[phenixbb] Xtriage systematic results is not consistent with HKL2000
Alex Lee
alexlee198609 at gmail.com
Sat Jan 23 09:11:05 PST 2016
Dear All,
I scaled a dataset of SG P2221 in HKL2000 and got systematic absence
results as below, it seems clearly HKL2000 showed the data had systematic
absence violations, but when I used the .sca file from HKL2000 as input in
Xtriage, the result did not show any systematic violations. Which result
should I rely on?
HKL200 Results:
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 Rmeas
Rpim CC1/2 CC*
50.00 5.60 2819.0 103.7 44.8 0.607 0.033 0.040 0.037
0.017 0.998 0.999
5.60 4.45 1801.5 63.8 28.1 0.914 0.043 0.050 0.048
0.022 0.997 0.999
4.45 3.88 1435.3 52.6 25.5 0.980 0.048 0.051 0.054
0.024 0.997 0.999
3.88 3.53 738.7 31.8 20.5 1.117 0.068 0.067 0.075
0.032 0.996 0.999
3.53 3.28 489.7 26.5 20.1 1.134 0.092 0.080 0.102
0.043 0.996 0.999
3.28 3.08 236.3 19.8 17.4 0.975 0.147 0.108 0.162
0.069 0.993 0.998
3.08 2.93 93.4 16.4 16.0 0.850 0.296 0.277 0.327
0.138 0.947 0.986
2.93 2.80 62.9 16.3 16.0 0.737 0.422 0.384 0.467
0.197 0.921 0.979
2.80 2.69 42.6 16.7 16.5 0.677 0.622 0.515 0.688
0.291 0.879 0.967
2.69 2.60 29.3 20.0 19.9 0.680 0.924 0.842 0.000
0.440 0.659 0.891
All reflections 798.1 37.4 22.6 0.873 0.064 0.050 0.068
0.031
Intensities of systematic absences
h k l Intensity Sigma I/Sigma
0 0 3 -0.4 1.3 -0.3
0 0 5 10.4 3.0 3.5
0 0 7 11.4 3.9 2.9
0 0 9 8.7 4.3 2.0
0 0 11 18.6 6.4 2.9
0 0 13 182.9 17.1 10.7
0 0 15 3.0 7.8 0.4
0 0 17 11.9 9.2 1.3
0 0 19 30.0 14.3 2.1
0 0 21 7.4 11.1 0.7
0 0 23 54.2 15.6 3.5
0 0 25 43.1 16.1 2.7
0 0 27 12.5 18.9 0.7
0 0 29 -16.6 20.9 -0.8
0 0 31 31.0 25.4 1.2
0 0 33 3.4 29.2 0.1
0 0 35 -24.2 32.0 -0.8
0 0 37 50.9 42.5 1.2
0 0 39 -53.3 66.4 -0.8
0 0 41 65.8 50.6 1.3
0 0 43 -24.3 46.8 -0.5
0 0 45 -6.1 48.3 -0.1
0 0 47 -14.8 45.8 -0.3
0 0 49 1.1 53.5 0.0
0 0 51 -7.9 64.2 -0.1
Phenix Xtriage Results:
----------Space group identification----------
Analyses of the absences table indicates a number of likely space group
candidates, which are listed below. For each space group, the number of
systematic absence violations are listed under the '+++' column. The number
of
non-absence violations (weak reflections) are listed under '---'. The last
column is a likelihood based score for the particular space group. Note
that
enantiomorphic spacegroups will have equal scores. Also, if absences were
removed while processing the data, they will be regarded as missing
information, rather then as enforcing that absence in the space group
choices.
-------------------------------------------------------------------------------------
| space group | # absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- |
score |
-------------------------------------------------------------------------------------
| P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 4 |
0.000e+00 |
| P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 4 |
0.000e+00 |
| P 2 21 2 | 5 | 3.07 | 16.77 | 5 | 4 |
1.038e+01 |
| P 2 21 21 | 5 | 3.07 | 16.77 | 5 | 4 |
1.038e+01 |
| P 21 2 2 | 5 | 1.89 | 15.21 | 5 | 4 |
1.250e+01 |
| P 21 2 21 | 5 | 1.89 | 15.21 | 5 | 4 |
1.250e+01 |
| P 21 21 2 | 10 | 2.48 | 15.99 | 10 | 4 |
2.288e+01 |
| P 21 21 21 | 10 | 2.48 | 15.99 | 10 | 4 |
2.288e+01 |
-------------------------------------------------------------------------------------
----------List of individual systematic absences----------
Note: this analysis uses the original input data rather than the filtered
data
used for twinning detection; therefore, the results shown here may include
more reflections than shown above.
P 2 2 2: no systematic absences possible
P 2 2 21 (input space group): no absences found
P 21 2 2
( 5, 0, 0): i/sigi = 21.0
( 7, 0, 0): i/sigi = 4.8
( 9, 0, 0): i/sigi = 14.3
( 11, 0, 0): i/sigi = 15.2
( 13, 0, 0): i/sigi = 18.3
( 15, 0, 0): i/sigi = 12.7
( 17, 0, 0): i/sigi = 4.1
P 2 21 2
( 0, 3, 0): i/sigi = 21.3
( 0, 5, 0): i/sigi = 21.4
( 0, 7, 0): i/sigi = 20.7
( 0, 9, 0): i/sigi = 21.4
( 0, 11, 0): i/sigi = 20.7
( 0, 13, 0): i/sigi = 14.5
( 0, 17, 0): i/sigi = 10.4
( 0, 21, 0): i/sigi = 14.4
( 0, 23, 0): i/sigi = 0.8
( 0, 25, 0): i/sigi = 2.3
( 0, 27, 0): i/sigi = 2.0
P 21 21 2
( 0, 3, 0): i/sigi = 21.3
( 0, 5, 0): i/sigi = 21.4
( 0, 7, 0): i/sigi = 20.7
( 0, 9, 0): i/sigi = 21.4
( 0, 11, 0): i/sigi = 20.7
( 0, 13, 0): i/sigi = 14.5
( 0, 17, 0): i/sigi = 10.4
( 0, 21, 0): i/sigi = 14.4
( 0, 23, 0): i/sigi = 0.8
( 0, 25, 0): i/sigi = 2.3
( 0, 27, 0): i/sigi = 2.0
( 5, 0, 0): i/sigi = 21.0
( 7, 0, 0): i/sigi = 4.8
( 9, 0, 0): i/sigi = 14.3
( 11, 0, 0): i/sigi = 15.2
( 13, 0, 0): i/sigi = 18.3
( 15, 0, 0): i/sigi = 12.7
( 17, 0, 0): i/sigi = 4.1
P 2 21 21
( 0, 3, 0): i/sigi = 21.3
( 0, 5, 0): i/sigi = 21.4
( 0, 7, 0): i/sigi = 20.7
( 0, 9, 0): i/sigi = 21.4
( 0, 11, 0): i/sigi = 20.7
( 0, 13, 0): i/sigi = 14.5
( 0, 17, 0): i/sigi = 10.4
( 0, 21, 0): i/sigi = 14.4
( 0, 23, 0): i/sigi = 0.8
( 0, 25, 0): i/sigi = 2.3
( 0, 27, 0): i/sigi = 2.0
P 21 2 21
( 5, 0, 0): i/sigi = 21.0
( 7, 0, 0): i/sigi = 4.8
( 9, 0, 0): i/sigi = 14.3
( 11, 0, 0): i/sigi = 15.2
( 13, 0, 0): i/sigi = 18.3
( 15, 0, 0): i/sigi = 12.7
( 17, 0, 0): i/sigi = 4.1
P 21 21 21
( 0, 3, 0): i/sigi = 21.3
( 0, 5, 0): i/sigi = 21.4
( 0, 7, 0): i/sigi = 20.7
( 0, 9, 0): i/sigi = 21.4
( 0, 11, 0): i/sigi = 20.7
( 0, 13, 0): i/sigi = 14.5
( 0, 17, 0): i/sigi = 10.4
( 0, 21, 0): i/sigi = 14.4
( 0, 23, 0): i/sigi = 0.8
( 0, 25, 0): i/sigi = 2.3
( 0, 27, 0): i/sigi = 2.0
( 5, 0, 0): i/sigi = 21.0
( 7, 0, 0): i/sigi = 4.8
( 9, 0, 0): i/sigi = 14.3
( 11, 0, 0): i/sigi = 15.2
( 13, 0, 0): i/sigi = 18.3
( 15, 0, 0): i/sigi = 12.7
( 17, 0, 0): i/sigi = 4.1
Thanks ahead
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