[phenixbb] how to apply phi/psi helical restraints

Daqi Tu daqi.tu at gmail.com
Tue Aug 2 08:28:39 PDT 2011

Yes, applying Ramachandran restraints alone is able to maintain helical 


On 7/29/2011 1:45 PM, Pavel Afonine wrote:
> Hi,
> 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 restraints.
> Pavel.
> 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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