[phenixbb] geometry in phenix.refine

[Jianghai Zhu]

The real question is then how to reduce the rmsd after using  
phenix.reduce.

Jianghai



On Feb 21, 2008, at 12:21 PM, Ralf W. Grosse-Kunstleve wrote:

> 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.
> Ralf
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