Hi Sun,
you could address this problem by using CNS omit maps during your
refinement. Resolve and Phenix offer same/similar options, the poor
man's omit option would be delete a stretch of residues manually and
re-refine. Omitting single residues is not enough, as a rule of thumb
you should omit ~5-10% of your structure randomly (don't recall where
I read that, but someone might come up with a reference for that).
Good luck with your refinement,
Jürgen
On 25 Jul 2008, at 22:53, Sun Tang wrote:
Hello Everyone,
I have a question about getting rid of model bias in refinement with
refmac. I solved the structure with molecular replacement. After
final refinement of the structure, I found out some key amino acids
in the structure and wanted to make sure their conformations are
correct. I omitted these amino acids (by setting occupancy to zero)
and refined the structure. I manually fit the amino acids into the
density and refined the structure again. I found these amino acids
return to the precious conformations even though the conformations I
fit were different. Should I omit these amino acids from the
beginning of the refinement? What is the best way to get rid of the
model bias? Your suggestions are greatly appreciated!
Best,
Sun
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
