[phenixbb] RMSD limit for negative eletron density

Pavel Afonine pafonine at lbl.gov
Sun Feb 7 14:01:03 PST 2016


above 3 "sigma" is alarming. Possibilities are:

- it is misplaced;
- parameters are not refined well (till convergence, for example);
- it is partially occupied so you need to refine occupancy (one q per 
entire ligand).


On 2/7/16 00:42, Singh, Bishal wrote:
> Dear all,
>   I am solving a structure at 1.28 Å. On the ligand, there are some patches
> of negative electron density till 3.5 RMSD. It will be highly appreciated
> if someone can tell the maximum RMSD of allowed negative electron density
> in structure. Thank you!
> With regards,
> Bishal Singh
> PhD student
> German cancer research center (DKFZ)
> University of Heidelberg, Germany
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