Hi, Elaine, I am not an expert, but had the same problem, solved by trial and error. It involves using alpha-fold independetly from Chimera, and uploading the result in Chimera X. I will be interested if there is a more direct way. Claudio On Mon, 15 Aug 2022 at 17:52, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Erik, Sorry, our AlphaFold / Colab expert is away this week, but I will try to answer.
As I understand it, the structure(s) should appear in ChimeraX automatically after a successful calculation. That they did not open automatically suggests there was some other problem. In addition, there should be a directory under ~/Downloads/ChimeraX/AlphaFold/ containing the results, as mentioned in the tutorial you were viewing: < https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html
I found this one post about saving intermediate results when there is a calculation failure... not sure if it pertains to your situation, however: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/004041.html>
If I come up with something more definitive, will let you know.
Maybe other users who regularly use AlphaFold via Colab can comment? Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 15, 2022, at 12:51 AM, Erik Werner via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Ladies and Gentlemen,
This weekend, I did an AlphaFold prediction run of the human Troponin complex (Troponin C, T and I, UniProt-Ids P63316, P45379, P19429, respectively) via a freshly installed ChimeraX (v 1.4)/Google Colab on macOS Catalina (10.15.7). It completed successfully after 8 hrs (see screenshot below) but I failed to locate the results.
<Screenshot%202022-08-14%20at%2021.48.30.png>
According to your tutorial (https://www.youtube.com/watch?v=6lXeCPuTePs and https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html), I was expecting the results in a Prediction#-folder within the Downloads folder, but ChimeraX had only saved the UniProt xml files there. Also, the notebook code indicated the download of a "results.zip" folder but that also cannot be found anywhere on the computer.
What have I done wrong? Would I have to edit the notebook? Specify a folder, and where? And: can I still recover the results from Google Colab servers? I copied the notebook to my GoogleDrive but was unable to identify a run-id or anything specific to my run.
I would really like to get this working as the prediction of complexes is such a fantastic resource!
Many thanks for your help, Erik Werner
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