An issue with using ChimeraX

[Huihui.Mu@…]

Dear ChimeraX team,
My name is Huihui Mu, and I am working in the Farzan Lab at Boston Children’s Hospital.
I have recently been having issues with fetching structures using ChimeraX, even after upgrading to the newest version of the software. I have been using ChimeraX for many years, and this is the first time I had this issue.
Could you guide me how to deal with this?
Thank you!
Best,
Huihui

[Screenshot 2026-04-15 at 4.39.46 PM.png]

[Huihui.Mu@…]

Added by email2trac

[Eric Pettersen]

Hi Huihui,

Thanks for reporting this problem. I was just now able to fetch 7tgy without problem. So one possibility is that it was a temporary problem with the RCSB web site and that it would work if you tried again. Another possibility is that it is some king of networking problem between (most likely a firewall issue) between Harvard and the RCSB. To test this out, go to your web browser and try to access ​http://files.rcsb.org/download/7tgy.cif . Does that work?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Huihui.Mu@…]

Hi Eric,
Thank you for helping me with this request.
I have had this issue for several weeks, so it might not be temporary. It seems my colleague can still fetch structures using ChimeraX.  I did not change any settings on my laptop, so I can not figure out this issue.
I pasted the link below into my browser and downloaded the file, which I can open in the software.
Best,
Huihui

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, April 16, 2026 at 4:43 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Mu, Huihui <Huihui.Mu@childrens.harvard.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #20181: An issue with using ChimeraX [EXTERNAL]

* External Email - Caution *


#20181: An issue with using ChimeraX
-----------------------------------+----------------------------
          Reporter:  Huihui.Mu@…   |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  feedback
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback

Comment:

 Hi Huihui,
         Thanks for reporting this problem.  I was just now able to fetch
 7tgy without problem.  So one possibility is that it was a temporary
 problem with the RCSB web site and that it would work if you tried again.
 Another possibility is that it is some king of networking problem between
 (most likely a firewall issue) between Harvard and the RCSB.  To test this
 out, go to your web browser and try to access
https://urldefense.com/v3/__http://files.rcsb.org/download/7tgy.cif__;!!NZvER7FxgEiBAiR_!rIepY-x5I-DVcAWYSn6hlREbUfFGsX6uHUEMEvrGsFGsuQGp5NBlDpfUZLP-OcMh8alvzqJPG1EsP63izZBVNwe3Vn0D9eY7wk2_IRh_x8c$  .  Does that work?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20181*comment:2__;Iw!!NZvER7FxgEiBAiR_!rIepY-x5I-DVcAWYSn6hlREbUfFGsX6uHUEMEvrGsFGsuQGp5NBlDpfUZLP-OcMh8alvzqJPG1EsP63izZBVNwe3Vn0D9eY7wk2_Er_JTN8$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!NZvER7FxgEiBAiR_!rIepY-x5I-DVcAWYSn6hlREbUfFGsX6uHUEMEvrGsFGsuQGp5NBlDpfUZLP-OcMh8alvzqJPG1EsP63izZBVNwe3Vn0D9eY7wk2_f-9B_Ns$ >
ChimeraX Issue Tracker

[Eric Pettersen]

Hi Huihui,

Has Harvard or your lab recently starting using an HTTP(s) proxy for web access? Might be a question you have to ask your sysadmin. If so, you need to inform ChimeraX about how to access the proxy by going to ChimeraX's preferences and in its Web Access category fill in the appropriate values for accessing your proxy.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Huihui.Mu@…]

Hi Eric,
Thank you for all the information. I will ask our IT about the usage of the HTTP proxy.
Best,
Huihui

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, April 16, 2026 at 5:02 PM
To: Mu, Huihui <Huihui.Mu@childrens.harvard.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #20181: An issue with using ChimeraX [EXTERNAL]

* External Email - Caution *


#20181: An issue with using ChimeraX
-----------------------------------+----------------------------
          Reporter:  Huihui.Mu@…   |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  feedback
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Comment (by Eric Pettersen):

 Hi Huihui,
         Has Harvard or your lab recently starting using an HTTP(s) proxy
 for web access?  Might be a question you have to ask your sysadmin.  If
 so, you need to inform ChimeraX about how to access the proxy by going to
 ChimeraX's preferences and in its Web Access category fill in the
 appropriate values for accessing your proxy.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20181*comment:4__;Iw!!NZvER7FxgEiBAiR_!rxqcHrdlNV5sIkY4rHrRkE-gbFuDvEuCIdsmZR7smcJ1Q95dbkRroRsRgRJDKY2VBqDuNJdfd0iGz0LQ8f-irvmwfbn1Nh2vvZiUlcx-U_0$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!NZvER7FxgEiBAiR_!rxqcHrdlNV5sIkY4rHrRkE-gbFuDvEuCIdsmZR7smcJ1Q95dbkRroRsRgRJDKY2VBqDuNJdfd0iGz0LQ8f-irvmwfbn1Nh2vvZiUTEF-qLQ$ >
ChimeraX Issue Tracker

[Tom Goddard]

My guess would be this fetch was blocked because of local firewall rules and ChimeraX is using unexpectedly using http and not https as shown in the screenshot (​http://files.rcsb.org). I tried the https url ​http://files.rcsb.org and it seems like we should be using https. The http url is in

chimerax/src/bundles/mmcif/src/mmcif.pyx