[phenixbb] difference map peaks

Pavel Afonine PAfonine at lbl.gov
Tue Oct 6 14:08:59 PDT 2009

Hi Ravi,

> 1. 
> 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:

> 2. 
> 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 
on this.


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