Hi Peter,
sorry for not answering exactly your question... but since this is
relevant I reply anyway:
The latest version of phenix.refine has an option "fix_rotamers=true",
that automatically fixes all side chain rotamers by going
residue-by-residue and choosing the best one based on density
Hi,
I'm working with a 1.8 A structure with Coot and Refmac, and there are
many sidechain rotamers that show very clear difference density peaks
for setting their correct positions. However, Refmac continuously
moves the rotamers back into negative density peaks. It's really
quite silly
Dear Peter,
This simply should not be happening.
The actual value of the weight term btw does not say much, what we
would need to know is the resulting rmsd, or the associated z-score.
For what you describe, weighting should not matter really - same goes
for the torsion restraint, that will
Is it possible there are alternate conformations
for these side chains? Refmac, or any other refinement program, will
try to fill one of the density regions with your side chain, but
because of partial occupancy, a negative difference map will result,
with accompanying positive density in the o
] How to fix sidechain rotamers for Refmac?
Hi,
I'm working with a 1.8 A structure with Coot and Refmac, and there are many
sidechain rotamers that show very clear difference density peaks for setting
their correct positions. However, Refmac continuously moves the rotamers back
into neg
It is hard to believe that REFMAC is being driven by rotamer
conformations - REFMAC weighting scheme gives a low priority to fitting
a preferred rotamer - quite rightly since the SD on rotamer angles is
high. The ideal is only "ideal" for a residue in a near vacuum - the
interactions with othe
Besides possibilities pointed, I would ask if your are using undue NCS
restraints, id est, between "rotamers" which are genuinely "different".
Anyway, at 1.8 A resolution, one should check the adequateness of using
NCS restraints.
J
Hi,
I'm working with a 1.8 A structure with Coot and Refmac,
