In the last months we have seen different versions of Refmac give different maps when displayed in Coot, i.e. one version giving "nicer" agreement and no difference peaks in some difficult areas and another version resulting in sharp differences where it was hard to build the protein. We did not investigate much further as most of the time use of two or three versions gave us a good picture of what's going on ..probably a feature which would disappear with newer versions anyway.
What's the version of Refmac you use, Petr? Jan Dohnalek On Thu, May 26, 2011 at 12:11 PM, 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 > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
