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Hi, all:
I collected Cu-MAD data, I tried to detect anomalous signals using
scalepack.
I followed tutorial: first: scale data with 'anomalous' checked, and chi
square around 1.
second: turn off 'anomalous' flag, and merge I+ and
I-.
Output is as follows:
Shell Summary of observation redundancies:
Lower Upper % of reflections with given No. of observations
limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 >19
total
99.00 5.48 1.8 22.8 75.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0
98.2
5.48 4.35 0.0 15.0 85.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
4.35 3.80 0.0 12.7 87.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
3.80 3.45 0.0 11.3 88.7 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
3.45 3.21 0.0 10.5 89.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
3.21 3.02 0.0 9.8 90.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
3.02 2.87 0.0 9.3 90.7 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
2.87 2.74 0.0 9.0 91.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
2.74 2.64 0.0 8.7 91.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0
100.0
2.64 2.54 2.5 8.3 89.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0
97.5
All hkl 0.4 11.9 87.7 0.0 0.0 0.0 0.0 0.0 0.0 0.0
99.6
Shell I/Sigma in resolution shells:
Lower Upper No. of reflections with I / Sigma less than
limit limit 0 1 2 3 5 10 20 >20 total
99.00 5.48 17 25 45 71 100 222 1790 2041 3831
5.48 4.35 13 21 30 43 65 174 953 2744 3697
4.35 3.80 19 40 68 100 168 345 1274 2364 3638
3.80 3.45 16 45 92 148 256 580 1761 1884 3645
3.45 3.21 23 76 164 245 469 961 2509 1105 3614
3.21 3.02 59 171 327 497 788 1533 3001 581 3582
3.02 2.87 98 287 528 751 1150 1978 3219 377 3596
2.87 2.74 153 413 762 1082 1552 2453 3335 233 3568
2.74 2.64 244 664 1131 1541 2175 3020 3511 77 3588
2.64 2.54 388 1049 1670 2107 2699 3232 3410 10 3420
All hkl 1030 2791 4817 6585 9422 14498 24763 11416 36179
Shell I/Sigma in resolution shells:
Lower Upper % of of reflections with I / Sigma less than
limit limit 0 1 2 3 5 10 20 >20 total
99.00 5.48 0.4 0.6 1.2 1.8 2.6 5.7 45.9 52.3 98.2
5.48 4.35 0.4 0.6 0.8 1.2 1.8 4.7 25.8 74.2 100.0
4.35 3.80 0.5 1.1 1.9 2.7 4.6 9.5 35.0 65.0 100.0
3.80 3.45 0.4 1.2 2.5 4.1 7.0 15.9 48.3 51.7 100.0
3.45 3.21 0.6 2.1 4.5 6.8 13.0 26.6 69.4 30.6 100.0
3.21 3.02 1.6 4.8 9.1 13.9 22.0 42.8 83.8 16.2 100.0
3.02 2.87 2.7 8.0 14.7 20.9 32.0 55.0 89.5 10.5 100.0
2.87 2.74 4.3 11.6 21.4 30.3 43.5 68.8 93.5 6.5 100.0
2.74 2.64 6.8 18.5 31.5 42.9 60.6 84.1 97.8 2.1 100.0
2.64 2.54 11.1 29.9 47.6 60.1 77.0 92.2 97.3 0.3 97.5
All hkl 2.8 7.7 13.3 18.1 25.9 39.9 68.1 31.4 99.6
Summary of reflections intensities and R-factors by shells
R linear = SUM ( ABS(I - <I>)) / SUM (I)
R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2)
Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) )
In all sums single measurements are excluded
Shell Lower Upper Average Average Norm. Linear Square
limit Angstrom I error stat. Chi**2 R-fac R-fac
99.00 5.48 8615.3 482.4 482.4 3.516 0.047 0.057
5.48 4.35 6515.9 285.4 285.4 0.825 0.020 0.022
4.35 3.80 3874.3 172.3 172.3 0.802 0.023 0.023
3.80 3.45 2386.9 113.4 113.4 0.926 0.029 0.030
3.45 3.21 1289.7 71.3 71.3 1.042 0.039 0.039
3.21 3.02 676.0 46.9 46.9 1.057 0.055 0.051
3.02 2.87 445.4 38.9 38.9 1.028 0.071 0.066
2.87 2.74 292.9 34.7 34.7 1.006 0.095 0.088
2.74 2.64 179.2 33.7 33.7 0.910 0.146 0.134
2.64 2.54 125.9 41.0 41.0 0.899 0.252 0.224
All reflections 2506.8 135.3 135.3 1.182 0.037 0.046
____________________________________________________________________________
_____
I am confused by Chi square and R factor values. It seems that at higher
resolution, R factor is very high, does it mean there is a big difference
between I+ and I-? Is it caused by synchrotron radiation damage? Besides,
what are the ideal values for R factors, should they be constant throughout
all resolution shells?
Meanwhile, Chi square values are mostly around 1, which should be indicative
of no anomalous signal. Where does chi square derive from? and, what is the
real meaning of it?
thank you very much
Yi
