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

[Scazzocchio Claudio]

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 at 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 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
>
>
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