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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users