I am learning to use the Rosetta3.1. I tried to use the relax application to refine my homology model, which is a complex of a hetero-trimer. The result seems to be quite impressive and almost all of the conflicts were resolved.
However, based on the manual, it reads : "The "relax" mode in Rosetta carries out the task of structural refinement of a monomeric protein."
I do not understand why this relax mode is only good for monomeric proteins? Is it because it does not deal with the quaternary structure, or something more fundamental in the relax protocol?
I would deeply appreciate any advice!