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 > [email protected] > http://kolda.webz.cz
