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

On Thu, Mar 1, 2012 at 2:53 PM, Yuri wrote:

 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