[phenixbb] Xtriage systematic results is not consistent with HKL2000
Peter Zwart
PHZwart at lbl.gov
Sat Jan 23 09:28:59 PST 2016
Hi Alex,
HKL2000 removes the systematic absences according to the p2221 spacegroup.
Xtriage doesn't see them and can't do anything with them. For this reason,
the Wilson statistics likelihood score used to determine the spacegroup for
P222 and P2221 are exactly the same.
Peter
On 23 January 2016 at 09:11, Alex Lee <alexlee198609 at gmail.com> wrote:
> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
--
-----------------------------------------------------------------
P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
SASTBX: http://sastbx.als.lbl.gov
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-----------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160123/0940faa4/attachment.htm>
More information about the phenixbb
mailing list