[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.
Pavel.
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