Hi Petr,
a few things to consider:
1) Fourier truncation ripples:
- CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
- Pages 52-55 here:
http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
- Oliver Einsle, et al. Science, 1696 (2002) 297
- Page 267 Figure 4:
Acta Cryst. (2004). D60, 260-274
2) Try:
- refine individual anisotropic ADP for these atoms (and isotropic for the
rest);
- occupancy;
- define charge in input PDB file;
- if it is anomalous scatterer use and refine f' and f''.
I see what you described very often, and typically following the suggestions
that I listed above eliminate the problem.
Pavel.
On Thu, May 26, 2011 at 3:11 AM, Petr Kolenko <kole...@imc.cas.cz> wrote:
> Dear colleagues,
>
> I have two problems in two structure refinements using REFMAC5.
>
> 1) 1.8A resolution, zinc in the active site. Refinement using work
> reflections - ADP for Zinc was about 14. Final refinement including
> all reflections increase ADP to 20 or even higher values - followed by
> very high positive difference density in position of the zinc. I have
> tried also PHENIX, the same thing. I changed ADP manually to 14 and
> only calculated maps (no refinement) look good. May I deposit the
> structure using "manually" fixed ADP according to the best agreement
> to the observed and difference electron density? By the way, it is
> clear that this is zinc.
>
> 2) 1.9A resolution, about 600AA, all of them OK in electron density.
> But, somehow, about ten atoms give very strong positive electron
> density suggesting they are not taken into account in refinement. On
> the other hand, ADPs are reasonable and seem to be refined. All of
> these atoms are fully occupied. I tried to omit whole residues and
> build them again, but the maxima appeared again. Using of PHENIX
> resulted in no difference electron density for these atoms. I have
> also tried to take PHENIX output to REFMAC, but the maxima are there
> again. It is always one or two atoms from the same residues -
> sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but
> still on the same five residues. Does anyone have any idea how to
> solve this problem?
>
> Many thanks for any response.
>
> Petr
>
>
> --
> Petr Kolenko
> petr.kole...@biochemtech.uni-halle.de
> http://kolda.webz.cz
>
