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

Pavel Afonine pafonine at lbl.gov
Thu Mar 1 15:04:58 PST 2012

Hi Yuri,

just add them to your model using phenix.ready_set and run refinement as 
I would expect (*) the R-factors drop by 1.5-2% or so.

Your crystals could probably diffract to a higher resolution limit, 
given how well the map looks like for H atoms and at this resolution.

(*) based on:

"On contribution of hydrogen atoms to X-ray scattering"


On 3/1/12 2:52 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

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