[phenixbb] positive density around heavy metals

Pavel Afonine pafonine at lbl.gov
Wed Mar 28 09:49:59 PDT 2012

Hi Subhani,

here is some text that I posted on a bb a while ago, so I'm copy-pasting 
it with some minor updates:

These could be Fourier series truncation ripples or residual density 
features that are typically more pronounced for heavier atoms at higher 
Some relevant information to have a look:

1) Pages 19-21, 30, 32, 33 here:

2) CCP4 Newsletter
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev

3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16
Å Resolution: A.
Oliver Einsle, et al. Science, 1696 (2002) 297

4) Page 267 Figure 4:
On the possibility of the observation of valence electron density for
individual bonds in proteins in conventional difference maps
P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev
Acta Cryst. (2004). D60, 260-274

Suggestions for refinement are:

1) make sure the atom is not pulled out of density by incorrectly 
defined/applied restraints or their absence.
2) if site may be partially occupied then try occupancy refinement;
3) refine anisotropic ADP for this site;
4) try f' and f'' refinement if applicable;
5) try more refinement macro-cycles: achieving convergence of refinement 
of occupancy/b-factor may take longer.
6) if none of 1)-5) helped and you are convinced that this is Fourier 
truncation effect then leave it alone.


On 3/28/12 9:05 AM, Subhani Bandara wrote:
> Hi everyone,
> I have refined a protein with a metal-chelate complex at 1.4 
> resolution and saw positive density around some metals that are on a 
> two fold. I refined those chelator complexes with fixed occupancy  to 
> avoid the negative density seen around it as they are partially 
> occupied. Also I had to avoid xyz refinement after fixing them on 
> special position, to avoid moving away from two fold. I have attached 
> a figure of one of those complexes. If I increase occupancy then it 
> shows negative density. How can I get rid of this positive density.
> Thanks in advance for the help
> Subhani

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