[phenixbb] riding hydrogens

Jianghai Zhu jzhu at idi.harvard.edu
Wed Aug 6 12:39:18 PDT 2008


I remember that I asked a question before which probably is related to  
this one.  The ideal bond distances between the riding hydrogen and  
its attached atom are different in phenix.reduce and mono library.   
That is why I got a huge RMSD bond value after phenix.reduce. It has  
been fixed after my question.  phenix.refine now put all bond distance  
back to what are defined in mono library.  However, a new problem  
rises from this fix.  When using MolProbity to get a new set of riding  
hydrogen atoms, it will give a pretty bad clash score.  If I would  
guess, the bond distance between the riding hydrogen and its attached  
atom is longer in phenix.reduce or MolProbity than the value in mono  
library.

I believe this is a general problem and a "standard" bond distance  
should be used in different programs, especially those programs in one  
package.

-- Jianghai

PS.  Pavel, I think you can test this one using any pdb file.  If you  
still need my file, I will be happy to send it to you.



On Aug 6, 2008, at 3:03 PM, Pavel Afonine wrote:

> 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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