Rosetta: Clustering

Hi,

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. 

Thank you,

Stephanie