Hi Jon,
These few rotamers which I fix in Coot, validate in Phenix, refine in
Refmac, and validate again in Phenix keep getting pushed into areas that
are not favored. I would love to hear some ideas as I'm out and this
model
is otherwise done.
did you try refining it in Phenix with or without "fix_rotamers=True"
option? This may help. Do these residues have good density (since you
say you do validate in Phenix, then you must have the real-space CC
computed and listed per residue/atom)? There are plenty of other options
to try out, such as changing weights, for example. Or fixing coordinates
of specific residues during refinement. You can do it in phenix.refine.
If nothing helps, you can send me the data and model files and I will
have a closer look - this may help us to improve the software too and
help you to resolve this problem. Let me know if you have questions.
Pavel.
