[Chimera-users] Can't open web file

Emma Belcher erb76 at cam.ac.uk
Fri May 13 08:35:27 PDT 2022

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,

Pronouns she/her
University of Cambridge
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, May 13, 2022 4:20:10 PM
To: Emma Belcher <erb76 at cam.ac.uk>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at 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.

- 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 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 at 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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