I have used rosetta protein-protein docking to generate 1000 models, and was hoping to use rosetta clustering to analyze the result.
I have read that rosetta clustering superimposes models for rmsd calculation by default, and I was hoping to find a way to change this default mode for my models.
Is there a way to turn this default mode off?
P.S. I do not have a native structure (protein-protein docked structure) for my proteins of interest, so my intent was to cluster them based on their non-superimposed rmsd values.
The option "-cluster:skip_align" should do a non-superimposed rmsd.