[phenixbb] how to apply phi/psi helical restraints

Daqi Tu daqi.tu at gmail.com
Wed Aug 3 05:00:46 PDT 2011

Yes, I did only apply to that helical region. The point is as long as 
there is reasonable density there the Ramachandran restraints are able 
to hold the secondary structure conformation.


On 8/3/2011 2:15 AM, Pavel Afonine wrote:
> Hi Daqi,
> oh good! Then I guess you simply need to apply Ramachandran restraints 
> to that helical region only (using rama_selection keyword).
> Pavel.
> 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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