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

[David Johnson <da.johnson.a AT gmail.com>]

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