[phenixbb] Real space refinement with helical symmetry

Pavel Afonine pafonine at lbl.gov
Sat Jun 29 14:50:17 PDT 2019

Hi Yangqi,

> I am trying to do a real space refinement with phenix and my map is a 
> filament and I have monomer model and I would like to refine against 
> my filament map. I am wondering how to impose the helical symmetry in 
> this case? (I have a pseudo filament model by copying multiple 
> subunits and aligned in Chimera using "fit in map").

If you start with the model that possesses correct symmetry and just run 
phenix.real_space_refine (command line or GUI) and make sure to disable 
refinement of the NCS operators (by using refine_ncs_operators=False; 
available command line or GUI), then that should just work.

Let us know if it doesn't do what you want!


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