[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
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.
More information about the phenixbb