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

[Tristan Croll]

Will probably have to wait for the ChimeraX team (after the holiday, I
expect)… but just to be clear: did you install the Clipper wheel before
trying to install ISOLDE? Clipper *must* be installed first.

On Thu, 29 Dec 2022 at 20:16, Jaime Jensen <JJensen@eidresearch.org> wrote:

> Thank you, Tristan. I am still obtaining a similar error in ChimeraX when
> trying to install ISOLDE manually:
>
>
>
>
>
> *toolshed
> install /Users/JJensen/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl*
>
> *Looking in indexes: https://pypi.org/simple <https://pypi.org/simple>,
> https://cxtoolshed.rbvi.ucsf.edu/pypi/
> <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
> <http://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
> <http://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
> <http://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$>
> in your web browser, navigate to and download the Clipper and ISOLDE
> bundles. Then in ChimeraX, type “toolshed install “ into the command line,
> drag-and-drop the ChimeraX_Clipper…whl file from your file browser and
> press return, then repeat for the ISOLDE file. Restart ChimeraX and you
> should be good to go.
>
>
>
> Best,
>
> Tristan
>
>
>
> On Thu, 29 Dec 2022 at 17:25, Jaime Jensen <JJensen@eidresearch.org>
> wrote:
>
> Hi Tristan,
>
>
>
> Thanks for your reply. I obtain nearly the same error when trying to
> install 1.5:
>
>
>
> Looking in indexes: https://pypi.org/simple
> <https://urldefense.com/v3/__https:/pypi.org/simple__;!!FykDdelvMO2VvRk!ykQbqiwk0rEcjbFQhCUKVs0CI1g0hRQrswYFG6aG1yDG2aso_rXn6JX9-dmQRTDkTvoyV18WQkKwho6fEbI$>,
> 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>
> *Date: *Thursday, December 29, 2022 at 11:34 AM
> *To: *Bobby Singh <bsingh@hjf.org>
> *Cc: *Jaime Jensen <JJensen@eidresearch.org>
> *Subject: *[EXTERNAL] Re: Issue with installation of ISOLDE on macOS
> 11.7.2
>
> ATTENTION: This email originated from outside of the organization.
> Do not open attachments or click on links unless you recognize the sender
> and know the content is safe.
>
>
>
> 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> 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$>
> (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
> ERROR: Could not install packages due to an OSError: Could not find a
> suitable TLS CA certificate bundle, invalid path:
> /etc/pki/ca-trust/source/anchors/ZscalerRootCertificate-2048-SHA256.crt”
>
>
>
> The Zscaler certificate is proxy certificate for Internet access. Any help
> would be appreciated.
>
>
>
> I sent the above to tic20@cam.ac.uk which has bounced back.
>
>
>
>
>
> Bobby Singh
>
> Sr. Infrastructure Engineer
>
> Phone: 240-694-2279
>
> Email: bsingh@hjf.org
>
>
>
> Henry M. Jackson Foundation for the Advancement of Military Medicine
>
>
> <https://www.google.com/maps/search/6720a%0D%0A+Rockledge+Drive,+Suite+100+%0D%0A+%0D%0A+Bethesda,%0D%0A+MD+20817?entry=gmail&source=g>6720a
> Rockledge Drive, Suite 100
> <https://urldefense.com/v3/__https:/www.google.com/maps/search/6720a*Rockledge*Drive,*Suite*100**A0D*0A*Bethesda,*MD*20817?entry=gmail&source=g__;KysrKyslJSsrKw!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx4XTghgFk$>
>
> <https://www.google.com/maps/search/6720a%0D%0A+Rockledge+Drive,+Suite+100+%0D%0A+%0D%0A+Bethesda,%0D%0A+MD+20817?entry=gmail&source=g>
>
> Bethesda, MD 20817
> <https://urldefense.com/v3/__https:/www.google.com/maps/search/6720a*Rockledge*Drive,*Suite*100**A0D*0A*Bethesda,*MD*20817?entry=gmail&source=g__;KysrKyslJSsrKw!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx4XTghgFk$>
>
> www.hjf.org
>
>
>
>
>
>

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

Followup to #8240