[chimerax-users] AlphaFold prediction of complex - results not downloaded

[Elaine Meng]

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 at 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