[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.


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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