[phenixbb] riding hydrogens

Pavel Afonine PAfonine at lbl.gov
Wed Aug 6 12:03:06 PDT 2008


Hi Jianghai,

thanks for finding this: you find exotic problems, as always! Could you 
please send us the files (after phenix.refine and after phenix.reduce) 
so we can have a close look at this particular problem ? I can't promise 
to look at it immediately, but it definitely will go into the list. May 
be developers at Duke volunteer looking at this problem.

Thanks!
Pavel.


On 8/6/2008 8:17 AM, Jianghai Zhu wrote:
> 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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>>>
>>>       
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>
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