Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps are constructed by
Fourier transform without the 0 0 0 reflection, they have mean of zero (because the mean of a
sinusoid over one period is zero). That means that any time you add positive (difference) density,
which raises the mean value of the absolute map, the Fourier map has to sink down a little to bring
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflection, this would move the floor down
everywhere by a small amount to balance the large increase at the local peak, and it would not go
below the negative contour limit. But without the ultra-low resolution amplitudes the FT cannot make
a constant offset, and instead you get sagging around the peak, like a water-bed sagging around the
spot where a child (the peak) is standing. This could lead to the sagging part going below the
negative contour and giving you the red density.
However I would not have expected the negative density to be quite so localized around the peak -
depending on your low-res cutoff. As John Bacik suggested you should check for a mis-modeled part of
a symm-related molecule, but if that were the case, you should see the red density even before
omitting the loop, and you should see the red density somewhere else on your model. If it just
appeared after omitting the loop, it could be due to the map sagging under the weight of the peak,
and should go away as soon as the residue is replaced.
eab
Renuka Kadirvelraj wrote:
Hi CCP4bb,
We would greatly appreciate your advice regarding an odd problem that has cropped up with one of our
crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in
the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to
rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit map showed the positive
density expected from the omission of the loop (colored green in attached pics). However, flanking
the positive density, there is a complimentary negative density (in red). We are puzzled as to the
cause of the appearance of the negative density. Can you help us?
Many thanks,
Renu
---------------------------------------------
Renu Kadirvelraj, Ph.D.
Research Scientist
A428, Biochemistry and Molecular Biology
120, East Green Street
University of Georgia
Athens, GA 30602
Tel: (706) 583 0303
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