[phenixbb] how to apply phi/psi helical restraints

Nathaniel Echols nechols at lbl.gov
Fri Jul 29 10:35:45 PDT 2011

On Fri, Jul 29, 2011 at 10:25 AM, Daqi Tu <daqi.tu at gmail.com> wrote:
> I was trying to restrain a relatively mobile region of my structure to be
> helical using Phenix secondary structure restraints. The result is very bad.
> It forces the N-O distance to be about 3A, but the phi/psi angles are all
> ugly. What is the way in Phenix I can apply phi/psi restraints just like in
> the old CNS, which had always worked nicely?

At present, I think your only options are

a) use the reference model feature (preferred, if you have a
higher-resolution structure - this can also be done with a model
optimized by another program, e.g. Rosetta)
b) Ramachandran restraints (potentially dangerous, should be used with
extreme caution)
c) enable use of the monomer library phi/psi restraints
(discard_psi_phi=False on the command line, or Settings->Advanced->PDB
file interpretation in the GUI)

We've discussed restraining phi/psi in secondary structure instead of
the hydrogen bonds, but nothing has been implemented yet.  If you're
willing to share your model and data with us for testing purposes, it
might speed things up.  (It sounds like maybe the existing secondary
structure restraints aren't working properly either - although our
tests have indicated that they can't do much with a poor input model.)


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