Dear Petr Newer version of refmac is 5.6 and it should be available from ccp4 soon. Meanwhile you can try this version from this website
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz There are versions for mac etc also. regards and I hope you will sort it out soon Garib On 27 May 2011, at 09:57, 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 >> > > > > -- > Petr Kolenko > kole...@imc.cas.cz > http://kolda.webz.cz
