Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
Application of secondary structure restraints depends on the quality of the
experimental data. The most basic parameter to consider would be a
resolution. For lower-resolution SS restraints might help to keep a
reasonable geometry of the structure. The bent DNA should also work fine
with SS since they are restraining base pairs and stacking pairs which
normally don't distort too much.
P.S. There is a separate bulletin board for Phenix-specific questions:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Best regards,
Oleg Sobolev.
> Thank you
> Dhiraj
>
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