60% occupied Zn site perhaps ? Q2 do you have leftover atoms from a previous dual conformation refinement ? Try deleting the corresponding residues in a texteditor and not coot to ensure they are really gone, then rebuild the section into the new diff- map.
Jürgen ...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On May 26, 2011, at 6:11, Petr Kolenko <[email protected]> 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
