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[ccp4bb]: maps have negative peaks around "heavy" atoms (Cu, Cl, S)



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Hello,

I've been refining a structure that contains Cu atoms. When I refine with refmac
(using the ccp4 interface), R, Rfree are quite low (0.16, 0.19), and the "heavy"
atoms (Cu, Cl, many S) have large (> 5 sigma) negative peaks around them. These
are the largest 12 peaks in the difference map. They are located essentially at
the atomic positions.

Data is complete to 1.7 A and was measured at a wavelength where Cu anomalous
scattering is maximized (1.37 A). I'm thinking the problem is related to the
wavelength used in data collection (refmac contains scattering factors and
dispersion terms for Cu, Mo radiation.)
CCP4 is using the proper Cu, Cl scattering factors (and anyway, if the
contributions from these atoms were calculated as carbon the difference map
peaks would be positive.) The temperature factors on the Cu, Cl, and
non-disordered S atoms look fine.

When I refine with shelxl, the maps look normal, but the R factor isn't quite so
good (0.17,
0.21). (The shelx faq says it also selects scattering factors for Cu, Mo, or Ag
radiation, in this case it would also choose Cu radiation.) So, if the problem
is related to scattering factors, wouldn't shelx show similar behavior?

Any ideas as to what I've missed and how to make refmac work?

Sue

--------------------------
Sue Roberts
Dept. of Biochemistry & Molecular Biophysics,
University of Arizona
suer@u.arizona.edu (520) 621-8171