[phenixbb] constraining alpha-helical geometry in phenix

[Jianghai Zhu]

H-bond restraints are much easier to define comparing to phi-psi angle  
restraints.   But I think the DEN restraints from Axel Brunger  
probably is the easiest way for secondary structure restraints at low  
or moderate resolution refinement, which also allows the breakdown of  
secondary structure if your experimental data really drives the way.   
I hope phenix.refine can implement this new algorithm in the future.

-- Jianghai






On Jun 10, 2008, at 5:08 PM, Sean Johnson wrote:

> This discussion has me wondering - is it better to restrain h-bonds or
> phi-psi angles during refinement at "moderate" resolution?
>
> Sean Johnson
>
>
> Ralf W. Grosse-Kunstleve wrote:
>> Hi Pascal,
>>
>>
>>> I am currently refining a structure at moderate resolution (~3.4A)
>>> which is mainly composed of alpha-helices . Is there a way to
>>> constrain the backbone geometry of the alpha helical regions in the
>>> model used for refinement.
>>>
>>
>> Luca Jovine has kindly contributed a perl script that converts HBPLUS
>> output to phenix geometry_restraints.edits. You can find it here:
>>
>>  http://www.phenix-online.org/contrib/hbplus2phenix_restraints.pl
>>
>> We don't have much practical experience with this approach yet,
>> other that it works at a technical level. If you get a chance to
>> try it out, we'd be interested to know how much it helps in your
>> case.
>>
>> Ralf
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>>
>
> -- 
> Sean Johnson, PhD
> R. Gaurth Hansen Assistant Professor
> Utah State University
> Department of Chemistry and Biochemistry
> 0300 Old Main Hill
> Logan, UT 84322-0300
> (435) 797-2089
> (435) 797-3390 (fax)
> sean.johnson at usu.edu
>
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