[phenixbb] how to apply phi/psi helical restraints

Pavel Afonine pafonine at lbl.gov
Fri Jul 29 10:45:03 PDT 2011


I can't see why doing both: defining custom bonds between N-O pairs that 
stabilize the helical region and using Ramachandran plot restraints 
would not work. Could you please try it? If it still doesn't work, then 
please send me the data and model, indicate the region that you want to 
be helical, and tell which command you used; then I will have a look.

Alternatively, as Nat suggested, you can use reference model restraints. 
Just create a PDB file containing idealized (the way you want it) 
helical region and supply it to phenix.refine for reference model 


On 7/29/11 10:35 AM, Nathaniel Echols wrote:
> 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.)
> -Nat
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