[phenixbb] geometry in phenix.refine

Pavel Afonine pafonine at lbl.gov
Thu Feb 21 12:28:46 PST 2008

Hi All,

the difference is most likely because of H atoms, indeed (deferent 
"ideal" values used by phenix.reduce and Monomer Library that is used in 
phenix.refine). In the next version of phenix.refine the geometry of H 
atoms will always be regularized (unless free refinement is requested at 
ultra-high resolution), so it will be always consistent with the Monomer 
Library definitions.

Also, I think H atoms should be excluded from geometry statistics 
calculations if riding model is used. I will add this as well.

If all you need is to regularize the geometry, I would use more specific 
tool for this:
% phenix.pdbtools model.pdb --geometry-regularization
You can do it with phenix.refine as well (using wxc_scale=0 and 
strategy=individual_sites), but don't expect the same outcomes since the 
default values of number of iterations and number of macro-cycles are 
different. Also, doing it through phenix.refine will be slower.


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