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2VB1: Difference between revisions
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SILICON=34.812736 ! account for theta-dependant absorption in the CCD's phosphor. The correction is only | SILICON=34.812736 ! account for theta-dependant absorption in the CCD's phosphor. The correction is only | ||
! significant for hi-res data; 34.812736=32*(value for silicon as printed to CORRECT.LP if SILICON= not given) | ! significant for hi-res data; 34.812736=32*(value for silicon as printed to CORRECT.LP if SILICON= not given) | ||
MAXIMUM_NUMBER_OF_PROCESSORS=4 ! for fast processing on a machine with many cores | MAXIMUM_NUMBER_OF_PROCESSORS=4 ! for fast processing on a machine with many cores (e.g. for 16 cores) | ||
MAXIMUM_NUMBER_OF_JOBS=6 ! | MAXIMUM_NUMBER_OF_JOBS=6 ! "overcommit" the available cores but on the whole this produces results faster (see below) | ||
SPACE_GROUP_NUMBER=1 ! this is known | SPACE_GROUP_NUMBER=1 ! this is known | ||
UNIT_CELL_CONSTANTS= 27.07 31.25 33.76 87.98 108.00 112.11 ! from 2vb1 | UNIT_CELL_CONSTANTS= 27.07 31.25 33.76 87.98 108.00 112.11 ! from 2vb1 | ||
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NUMBER OF UNIQUE ACCEPTED REFLECTIONS 171714 | NUMBER OF UNIQUE ACCEPTED REFLECTIONS 171714 | ||
=== further optimization === | |||
Another round of optimization again improves the R-factors and I/sigma at high resolution a bit, but it also increased the misfits back to 8200. At this point I decided to switch to FRIEDEL'S_LAW=FALSE, and the resulting table is: | |||
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 | |||
1.77 9599 9023 19002 47.5% 1.5% 1.5% 1152 36.81 2.1% 1.6% 0% 0.000 0 | |||
1.26 31196 28239 33446 84.4% 1.4% 1.6% 5914 34.40 2.0% 1.6% 0% 0.000 0 | |||
1.03 40125 35205 43274 81.4% 1.7% 1.7% 9840 30.09 2.4% 2.0% 0% 0.000 0 | |||
0.89 46987 40188 51124 78.6% 2.3% 2.3% 13598 22.03 3.2% 3.4% 0% 0.000 0 | |||
0.80 52229 43723 57738 75.7% 3.9% 3.9% 17012 14.44 5.5% 6.6% 0% 0.000 0 | |||
0.73 56830 46674 64088 72.8% 7.1% 6.8% 20312 9.30 10.1% 13.2% 0% 0.000 0 | |||
0.68 60488 48814 69544 70.2% 13.9% 13.5% 23348 5.26 19.6% 27.1% 0% 0.000 0 | |||
0.63 36190 28598 74736 38.3% 28.2% 29.7% 15184 2.70 39.8% 57.3% 0% 0.000 0 | |||
0.60 9246 7246 79466 9.1% 57.8% 62.4% 4000 1.26 81.8% 122.0% 0% 0.000 0 | |||
total 342890 287710 492418 58.4% 2.8% 2.8% 110360 16.19 3.9% 9.9% 0% 0.000 0 | |||
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 345355 | |||
NUMBER OF REJECTED MISFITS 2448 | |||
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 | |||
NUMBER OF ACCEPTED OBSERVATIONS 342907 | |||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 287724 | |||
Indeed this brings the number of misfits to well below 1%, and it does make some sense. | |||
== XSCALE results == | == XSCALE results == | ||
a | The same strategy as shown for sweep e was used for sweeps a-d and f-h. XSCALE.INP is: | ||
=== main table === | SPACE_GROUP_NUMBER= 1 | ||
UNIT_CELL_CONSTANTS= 27.07 31.25 33.76 87.98 108.00 112.11 ! from 2vb1 PDB entry | |||
! cellparm for a-h gives 27.083 31.269 33.773 87.978 107.998 112.133 | |||
OUTPUT_FILE=lys-xds.ahkl | |||
FRIEDEL'S_LAW=TRUE | |||
RESOLUTION_SHELLS=2.91 2.06 1.68 1.45 1.30 1.19 1.10 1.03 0.97 0.92 0.88 0.84 0.81 0.78 0.75 0.73 0.71 0.69 0.67 0.65 | |||
INPUT_FILE=../a/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../b/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../c/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../d/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../e/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../f/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../g/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
INPUT_FILE=../h/XDS_ASCII.HKL | |||
INCLUDE_RESOLUTION_RANGE=30 0.65 | |||
=== XSCALE.LP main table === | |||
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total 1433128 190017 191232 99.4% 3.3% 3.5% 1431595 33.18 3.5% 3.5% 2% 0.801 170074 | total 1433128 190017 191232 99.4% 3.3% 3.5% 1431595 33.18 3.5% 3.5% 2% 0.801 170074 | ||
Remark: The first frames of sweeps g and h show a shadow in one corner of the detector. Nothing was done by me to exclude this shadow from processing (but one should do so if the resolution should be expanded beyond 0.65 A which the XSCALE statistics suggest to be possible). There is however no facility in XDS to exclude bad areas of specific frames in a dataset; one would need to chop the dataset into two parts. | |||
== Comparison of data processing: published (2006) ''vs'' XDS results == | == Comparison of data processing: published (2006) ''vs'' XDS results == | ||