Slabs are almost always due to rogue huge reflection(s).
If you run mtzdump on the refmac_output.mtz you will find the maximum
value and average value of each column.
If you run
fft hklin refmac_output.mtz
LABI F1=FWT PHI=PHWT then the log file gives you the indices of the
largest reflection.
(search for "largest" in the log file..)
If that term is >>> than the mean there might well be something wrong -
you will have to track back through the data processing to find out what..
If you have used scala the input mtz will have listed all measurements
of that reflection.
(You can use mtzdump with keyword START h k l to see what its value is..)
Eleanor
hayato Jumonji wrote:
Dear all, I've phased 3 wavelength SeMet dataset with SHELX and the
resulting mtz on Coot shows ~5.4 A apart slabs in water channel. I've
captured part of the electron density at 0.4sigma. The slabs appear through
out the electron density and parallel to AB plane (space group P21212). Most
of the electron density in the protein region looks good. But about 30% of
the protein region is affected by this regular noise and appeared choppy.
Although the protein region is still choppy, I do not see the slabs on
another dataset. Could anyone suggest where I am getting this noise and how
to avoid it ? Thanks in advance.
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