[chimerax-users] AlphaFold

[Tom Goddard]

Hi Hernando,

  I have not seen that problem.  Does that always happen when you run an AlphaFold prediction?  What operating system are you on?  Mac?  I have seen Mac ask for permission to download from a web site the first time you download from that site.  It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask.  But it doesn't make much sense because I do not observe this.  Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine.  If it is sleeping you might want to set your machine not to sleep during the run.  This can also be important to avoid Google Colab dropping your job entirely due to inactivity.  I guess another possibility is that it could be a firewall problem where your network firewall blocks the download.  Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem.

  At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes.  There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file.  Try that.  ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N.  It may also hang if there is some issue that prevents the downloads.  Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem.

	Tom


> On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
>       Dear Chimera/ChimeraX, 
> 
> I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot).  Is this a known issue? is there a workaround ?
> 
> Thanks
> 
> Hernando
> 
> <image.png>
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