You stated that you have only performed one B-overall refinement. This means that your B-factors are all way off, and your minimization may be stuck in a local minimium. First check to see if you have the energy calculation error suggested by Ed Berry. At your resolution you should perform rounds of B-factor refinement between each minimization run. The refinement will take many cycles to come to convergence. Programs like SHELX and REFMAC do this automatically, in CNS you must do it explicitly. At 1.4A resolution it may be better to use one of these programs instead, as suggested by Fred Vellieu. However, if you are using CNS remember it will take many cycles of refinement (bindividual & minimize) for the minimization to come to convergence. I have written a wrapper for CNS, called PMB, which simplifies the refinement procedure and incorporates some improvements, especially for higher resolution structures. You may want to try it on your model. It is available for download at:
http://xray.utmb.edu/PMB/
Good Luck,
Mark
PS. There is a BB at yahoo for CNS questions. I have included the address in the CC.
On Wed, 2006-06-14 at 12:48 +0800, Yuhe Liang wrote:
*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi, Sorry for a none CCP4 question. I am refining a 1.4A resolution structre with CNS. The model is now almost ok and the Rfree is around 0.23. The problem now is the atom coordinates of the model don't change when I do minimize job, only a overall B-factor refinement was done. And the minimize procedure terminated after 5 steps when Rfactor didn't change. I tried to change the resolution limit and wa setup, but it doesn't work. Simulated annealing can change the coordinates, but after that, minimizing can't refine more on the results. I also tried to use a not-well-refined model as the input model, then the minimizing had effect!? Is there any suggestion? Thanks a lot! 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
|
Sincerely yours, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics' X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-4745 mailto://[EMAIL PROTECTED] http://xray.utmb.edu http://xray.utmb.edu/~white |
