[chimerax-users] ChimeraX Alphafold Multiple jobs

[Tom Goddard]

Hi Rayees,

  ChimeraX can only run one AlphaFold prediction at a time.

  I tried various tricks to run two predictions at a time and they did not work.  I tried starting two copies of ChimeraX and running a different AlphaFold prediction in each.  Both ChimeraX instances just showed the AlphaFold run progress from the first prediction until it completed, then it hung trying to download the result, and at the same time the second prediction started up.  The download of the first probably hung because the second prediction deleted the results of the first one before it was done.  Then when the second prediction finished, both ChimeraX instances start downloading the results and both crashed.  I also tried running two predictions in a single ChimeraX.  ChimeraX was supposed to give an error when submitting the second prediction that the first was not done yet.  But it didn't, instead the AlphaFold run panel raised an error.  That is a bug.  I'll try to fix that.

  I know with Colab Pro you can have two sessions going at the same time but ChimeraX does not know how to start a second session.

  To avoid getting disconnected from Google Colab when you are running a prediction I think it is important to not let your computer sleep.  Google Colab is intended for interactive use and Google says they will kick you off if idle.  So I set my computer not to sleep during an AlphaFold prediction.  Even if I don't touch the computer after that I have never had Colab disconnect me.  And I think it is fine to iconify ChimeraX, it has not disconnected me unless the computer sleeps.

	Tom




> On Dec 15, 2022, at 11:07 PM, Rayees Mattoo via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I was wondering if I could run multiple Alphafold jobs via ChimeraX using my Colab Pro. Also, very often Alphafold job submitted gets disconnected after some time (15 min or so) without completing the job, any solution to that?
> 
> 
> Best
> Rayees
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