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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