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

[Tristan Croll]

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/ 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://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
> /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
> (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
> (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
> (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$>
> (from ChimeraX-ISOLDE==1.2.2) (1.2.5)
> ERROR: Could not install packages due to an OSError: Could not find a
> suitable TLS CA certificate bundle, invalid path:
> /etc/pki/ca-trust/source/anchors/ZscalerRootCertificate-2048-SHA256.crt”
>
>
>
> The Zscaler certificate is proxy certificate for Internet access. Any help
> would be appreciated.
>
>
>
> I sent the above to tic20@cam.ac.uk which has bounced back.
>
>
>
>
>
> Bobby Singh
>
> Sr. Infrastructure Engineer
>
> Phone: 240-694-2279
>
> Email: bsingh@hjf.org
>
>
>
>
> <https://www.google.com/maps/search/6720a%0D%0A+Rockledge+Drive,+Suite+100+%0D%0A+%0D%0A+Bethesda,%0D%0A+MD+20817?entry=gmail&source=g>
>
>
> <https://www.google.com/maps/search/6720a%0D%0A+Rockledge+Drive,+Suite+100+%0D%0A+%0D%0A+Bethesda,%0D%0A+MD+20817?entry=gmail&source=g>Henry
> M. Jackson Foundation for the Advancement of Military Medicine
>
> 6720a Rockledge Drive, Suite 100
> <https://urldefense.com/v3/__https:/www.google.com/maps/search/6720a*Rockledge*Drive,*Suite*100**A0D*0A*Bethesda,*MD*20817?entry=gmail&source=g__;KysrKyslJSsrKw!!FykDdelvMO2VvRk!161hauhA2b56LC2rSJz5Ww5N3-1hRNVF3BdeCgcVsaWrv45-YRFClmOdwgDuP59-GsRAohU9SOx4XTghgFk$>
>
> 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]

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