[modeller_usage] Make non-adjacent mutations, preserve backbone and avoid clashes

I would like to make a handful of mutations that are not necessarily in sequential order in the primary structure. I would like to preserve the backbone of the model and to keep fixed all side-chains except those of the mutations and possibly nearby residues, which are to be moved ONLY if necessary to void steric clashes.

Thus far I have tried Selecting all but the mutated atoms and setting env.edat.nonbonded_sel_atoms = 2 a.library_schedule = autosched.slow a.md_level = None OR a.md_level = refine.very_fast a.repeate_optimization = 3

It is not clear to me exactly what each refinement protocol does. I would appreciate any assistance in understanding this.

David