I am using the energy_based_clustering application to cluster results from a protein-protein global docking job. One of the partners is kept fixed, so I would like to cluster based on the RMSD of the moving partner alone, without any alignment. I assume that the clustering algorithm is aligning the whole structure to minimize RMSD. Is this correct? If it is, is there a way to skip the alignment and calculate the RMSD directly from the input structures?
A related question is about the cluster:energy_based_clustering:chains_to_ignore flag. I want to use it so it calculates the RMSD only for the moving protein. It needs a list of chains as an integer vector, but it's not clear in what format and how to specify the chains.