[phenixbb] helix deformed during refinement in phenix

[Raja Dey]

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