[phenixbb] constraining alpha-helical geometry in phenix

Pavel Afonine PAfonine at lbl.gov
Thu Jun 5 09:28:23 PDT 2008

Hi Pascal,

it's not automated yet, but you can do it manually. In phenix.refine you 
can define "custom bonds" and "custom angles". So in your case you can 
just define such kind of pseudo-bonds between atom pairs that stabilize 
the secondary structure.

Look the manual for more informations:

Please let me know if you have any questions!

On 6/4/2008 2:29 PM, Pascal EGEA wrote:
> Dear All,
> 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.
> Many Thanks,
> Pascal F. Egea, PhD
> Post Doctoral Researcher
> University of California San Francisco
> Department of Biophysics and Biochemistry
> Robert Stroud Laboratory
> pascal at msg.ucsf.edu <mailto:pascal at msg.ucsf.edu>
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