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I believe I figured out the reason (but not the solution) to this problem:
2) This is unrelated to SHELX: I integrated and scaled in HKL2000 and then
converted to MTZ format. All of the CCP4 programs say that my data is
incomplete, but the scalepack log file says I'm 100% complete in all shells.
I looked at the MTZ file with mtzdump and it says I'm missing data around
1.7-1.5A, but not in higher-resolution shells. Anyone have an idea what's
going on?
The problem is that when I merge the high-res and low-res wedges, HKL2000
scales the intensities such that the range starts very low:
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
50.00 2.11 38.3 0.5 0.3 1.540 0.041 0.049
2.11 1.68 9.5 0.2 0.1 1.112 0.077 0.081
1.68 1.46 3.7 0.1 0.1 1.063 0.097 0.132
1.46 1.33 2.2 0.1 0.1 0.997 0.084 0.087
1.33 1.23 1.6 0.1 0.1 0.963 0.109 0.114
1.23 1.16 1.3 0.1 0.1 0.938 0.134 0.126
1.16 1.10 1.0 0.1 0.1 0.865 0.165 0.155
1.10 1.06 0.6 0.1 0.1 0.754 0.253 0.239
1.06 1.02 0.4 0.1 0.1 0.674 0.374 0.363
1.02 0.98 0.2 0.1 0.1 0.627 0.543 0.484
This is not a problem when processing the high-res data separately; I
have, on the other hand, observed this result for other proteins where I
had high- and low-res wedges.
The missing reflections arise from HKL2000 setting sigma(I) to 0.0 in
cases where it was very low - I assume this is just rounding down. This
has not happened with similar data in the past, but for this crystal (my
best for that protein!) more than 10% of the reflections have this
problem. scalepack2mtz treats all reflections with sigI=0 as missing
(based on the output, and the source code - this is ccp4 5.0.2).
I guess I have three choices:
1) Tell HKL2000 to *not* scale everything down so much. (Is this even
possible? FYI, ighest intensity is 1665, which is the only intensity
above 1000.)
2) Modify scalepack2mtz to keep reflections with sigI=0. I have no idea
what the effect would be on other programs of zero sigma values.
3) Change sigI to 0.1 in all cases where it's 0.0. I suspect this is
probably a bad idea.
Any thoughts?
thanks,
Nat
