<div dir="ltr"><div>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.</div><div>Claudio<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 15 Aug 2022 at 17:52, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Erik,<br>
Sorry, our AlphaFold / Colab expert is away this week, but I will try to answer.<br>
<br>
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:<br>
<<a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html</a>><br>
<br>
I found this one post about saving intermediate results when there is a calculation failure... not sure if it pertains to your situation, however:<br>
<<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/004041.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/004041.html</a>><br>
<br>
If I come up with something more definitive, will let you know.<br>
<br>
Maybe other users who regularly use AlphaFold via Colab can comment?<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Aug 15, 2022, at 12:51 AM, Erik Werner via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Ladies and Gentlemen,<br>
> <br>
> 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.<br>
> <br>
> <Screenshot%202022-08-14%20at%2021.48.30.png><br>
> <br>
> According to your tutorial (<a href="https://www.youtube.com/watch?v=6lXeCPuTePs" rel="noreferrer" target="_blank">https://www.youtube.com/watch?v=6lXeCPuTePs</a> and <a href="https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html</a>), 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.<br>
> <br>
> 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.<br>
> <br>
> I would really like to get this working as the prediction of complexes is such a fantastic resource!<br>
> <br>
> Many thanks for your help,<br>
> Erik Werner<br>
<br>
<br>
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</blockquote></div>