On Wed, Mar 23, 2011 at 10:17 AM, Ed Pozharski
Does refine restrains side chain rotamers to, say, the closest one from the rotamer dictionary or, perhaps, the starting coordinates (I find this less likely, of course)?
No, except to the extent that the standard monomer library dihedral restraints will often drive sidechains to rotameric conformations. I've been playing with multi-angle restraints using e.g. the Molprobity distributions, similar to what we've done for Ramachandran restraints, but nothing working yet.
Do I understand correctly that the real-space refinement for the side chains is on by default, which means that disordered side chains would tend to stay within their biased density?
Real-space refinement for the entire structure is on by default (strategy=individual_sites_real_space, subject to resolution and R-factor cutoffs) - individual rotamer fitting needs to be explicitly enabled (fix_rotamers=True). -Nat