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Thanks for all kind replies, I changed the matrix value to 0.05, and it works. Best regards, Yuhe Liang, PhD Structural Biology Lab College of Life Sciences Peking University Beijing, 100871 P.R.China Tel: 86-10-62755714 Fax: 86-10-62765669 =======In your last mail at 2005-12-02 11:42:00 ======= >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > > >On Dec 2, 2005, at 10:21, Tim Gruene wrote: > >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> Hello, >> >> you have to lower the weight between crystrallographic and geometric >> data. >> That is the matrix keyword. I think the default is 0.3, which in my >> experience is much to high at the beginning of refinement. > >Its completely resolution dependent. > >MATRIX 0.3 is correct for about 2.0 A. >for 2.5 A you sometimes need 0.05. >for 1.5 A, 0.5-0.7 tends to be OK. > >I would suggest to aim for 1-2 distances rms between 0.015-0.020 and >angles about 1.5 degrees. > > >> You can try >> setting it to AUTO instead of a number and let refmac figure it out for >> you. If the protein is still distorted, lower the value until the >> geometric statistics look reasonable. >> > >AUTO is great as a rough guess - in my experience towards the end of >refinement you better tune yourself. > > Tassos > >> Tim >> >> -- >> Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> >> On Fri, 2 Dec 2005, [gb2312] 李昂 wrote: >> >>> I used refmac5 to refine a structure out from MR. But it seems >>> the geometric parameters of the output model are really bad, >>> only 50 residues are in core region of Ramachandrans plot, all >>> output from procheck are not good, Rfree value of the model is about >>> 45. Can someone give any suggestions? Is there any special >>> parameters needed when the refinement is on some initial moder? >>> I didn't met such problem on models that are almost correct. >>> >>> Any help are thankful! >>> >>> Yuhe Liang >>> >>> >>> >>> >> = = = = = = = = = = = = = = = = = = = =
