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

[Sue Roberts <suer@email.arizona.edu>]

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In reply to the comments, I've received (quickly! you guys are fast),

Ed Berry: 
The peaks are at the atom positions. They're not hollow shells (which series
termination effects usually show up as). There is no positive (or zero) density
at the atomic center, just the negative density.

bds:
I have entered the wavelength in shelx. The shelx maps are OK. It's the refmac
maps that have problems. Scattering factors for Cu are being used in refmac/fft
(according to the log file) If Cu were being modeled as C, the difference peaks
would be positive and/or B would be very low (been there, done that with Fe). 

bds said in his reply that, if the wavelength in shelx is entered the proper
dispersion terms will be selected. This isn't what the shelx faq says and, if
it's true, may explain the different behavior of the two programs. (Yes, I know
I could have entered a DISP term in shelx,, but everything is OK in shelx, so I
didn't bother.)

Bart Hazes:
1.7 is pretty much the resolution limit, (I/sig(I) = 1.5 unmerged, Rmerge = 0.25
in shell).

This problem is specific to a data set collected to maximize the anomalous
scattering from the metal (yes, in retrospect not a good idea, but the identity
of the metal is unambiguous).
Other data sets (different crystal conditions) collected with 1 A x-rays don't
have this problem. If it's in the dispersion correction, I could change the
scattering factor library. I also can't find anyplace that refmac asks for the
x-ray wavelength. It doesn't seem to be in the mtz file (or am I missing that
too?)

Since shelx seems to give me answers I like, I'll continue refining that way,
but it'd be nice to get equivalent difference maps (within reason) with refmac.

Sue




"Edward A. Berry" wrote:
> 
> Sue,
> Are there discrete negative peaks near the atom position
> in the difference map, or shells of negative density
> surrounding a positive peak at the atom position?
> I have the latter (or vice versa) at iron positions
> in a cytochrome, which I attribute to scalling problems.
> Manually adjusting the B-factor for Fcalc in FFT can
> smooth it out.
> 
> Ed
> 
> Sue Roberts wrote:
> >
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > 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

-- 

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