[phenixbb] difference map peaks
PAfonine at lbl.gov
Tue Oct 6 14:08:59 PDT 2009
> I am getting difference map peaks (in Coot) of magnitude less than -5
> sigmas (0.24 e/A3) (~10 or more peaks) and equal number of positive
> peaks of same magnitudes.
> The positive peaks hardly have 2fo-fc of more than 1.0 sigma level. I
> presumed this well could be due to bulk solvent or improper mask.
> Therefore I optimized the mask parameters (by giving option under
> "General refinement parameters" in phenix.refine GUI). I could get my
> R free lower as expected but I still got these peaks back. Although I
> am not absolutely sure, but positive peaks are more in polar pocket
> of protein and negative peaks are more in non-polar and aromatic
> pockets. I have PEG, Na acetate in my crystal soup. What these
> negative peaks represent for?
Compute 2mFo-DFc and mFo-DFc Average Kick maps and see if these peaks
are still there. If they disappear - lucky you, if not, then will think
more. If you do not know what an Average Kick map is, check slide #20 here:
> During addition of atoms like Na+, Cl- in map, do one need to careful
> about of the its coordination valency in surrounding pocket. ?
Not 100% sure, but at 3A resolution yes... Hope some one else comments
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