[phenixbb] geometry in phenix.refine

Jianghai Zhu jzhu at cbr.med.harvard.edu
Thu Feb 21 10:18:44 PST 2008

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


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list