[phenixbb] Torsion angels refinement question

Pavel Afonine PAfonine at lbl.gov
Sat Apr 3 19:32:06 PDT 2010

Hi Peter,

when using torsion angle parameterization you need to use simulated 
annealing based refinement. Gradient-driven minimization (without using 
second derivatives) will not perform well.

To enable it in your refinement:

phenix.refine model.pdb data.mtz simulated_annealing_torsion=true

I would recommend running a SA refinement in Cartesian space too - just 
for comparison:

phenix.refine model.pdb data.mtz simulated_annealing=true

Please let me know if you have any questions or would like to discuss 
this subject some more.


> I try to refine a big complex at low resolution. I am a little 
> confused about the syntax of using torsion angels gradient-driven 
> refinement. Is it now the default for individual sites refinement 
> instead of  cartesian ? If not, should I add :  
> sites.Torsion_angles=all for example ? Could you shed some light on this,

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