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3CSL: Difference between revisions
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The verdict is clear: bad ISa, anomalous correlation > 30% only to about 5 A. The reason becomes clear if we load FRAME.cbf into [[XDS-Viewer]], and zoom in: | The verdict is clear: bad ISa, anomalous correlation > 30% only to about 5 A. The reason becomes clear if we load FRAME.cbf into [[XDS-Viewer]], and zoom in: | ||
[[File:3csl-frame.png]] | [[File:3csl-frame.png]] | ||
It is clear that these split reflections provide bad data. Fortunately it seems that in other areas of the detector, the reflections look better. | It is clear that these split reflections provide bad data. Fortunately it seems that in other areas of the detector, the reflections look better. | ||
We can use the "scalefactors" [[jiffies|jiffy]] to investigate the scale factor, and the estimates for mosaicity and beam divergence of each frame: | |||
[[File:3csl-pk-scalefactors.png]] | |||
[[File:3csl-pk-mosaicity.png]] | |||
[[File:3csl-pk-beamdiv.png]] | |||
Next, we can use xdsstat to get frame-wise statistics from XDS_ASCII.HKL: | |||
[[File:3csl-pk-xdsstat1.png]] | |||
This shows a "jump" around frame 225 which is always bad for experimental phasing! | |||
[[File:3csl-pk-xdsstat2.png]] | |||
Around frame 225 the data are weakest, but they recover. | |||
[[File:3csl-pk-xdsstat3.png]] | |||
In particular the correlation against standard profiles (blue curve) is ''really'' low. | |||
[[File:3csl-pk-xdsstat4.png]] | |||
R-factors peak around frame 225. | |||
[[File:3csl-pk-rd.png]] | |||
R_d helps to quantify radiation damage. Unfortunately, for this dataset this "R-factor as a function of frame number difference" behaves wildly, so we cannot use 0-dose extrapolation, like we successfully did for [[1Y13]]. | |||
=== Inflection === | === Inflection === | ||
360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/3csl-ip.tar here] (1.8 Gb). | 360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/3csl-ip.tar here] (1.8 Gb). | ||
CORRECT.LP has: | |||
a b ISa | |||
6.514E+00 5.329E-04 16.97 | |||
... | |||
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 | |||
8.28 26530 7039 7111 99.0% 4.4% 4.6% 26516 23.79 5.2% 3.7% 57% 1.526 3211 | |||
5.90 48700 12589 12598 99.9% 8.7% 8.5% 48700 14.00 10.2% 9.2% 23% 1.052 5989 | |||
4.83 62546 16177 16208 99.8% 12.0% 11.5% 62546 10.85 13.9% 14.5% 12% 0.912 7784 | |||
4.18 72644 19076 19117 99.8% 13.6% 13.1% 72637 9.64 15.9% 17.3% 8% 0.850 9229 | |||
3.75 80829 21710 21740 99.9% 23.8% 24.0% 80829 5.92 27.9% 32.0% 1% 0.770 10553 | |||
3.42 86652 23874 23917 99.8% 38.5% 39.9% 86652 3.71 45.2% 53.8% 3% 0.737 11620 | |||
3.17 73630 25264 26115 96.7% 64.4% 68.0% 71837 1.82 78.5% 109.4% 3% 0.693 10945 | |||
2.96 48079 22582 28004 80.6% 99.2% 107.3% 43325 0.86 129.6% 186.7% 3% 0.654 7797 | |||
2.80 28417 17801 29828 59.7% 155.6% 168.5% 20099 0.43 214.2% 307.3% 3% 0.613 3713 | |||
total 528027 166112 184638 90.0% 17.6% 17.8% 513141 5.98 20.9% 38.7% 10% 0.816 70841 | |||
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 534898 | |||
NUMBER OF REJECTED MISFITS 6486 | |||
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 | |||
NUMBER OF ACCEPTED OBSERVATIONS 528412 | |||
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 166224 | |||