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






_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb

      
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb

    

_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb