldefense.com/v3/__https:/pypi.org/simple__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKwho6fEbI$>, https://cxtoolshed.rbvi.ucsf.edu/pypi/<https://urldefense.com/v3/__https:/cxtoolshed.rbvi.ucsf.edu/pypi/__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKwWo2RIVs$>
Processing /Users/JJensen/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in /private/var/folders/3h/hh3v85xj3q53ld5jv96yjwk80000gp/T/AppTranslocation/E20A8FCD-E5C4-4780-87CE-DAD711C8B2EB/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages<https://urldefense.com/v3/__http:/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKw0qFjbZU$> (from ChimeraX-ISOLDE==1.5) (8.0.3)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in /private/var/folders/3h/hh3v85xj3q53ld5jv96yjwk80000gp/T/AppTranslocation/E20A8FCD-E5C4-4780-87CE-DAD711C8B2EB/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages<https://urldefense.com/v3/__http:/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKw0qFjbZU$> (from ChimeraX-ISOLDE==1.5) (1.41.5)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /private/var/folders/3h/hh3v85xj3q53ld5jv96yjwk80000gp/T/AppTranslocation/E20A8FCD-E5C4-4780-87CE-DAD711C8B2EB/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages<https://urldefense.com/v3/__http:/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKw0qFjbZU$> (from ChimeraX-ISOLDE==1.5) (1.0)
ERROR: Could not install packages due to an OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/pki/ca-trust/source/anchors/ZscalerRootCertificate-2048-SHA256.crt


From: Tristan Croll <tcroll@altoslabs.com<mailto:tcroll@altoslabs.com>>
Date: Thursday, December 29, 2022 at 11:34 AM
To: Bobby Singh <bsingh@hjf.org<mailto:bsingh@hjf.org>>
Cc: Jaime Jensen <JJensen@eidresearch.org<mailto:JJensen@eidresearch.org>>
Subject: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2
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Hi Bobby, Jaime,

It looks to me that the most likely issue is the very old version of ChimeraX (1.2.5). Could you try updating to the latest version (1.5) and see if you can install ISOLDE into that?

Best,
Tristan

On Thu, 29 Dec 2022 at 15:38, Bobby Singh <bsingh@hjf.org<mailto:bsingh@hjf.org>> wrote:
Hello,
One of our users (Jamie Jensen, cced in the email)  is having an issue while trying to install ISOLDE through ChimeraX toolbox. She is on macOS 11.7.2. The following error is generated during the installation:

“Looking in indexes: https://pypi.org/simple<https://urldefense.com/v3/__https:/pypi.org/simple__;!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx43NKDqdM$>, https://cxtoolshed.rbvi.ucsf.edu/pypi/<https://urldefense.com/v3/__https:/cxtoolshed.rbvi.ucsf.edu/pypi/__;!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx4AwA1-KA$>
Processing /Users/JJensen/Downloads/ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl
Requirement already satisfied: ChimeraX-Core~=1.2.0 in /Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages<https://urldefense.com/v3/__http:/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages__;!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx45v47DZU$> (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
ERROR: Could not install packages due to an OSError: Could not find a suitable TLS CA certificate bundle, invalid path: /etc/pki/ca-trust/source/anchors/ZscalerRootCertificate-2048-SHA256.crt”

The Zscaler certificate is proxy certificate for Internet access. Any help would be appreciated.

I sent the above to tic20@cam.ac.uk<mailto:tic20@cam.ac.uk> which has bounced back.


Bobby Singh
Sr. Infrastructure Engineer
Phone: 240-694-2279
Email: bsingh@hjf.org<mailto:bsingh@hjf.org>

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