regarding the first question - is it now not much more common to refine only against work reflections, and not do a final refinement agains all reflections?
(avoids the problem rather than solve it, I admit)
regarding the second question - if you take the model from refmac and calculate a map using that and the original processed dataset (i.e. before it has "seen" refmac), do the peaks also show up?
(I guess you have checked the pdb-file output from refmac carefully in a text editor?)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 26 May 2011, at 12:11, Petr Kolenko 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
> [log in to unmask]
> http://kolda.webz.cz
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