[phenixbb] riding hydrogens

Jianghai Zhu jzhu at idi.harvard.edu
Wed Aug 6 08:17:40 PDT 2008


Yes, I think the phenix group should figure that out :)

-- Jianghai






On Aug 6, 2008, at 5:12 AM, Pavel Afonine wrote:

> 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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