[phenixbb] rotamers

Nathaniel Echols nechols at lbl.gov
Wed Mar 23 10:50:28 PDT 2011

On Wed, Mar 23, 2011 at 10:17 AM, Ed Pozharski <epozh001 at umaryland.edu> wrote:
> 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).


More information about the phenixbb mailing list