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3CSL: Difference between revisions
→Scaling
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== Scaling == | == Scaling == | ||
This is XSCALE.INP - we don't try anything fancy: | |||
SPACE_GROUP_NUMBER= 22 | |||
UNIT_CELL_CONSTANTS= 156.80 163.12 595.87 90.000 90.000 90.000 | |||
OUTPUT_FILE=hr.ahkl | |||
INPUT_FILE=../xds.hr1/XDS_ASCII.HKL | |||
OUTPUT_FILE=pk.ahkl | |||
INPUT_FILE=../xds.pk/XDS_ASCII.HKL | |||
OUTPUT_FILE=ip.ahkl | |||
INPUT_FILE=../xds.ip/XDS_ASCII.HKL | |||
and this is an excerpt from XSCALE.LP: | |||
CORRELATIONS BETWEEN INPUT DATA SETS AFTER CORRECTIONS | |||
DATA SETS NUMBER OF COMMON CORRELATION RATIO OF COMMON B-FACTOR | |||
#i #j REFLECTIONS BETWEEN i,j INTENSITIES (i/j) BETWEEN i,j | |||
1 2 38920 0.986 1.0028 -0.1467 | |||
1 3 36555 0.985 0.9971 0.2041 | |||
2 3 35630 0.989 1.0038 -0.0116 | |||
These correlations are worse than what I like to see from MAD datasets. Some of the badness is maybe due to the fact that we used an unrealistic high-resolution limit. If we use INCLUDE_RESOLUTION_RANGE=50 3 the correlations are | |||
The file further reports CHI^2-VALUE OF FIT OF CORRECTION FACTORS around 1.15 which indicates that the scaling model is not entirely adequate, but it is unclear what to change, so we leave it at that (we could use STRICT_ABSORPTION_CORRECTION=TRUE to bring the number closer to 1). | |||
Then we learn | |||
****************************************************************************** | |||
CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES | |||
****************************************************************************** | |||
The variance v0(I) of the intensity I obtained from counting statistics is | |||
replaced by v(I)=a*(v0(I)+b*I^2). The model parameters a, b are chosen to | |||
minimize the discrepancies between v(I) and the variance estimated from | |||
sample statistics of symmetry related reflections. This model implicates | |||
an asymptotic limit ISa=1/SQRT(a*b) for the highest I/Sigma(I) that the | |||
experimental setup can produce (Diederichs (2010) Acta Cryst D66, 733-740). | |||
Often the value of ISa is reduced from the initial value ISa0 due to systematic | |||
errors showing up by comparison with other data sets in the scaling procedure. | |||
(ISa=ISa0=-1 if v0 is unknown for a data set.) | |||
a b ISa ISa0 INPUT DATA SET | |||
6.329E+00 3.527E-04 21.17 22.36 ../xds.hr1/XDS_ASCII.HKL | |||
7.255E+00 8.432E-04 12.79 13.43 ../xds.pk/XDS_ASCII.HKL | |||
6.151E+00 6.548E-04 15.76 16.97 ../xds.ip/XDS_ASCII.HKL | |||
which says that the high-remote indeed scales best of the three datasets, and the peak the worst. This is the output for high-remote - not too impressing! | |||
****************************************************************************** | |||
STATISTICS OF SCALED OUTPUT DATA SET : hr.ahkl | |||
FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=FALSE | |||
450 OUT OF 419653 REFLECTIONS REJECTED | |||
419203 REFLECTIONS ON OUTPUT FILE | |||
****************************************************************************** | |||
... | |||
NOTE: Friedel pairs are treated as different reflections. | |||
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION | |||
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno | |||
Nano | |||
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr | |||
12.39 5724 2008 2112 95.1% 2.5% 3.2% 5674 30.03 3.2% 2.3% 67% 1.522 850 | |||
8.76 10864 3684 3837 96.0% 3.0% 3.5% 10807 26.32 3.7% 3.0% 62% 1.615 1649 | |||
7.15 13926 4749 4984 95.3% 4.3% 4.3% 13862 21.17 5.3% 5.0% 47% 1.397 2149 | |||
6.19 16773 5747 5895 97.5% 5.8% 5.6% 16708 16.66 7.1% 7.2% 30% 1.135 2664 | |||
5.54 19099 6546 6690 97.8% 6.8% 6.5% 19008 14.51 8.4% 9.1% 24% 1.078 3041 | |||
5.06 20933 7167 7374 97.2% 6.9% 6.7% 20828 14.04 8.6% 10.2% 17% 0.999 3321 | |||
4.68 22497 7721 7993 96.6% 6.5% 6.2% 22372 14.51 8.1% 9.9% 15% 0.957 3564 | |||
4.38 24415 8374 8666 96.6% 6.9% 6.6% 24280 13.74 8.5% 10.7% 12% 0.919 3870 | |||
4.13 26251 8985 9164 98.0% 8.7% 8.4% 26113 11.47 10.7% 13.9% 8% 0.863 4203 | |||
3.92 28037 9562 9686 98.7% 11.0% 10.8% 27878 9.38 13.5% 17.9% 6% 0.829 4485 | |||
3.74 29520 10119 10241 98.8% 13.3% 13.4% 29337 7.75 16.4% 22.1% 6% 0.813 4746 | |||
3.58 30822 10537 10662 98.8% 15.9% 15.9% 30639 6.74 19.6% 26.3% 8% 0.818 4933 | |||
3.44 32336 11005 11104 99.1% 21.2% 21.6% 32151 5.20 26.0% 35.8% 5% 0.786 5164 | |||
3.31 32608 11518 11593 99.4% 26.8% 27.5% 32195 4.07 33.1% 48.5% 3% 0.764 5248 | |||
3.20 27228 11396 11998 95.0% 33.2% 34.5% 25691 2.79 42.5% 66.2% 4% 0.729 4287 | |||
3.10 22192 10787 12431 86.8% 41.3% 43.7% 19573 1.94 54.3% 83.7% 1% 0.711 3403 | |||
3.00 18768 10018 12806 78.2% 53.3% 56.5% 15662 1.49 71.6% 110.8% -3% 0.669 2893 | |||
2.92 15878 9250 13096 70.6% 67.6% 71.8% 12570 1.09 93.3% 141.2% -1% 0.670 2408 | |||
2.84 13496 8654 13568 63.8% 74.1% 78.5% 9579 0.88 104.4% 158.4% 1% 0.662 1796 | |||
2.77 7836 6348 13844 45.9% 97.6% 103.5% 2966 0.58 137.9% 207.6% 1% 0.657 545 | |||
total 419203 164175 187744 87.4% 10.2% 10.4% 397893 7.99 12.8% 24.6% 14% 0.882 65219 | |||
== Structure solution == | == Structure solution == | ||