[phenixbb] anisotropic ADP factor refinement and optimize_wxc

Joyce, Gordon M. (NIH/NIAID) [F] joycego at niaid.nih.gov
Tue Jul 21 21:08:11 PDT 2009

Dear All,

I have just recently started using phenix.refine and I hope I can get some advice. 

I am trying to refine my structure with anisotropic ADP factors while also optimizing the weighting parameters.When I give the following command, anisotropic refinement is carried out but optimization is not carried out as far as I can see (ie the rms bond and angles are not reduced, which is one of my concerns at the moment). 

phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true strategy=individual_adp adp.individual.anisotropic="not element H" optimize_wxc=true --overwrite

pdb output values

REMARK Start: r_work = 0.1952 r_free = 0.2388 bonds = 0.015 angles = 1.646
REMARK Final: r_work = 0.1413 r_free = 0.2448 bonds = 0.015 angles = 1.646

If I give the following command, optimization occurs and rms bond and angle values decrease.

phenix.refine protein1.pdb 072109checks.mtz optimize_wxc=true --overwrite

REMARK Start: r_work = 0.2048 r_free = 0.2388 bonds = 0.015 angles = 1.646
REMARK Final: r_work = 0.1917 r_free = 0.2352 bonds = 0.009 angles = 1.301

Is it possible to refine both anisotropic B factors and optimize ADP factors in the same run.

Any advice would be great.


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