[phenixbb] geometry in phenix.refine

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Feb 21 09:21:16 PST 2008

Hi Jianghai,
> Shouldn't the hydrogen atoms be added with perfect geometry?
phenix.refine uses the monomer library definitions, phenix.reduce
has its own internal database. Since nobody really knows what
"perfect" is, these (probably) don't agree exactly (but I haven't
actually checked).
BTW: older versions of phenix.refine reported mean deviations
instead of root-mean-squared deviations. This could be another
source of mismatching numbers.

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