Hi there, I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1). When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message: Error reading consurf_1652376787.chimerax: Couldn't find url 'https://consurf.tau.ac.il/results/1652376787/msa_file_fasta.aln.clustalw': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661) I have no idea what this means or how to fix it, so would appreciate any tips! Thank you, Emma Belcher
Hi Emma, I can only guess it's exactly what the message says, it can't read that URL. Possibilities: - you have a very, very old Chimera that can't read https. Must use Chimera 1.12 or newer. - that URL is not available (did you try entering it into a web browser)? They may only keep results for a certain amount of time. If you did the calculation many days ago, they may have removed the data from their website. To save the data longer-term after a web service calculation, you should open it in Chimera while the data is "fresh" and then save your Chimera session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2022, at 4:26 AM, Emma Belcher via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi there,
I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1).
When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message:
Error reading consurf_1652376787.chimerax: Couldn't find url 'https://consurf.tau.ac.il/results/1652376787/msa_file_fasta.aln.clustalw': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)
I have no idea what this means or how to fix it, so would appreciate any tips!
Thank you, Emma Belcher
Hi Elaine, Thanks for getting back to me so quickly. I’m running Chimera 1.16 and the URL opens to the webpage fine (I ran the Consurf calculation today). I downloaded it from and opened it with Safari, but don’t know why the browser would make a difference. Not sure what else to try! Best wishes, Emma Pronouns she/her University of Cambridge ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, May 13, 2022 4:20:10 PM To: Emma Belcher <erb76@cam.ac.uk> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Can't open web file Hi Emma, I can only guess it's exactly what the message says, it can't read that URL. Possibilities: - you have a very, very old Chimera that can't read https. Must use Chimera 1.12 or newer. - that URL is not available (did you try entering it into a web browser)? They may only keep results for a certain amount of time. If you did the calculation many days ago, they may have removed the data from their website. To save the data longer-term after a web service calculation, you should open it in Chimera while the data is "fresh" and then save your Chimera session. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2022, at 4:26 AM, Emma Belcher via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi there,
I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1).
When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message:
Error reading consurf_1652376787.chimerax: Couldn't find url 'https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fconsurf.tau.ac.il%2Fresults%2F1652376787%2Fmsa_file_fasta.aln.clustalw&data=05%7C01%7Cerb76%40universityofcambridgecloud.onmicrosoft.com%7Cd986033428f04d52880408da34f42645%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637880520886351409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tYqnSzxd6dCdFKafpfAGk4AKs1pq2AS1JQmmKcwkuRw%3D&reserved=0': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)
I have no idea what this means or how to fix it, so would appreciate any tips!
Thank you, Emma Belcher
Hi Emma, Do you mind sharing the .chimerax file? Then we can actually try ourself and see if we have the problem. You can send it to just my e-mail rather than the whole list if you prefer... Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2022, at 8:35 AM, Emma Belcher via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks for getting back to me so quickly. I’m running Chimera 1.16 and the URL opens to the webpage fine (I ran the Consurf calculation today). I downloaded it from and opened it with Safari, but don’t know why the browser would make a difference. Not sure what else to try!
Best wishes, Emma
Pronouns she/her University of Cambridge From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, May 13, 2022 4:20:10 PM To: Emma Belcher <erb76@cam.ac.uk> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Can't open web file
Hi Emma, I can only guess it's exactly what the message says, it can't read that URL.
Possibilities: - you have a very, very old Chimera that can't read https. Must use Chimera 1.12 or newer. - that URL is not available (did you try entering it into a web browser)? They may only keep results for a certain amount of time. If you did the calculation many days ago, they may have removed the data from their website. To save the data longer-term after a web service calculation, you should open it in Chimera while the data is "fresh" and then save your Chimera session.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 13, 2022, at 4:26 AM, Emma Belcher via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi there,
I am a complete beginner with Chimera so apologies for the very basic question. I am trying to open a Consurf output which is a .chimerax file. I have downloaded Chimera to do this and have not changed any default settings (running MacOS Monterey 12.2.1).
When I try to open the file (either by clicking “Open with Chimera” on the file or opening Chimera and going File > Open… and selecting the file), it comes up with the following error message:
Error reading consurf_1652376787.chimerax: Couldn't find url 'https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fconsurf.tau.ac.il%2Fresults%2F1652376787%2Fmsa_file_fasta.aln.clustalw&data=05%7C01%7Cerb76%40universityofcambridgecloud.onmicrosoft.com%7Cd986033428f04d52880408da34f42645%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637880520886351409%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tYqnSzxd6dCdFKafpfAGk4AKs1pq2AS1JQmmKcwkuRw%3D&reserved=0': [Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)
I have no idea what this means or how to fix it, so would appreciate any tips!
Thank you, Emma Belcher
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participants (2)
-
Elaine Meng -
Emma Belcher