Dear colleagues, regarding Q2:
I do not use TLS parameters, the space group is P1, and yesterday I tried to refine the structure with anisotropic ADP (60,000 reflections against 50,000 parameters) - no positive maximums. Then I used the anisotropic model as input and refined isotropically, the maximums are there again. I use refmac5.5.0100, is it really too late version? Seems to be current version according the websites. Many thanks. Petr 2011/5/27 Jan Dohnalek <dohnalek...@gmail.com>: > 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 > -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
