[chimerax-users] problem on Protein complex prediction

[Tom Goddard]

Hi Bing,

  Your AlphaFold prediction did not finish.  It needs to do energy minimization and then say "Structure prediction completed" at the bottom of the AlphaFold Run log.  I attach an image of a finished job.  The status at the bottom of the AlphaFold Run window that says "completed at 4:15 PM" is something Google Colab shows and it says that even when Google terminated the calculation.  But if Google terminates it you usually get a popup window that says "Google Colab runtime disconnected.  Reconnect?".  Did you get that popup.  ChimeraX has no way to control Google terminating your job because it runs too long, and ChimeraX does not control the misleading Google Colab status message that says "completed...".  Google Colab has lots of problems.  Notice in my attached log it claims it took 455118 hours to run -- which is just nonsense -- it took a couple hours for that run.

  Two things I do which probably helps not get the job terminated by Google Colab is I tell my computer not to sleep.  I am not sure if Google Colab will terminate your job if it cannot connect to the AlphaFold Run web browser panel -- it might -- Google doesn't document how Colab behaves.  Another thing that probably helps my jobs always succeed is I pay $10 per month to Google for Colab Pro service.

  You may be better off running AlphaFold directly with the Google server and not in ChimeraX.

	https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb <https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb>

  I don't know why your AlphaFold Run panel appears black.  I have never seen that, but I use Mac and from your image I see you are using Windows or Linux.  You might want to use ChimeraX Help / Report a Bug... to report that black panel then I will know what operating system and ChimeraX version you are using.  But it is either a Qt window toolkit problem or Google Colab problem and neither of those are things that can be fixed in ChimeraX.

  Tom



> On Dec 30, 2021, at 3:16 PM, Bing Xu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX Staff,
> I tried to used ChimeraX to predict to two proteins complex. After Alfafold Run finished, I can’t find the result. Alfafold Run window showed that the prediction was completed. I attached the pictures of Alfafold Run window. Could you please help me to figure out what is wrong with ChimeraX?   I do appreciate your help.
>  
> Thanks and Happy New Year!
>  
> Bing
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