Hi Sun:
It might be worth doing a simulated annealing omit refinement in
phenix or CNS, with the residues in question omitted. CNS also allows
you to make a composite-omit map. I haven't seen that in phenix yet
but presumably it is doable.
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 25, 2008, at 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
