[phenixbb] riding hydrogens
Pavel Afonine
pafonine at lbl.gov
Wed Aug 6 02:12:24 PDT 2008
Hi Jianghai,
phenix.refine idealizes the geometry of hydrogen atoms using the Monomer
Library definitions for ideal values (if riding model is used). I
presume that phenix.reduce uses some other values when adding H atoms.
So it is not too surprising that the geometries of H atoms are different
after phenix.reduce and phenix.refine.
What is interesting though is why this has a significant impact on the
clash scores.
Pavel.
On 8/5/2008 1:38 PM, Jianghai Zhu wrote:
> Hi,
>
> I used phenix.reduce to add riding hydrogens. After phenix.refine,
> the structure got a good score from MolProbity. However, if I
> stripped the riding hydrogens from the structure and let MolProbity to
> add hydrogens before the analysis, I got a much worse score,
> especially the clash score. Does phenix.refine refine the hydrogen
> positions?
>
> -- Jianghai
>
>
>
>
>
>
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