[phenixbb] helix deformed during refinement in phenix
PAfonine at lbl.gov
Mon Oct 13 16:03:26 PDT 2008
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 Dey, Ph.D.
> Research Associate
> Molecular and Computational Biology
> University of Southern California
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