[phenixbb] helix deformed during refinement in phenix

Pavel Afonine PAfonine at lbl.gov
Mon Oct 13 16:03:26 PDT 2008

Hi Raja,

it's still not available, and we still plan to add it in future.

Currently the only way of doing it is to define pseudo-bonds between the 
pairs of atoms that stabilize the secondary structure elements. For more 
informations please look "Definition of custom bonds and angles" section 
in phenix.refine manual 


On 10/13/2008 3:55 PM, Raja Dey wrote:
> Dear All,
>             I am using phenix to refine a long helix of about 120 residues in a complex structure, but in course of refinement the helix becoming distorted from helical geometry. As a result when I am displaying the refined structure in pymol as cartoon one long helix showed 3/4 discontinuous helices in a single chain. Is there any way to constrain or restrain the helix during refinement, so that refinement process can maintain the helical geometry? Any suggestion is well appreciated. 
> With regards...
> Raja
> Raja Dey, Ph.D.
> Research Associate 
> Molecular and Computational Biology
> University of Southern California
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