I am doing SymDock using Rosetta 3.5. I wonder what the option really does:
-symmetry:initialize_rigid_body_dofs - Initialize the rigid body configuration according to the symmetry definition file.
I actually ran SymDock using diff. option combinations. When initialize_rigid_body_dofs is set, the assemblies look very different, otherwise more homogeneous. So I concluded that the option does initialization.
But, when I also set some distance constraints that the original orientation of the input rigid body wouldn't satisfy, SymDock could also generate assemblies satisfying the distance constraints, although initialize_rigid_body_dofs was NOT set. In all experiments, perturb_rigid_body_dofs was not set.
So my question is, why is the input rigid body initialized/randomized no matter the option is set or not?