After many warning messages, I think I have to clarify the meaning of
my question. After careful refining, in a low resolution structure
often many residues (mainly in loop regions) can still adopt
different dihedral conformations which are equally compatible with a
low resolution electron
Remember that phi-psi angels are excellent for validation purposes,
but only when they are unrestrained, so if you restrain them you
lose this option.
The above is a very important point!
Having now said that, restraining alpha-helices hydrogen bonding, and
beta-sheet cross-strand hydrog
Hi Mario
Maintaining the secondary structure of your protein when refining against weak
data can be really challenging.
There are some options, but in the end you might have to accept a fairly large
number of Ramachandran plot outliers.
Try phenix.refine with the keyword "discard_psi_phi=Fals
Hi,
it could be really useful in refining low resolution structure (with
poor electron density map) to have a refinement program that can
restrain phi and psi angles to follow Ramachandran plot. Does anyone
know if such program exist?
Thank you,
mario
Mario Milani, PhD
University of Milan
