Dear colleagues, Q2 is solved by new installation of Refmac. Many thanks for your time and effort. I appreciate all your comments.
Petr 2011/5/27 David Cobessi <david.cobe...@ibs.fr>: > Dear Petr, > Before running Refmac, you have to remove the ANISOU line using pdbset for > example. In fact you should not add the TLS contribution to the output > coordinates when you use Refmac except in the last run before to deposit the > file into to PDB. Phenix removes it automatically. > Kind regards, > David > > On 05/27/2011 10:57 AM, Petr Kolenko wrote: >> >> 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 >>> >> >> > > > -- > David Cobessi > Institut de Biologie Structurale > 41, Rue Jules Horowitz > 38027 Grenoble Cedex-1, France > Tel:33(0)438789613 > 33(0)608164340 > Fax:33(0)438785122 > > -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
