[chimerax-users] AlphaFold Prediction

[Tom Goddard]

Hi Raihan,

The ChimeraX AlphaFold prediction produces 5 models but it only automatically opens the best model.  All 5 models are in the ~/Downloads/ChimeraX/AlphaFold/prediction directory after the job completes.  There is no option to run fewer models.  Running AlphaFold not through ChimeraX also produces 5 models.  This is because AlphaFold works by running 5 slightly differently trained neural networks and the best is chosen.  If you install your own AlphaFold (a somewhat difficult task, needs Linux and an Nvidia GPU and a few Tbytes of disk for databases) then you can modify the AlphaFold Python code to predict only one or a few models by choosing which of the 5 networks it should run.

	Tom

> On Oct 31, 2022, at 1:39 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi!
> Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. 
> 
> Regards, 
> Raihan
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users