Alphafold prediction send sequence to Google Colab returned: None

[danesh_moazed@…]

Hi,

I am trying to do structure predictions using AlphaFold in ChimeraX_Daily.

I get the following message: Alphafold prediction send sequence to Google Colab returned: None

Can you please help? I used to do this routinely without any problems.

Thank you,
Danesh

——
Danesh Moazed
Harvard Medical School/HHMI
danesh@…

[Tom Goddard]

Are you using a current ChimeraX daily build? It would be best to use menu Help / Report a Bug so we get your ChimeraX version, operating system, and other details.

I just tried AlphaFold prediction and got no errors.

The error message you get means when ChimeraX tried to send the sequence to predict to the Google Colab virtual machine it failed. I'm not sure why that would happen. Did you log into Google in the AlphaFold Run window? Have you used ChimeraX AlphaFold prediction successfully in the past?

[danesh_moazed@…]

Thank you for responding.

Yes I downloaded the latest version of ChimeraX_Daily.  And also logged into Google in the AlphaFold run window.  I have used ChimerX AlphaFold predictions successfully in the past (for several dozen pairwise interactions) without any trouble, but not over the last about 3 months.


——
Danesh Moazed
Harvard Medical School/HHMI
danesh@hms.harvard.edu





On Apr 12, 2024, at 3:07 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#14963: Alphafold prediction send sequence to Google Colab returned: None
-------------------------------------------+-------------------------
         Reporter:  danesh_moazed@…       |      Owner:  Tom Goddard
             Type:  defect                |     Status:  assigned
         Priority:  normal                |  Milestone:
        Component:  Structure Prediction  |    Version:
       Resolution:                        |   Keywords:
       Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
          Project:  ChimeraX              |
-------------------------------------------+-------------------------
Changes (by Tom Goddard):

* component:  Unassigned => Structure Prediction
* owner:  (none) => Tom Goddard
* platform:   => all
* project:   => ChimeraX
* status:  new => assigned
* summary:  AlphaFold not working => Alphafold prediction send sequence to
    Google Colab returned: None

Comment:

Are you using a current ChimeraX daily build?  It would be best to use
menu Help / Report a Bug so we get your ChimeraX version, operating
system, and other details.

I just tried AlphaFold prediction and got no errors.

The error message you get means when ChimeraX tried to send the sequence
to predict to the Google Colab virtual machine it failed.  I'm not sure
why that would happen.  Did you log into Google in the AlphaFold Run
window?  Have you used ChimeraX AlphaFold prediction successfully in the
past?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14963#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Did you use menu Help / Report a Bug as I suggested? I don't even know what operating system (Mac, Windows, Linux) you are using. It could also be helpful to attach a screenshot of the AlphaFold Run window.

On Mac with the current ChimeraX daily build I just ran AlphaFold prediction from ChimeraX and had no problems. The error you get means that ChimeraX cannot send the sequence to Google Colab. The way it sends the sequence is it runs some JavaScript code on the Google Colab web page shown in the AlphaFold Run window. So if your Google Colab web page looks different (not sure why, maybe you have Colab configured in some custom way), or if you have some permissions restriction that prevents ChimeraX from running that JavaScript in the Colab page, then that would explain the failure. Certainly something is different about your computing environment. Maybe it is network security restrictions at your site.

[Tom Goddard]

No reply from reporter.