[phenixbb] how to apply phi/psi helical restraints

Pavel Afonine pafonine at lbl.gov
Tue Aug 2 23:15:57 PDT 2011

Hi Daqi,

oh good! Then I guess you simply need to apply Ramachandran restraints 
to that helical region only (using rama_selection keyword).


On 8/2/11 8:28 AM, Daqi Tu wrote:
> Yes, applying Ramachandran restraints alone is able to maintain 
> helical conformation.
> Cheers,
> Daqi
> 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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