Hi Sun,
you may also want to have a look at this paper:
Acta Cryst. (2008). D64, 515-524.
Iterative-build OMIT maps: map improvement by iterative model building
and refinement without model bias.
Pavel.
On 7/25/2008 10:53 PM, 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
