[phenixbb] Hi Res Model. Maybe its time to Include Hydrogens?

Roberts, Sue A - (suer) suer at email.arizona.edu
Thu Mar 1 15:13:42 PST 2012

Hi Yuri,

Are you sure that the hydrogen atoms are included when the difference map is calculated (and/or when the map coefficients are calculated), not just in the refinement? Even for small molecule structures with resolutions better than 0.85 A riding hydrogen atoms usually account for the electron density very well, especially for phenyl rings. Iin phoenix, the geometry will be restrai


On Mar 1, 2012, at 3:52 PM, Yuri wrote:

> Dear users,
> I am refining a 400 aa protein with data out to 1.16 A (real data). I 
> am almost finished with refinement. I have good geometry, complete model 
> and ligands Rw 0.11 Rf 0.13.
> Difference maps seem to be asking for more. See attached screen 
> shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma.
> How should I handle this? I have used hydrogens all along (riding).
> Thanks for your time
> -- 
> Yuri Pompeu
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Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1041 E. Lowell St.,  Tucson, AZ 85721
Phone: 520 621 8171
suer at email.arizona.edu

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