Hi Res Model. Maybe its time to Include Hydrogens?
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
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
On Thu, Mar 1, 2012 at 2:53 PM, Yuri
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).
I have no idea if this will help, but there are some parameters in the scope refinement.hydrogens (in GUI: Settings menu-->Advanced-->Hydrogens) that might make a difference. Among other options, you could try refining the hydrogens individually - but note that you should still leave them isotropic. -Nat
Hi Yuri, just add them to your model using phenix.ready_set and run refinement as usual. 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" http://phenix-online.org/newsletter/ Pavel 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
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 Sue 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 [email protected] http://www.biochem.arizona.edu/xray
Hi Yuri, try: hydrogens.refine=individual and let me know if that improves the maps. I found a bug such that if hydrogens.refine=riding then H atom scattering contribution is not included into map (but included everywhere else). I will fix this bug within a week or so. Pavel 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
participants (4)
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Nathaniel Echols -
Pavel Afonine -
Roberts, Sue A - (suer) -
Yuri