Opened 23 months ago

Closed 23 months ago

#10402 closed defect (fixed)

AlphaFold colab problem?

Reported by: anapap@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Hello,

Although I have used ChimeraX before to run AlphaFold predictions successfully, I just encounter a problem and I cannot longer run any predictions. I tried both 1.6 and 1.7.

Please see attached the error I received from the colab notebook. I wonder if something has changed in the colab and ChimeraX has to be fixed

Thank you

Tassos Papageorgiou

Screenshot 2023-12-25 at 18.47.38.png​

Attachments (1)

Screenshot 2023-12-25 at 18.47.38.png​ (92.8 KB ) - added by anapap@… 23 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by anapap@…, 23 months ago

Attachment: Screenshot 2023-12-25 at 18.47.38.png​ added

Added by email2trac

comment:1 by Tom Goddard, 23 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned

comment:2 by Tom Goddard, 23 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

AlphaFold prediction failed because ColabFold installs latest Biopython 1.82 which does not include SCOPData required by AlphaFold. I made it install Biopython 1.81. Unfortunately Colabfold does not pin the versions of its dependencies so it is prone to breaking whenever those dependencies are updated.

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