[chimerax-users] AlphaFold predictions

Tue Sep 6 11:45:19 PDT 2022

Hi Hernando,

  It is hard to explain how a 400 residue AlphaFold prediction downloads automatically, but a 1500 residue prediction hangs downloading.  It only downloads once the job finishes.  But that is a bit suspicious because I have never seen Google Colab succeed with 1500 residues.  The GPUs it offers are just too old, even with Colab Pro (which is what I use) -- I only get GPUs with 16 GB memory that can handle about 1200 residues -- larger runs don't have enough GPU memory.  Here are some test runs of AlphaFold prediction on Google Colab Nvidia P100 (16 GB) and on a desktop PC Nvidia RTX 3090 (24 GB) and on a server Nvidia A40 (48 GB).  The A40 can handle over 3000 residues.

	https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html>

I think your download problem is a Google Colab issue.  Unfortunately Google Colab is an erratic service, although the price (free) is right.

  Tom

> On Sep 4, 2022, at 6:51 AM, Hernando J Sosa <hernando.sosa at einsteinmed.edu> wrote:
> 
> Thanks Tom,
> 
> I've run successfully other predictions but of smaller sequences (~400 residues). This happened with a larger but not huge complex ( ~1500 residues total).  I've tried others runs  but they crashed with an error message saying that RAM was insufficient, even though the goggle account was upgraded to pro (not pro+).  
> 
> I am using a windows 10 computer and it was not in screen saving mode, but  I was using the multiple desktop feature. It is likely that when the run finished the desktop with chimera and the google colab window was not the one that was on display. Would this be an issue  ??
> 
> Best
> 
> Hernando
> 
> ___________________________________
> Hernando Sosa                                                           
> Dept. of Biochemistry
> Albert Einstein College of Medicine
> 1300 Morris Park Av.
> Bronx NY 10461
> phone (718) 430-3456
> emai:  hernando.sosa at einsteinmed. <mailto:hernando.sosa at einsteinmed.org>edu
> ___________________________________
> 
> 
> From: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
> Sent: Friday, September 2, 2022 5:17 PM
> To: Hernando J Sosa <hernando.sosa at einsteinmed.edu <mailto:hernando.sosa at einsteinmed.edu>>
> Cc: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] AlphaFold
>  
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> 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 <mailto: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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