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1Y13: Difference between revisions
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The easiest thing one can do is to inspect INTEGRATE.LP - this lists scale factor, beam divergence and mosaicity for every reflection. There's a [[jiffies|jiffy]] called "scalefactors" which grep's the relevant lines from INTEGRATE.LP ("scalefactors > scales.log"). This shows the scale factor (column 3): | The easiest thing one can do is to inspect INTEGRATE.LP - this lists scale factor, beam divergence and mosaicity for every reflection. There's a [[jiffies|jiffy]] called "scalefactors" which grep's the relevant lines from INTEGRATE.LP ("scalefactors > scales.log"). This shows the scale factor (column 3): | ||
[[File:1y13-e1-scales.png]] | [[File:1y13-e1-scales.png]] | ||
demonstrating that "something happens" between frame 372 and 373 (of course one has to look at the table to find the exact numbers). | demonstrating that "something happens" between frame 372 and 373 (of course one has to look at the table to find the exact numbers). | ||
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Running "[[xdsstat]] > XDSSTAT.LP" in the e1_1-372 and e2_1-369 directories, we obtain statistics output not available from CORRECT. We open XDSSTAT.LP with the CCP4 program "loggraph", and take a look at [[misfits.pck]], [[rf.pck]], and the other files produced by [[xdsstat]], using [[VIEW]] or [[XDS-Viewer]]: | Running "[[xdsstat]] > XDSSTAT.LP" in the e1_1-372 and e2_1-369 directories, we obtain statistics output not available from CORRECT. We open XDSSTAT.LP with the CCP4 program "loggraph", and take a look at [[misfits.pck]], [[rf.pck]], and the other files produced by [[xdsstat]], using [[VIEW]] or [[XDS-Viewer]]: | ||
[[File:e1_1-372-xdsstat1.png]] Reflections and misfits, by frame - looks normal | [[File:e1_1-372-xdsstat1.png]] | ||
[[File:e1_1-372-xdsstat2.png]] Intensity and sigma by frame - looks normal | |||
[[File:e1_1-372-xdsstat3.png]] "partiality" and profile agreement, by frame - looks good but it's clear that the profiles at high frame number agree worse with the average profiles, possibly due to radiation damage | Reflections and misfits, by frame - looks normal | ||
[[File:e1_1-372-xdsstat4.png]] R_meas, by frame, clearly showing good R_meas in the middle of the dataset | |||
[[File:e1_1-372-xdsstat-raddam.png]] R_d - an R-factor which directly depends on radiation damage. This is calculated as a function of frame number difference and the linear rise indicates significant radiation damage that should be correctable in [[XSCALE]], using the CRYSTAL_NAME keyword. | [[File:e1_1-372-xdsstat2.png]] | ||
[[File:e1_1-372-misfits.png]] | |||
[[File:e1_1-372-rf.png]] R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings. | Intensity and sigma by frame - looks normal | ||
[[File:e1_1-372-xdsstat3.png]] | |||
"partiality" and profile agreement, by frame - looks good but it's clear that the profiles at high frame number agree worse with the average profiles, possibly due to radiation damage | |||
[[File:e1_1-372-xdsstat4.png]] | |||
R_meas, by frame, clearly showing good R_meas in the middle of the dataset | |||
[[File:e1_1-372-xdsstat-raddam.png]] | |||
R_d - an R-factor which directly depends on radiation damage. This is calculated as a function of frame number difference and the linear rise indicates significant radiation damage that should be correctable in [[XSCALE]], using the CRYSTAL_NAME keyword. | |||
[[File:e1_1-372-misfits.png]] | |||
misfits mapped on the detector, showing ice rings. | |||
[[File:e1_1-372-rf.png]] | |||
R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings. | |||
== Solving the structure == | == Solving the structure == | ||
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Although we could now think of using these two files ("firstparts" and "secondparts" merged) and assume that they are peak and inflection wavelengths, it appears more reasonable to try and solve the structure with SAD - which means using "firstparts" only. | Although we could now think of using these two files ("firstparts" and "secondparts" merged) and assume that they are peak and inflection wavelengths, it appears more reasonable to try and solve the structure with SAD - which means using "firstparts" only. | ||
Let's look at the XSCALE statistics for "firstparts": | |||
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 | |||
9.40 6122 844 883 95.6% 2.9% 3.5% 6111 54.76 3.2% 1.4% 79% 2.137 313 | |||
6.64 12037 1611 1621 99.4% 2.9% 3.6% 12035 51.54 3.1% 1.5% 80% 2.259 684 | |||
5.43 15348 2065 2086 99.0% 3.5% 3.7% 15347 47.79 3.7% 1.7% 78% 2.294 908 | |||
4.70 18714 2487 2498 99.6% 3.0% 3.7% 18711 49.55 3.2% 1.5% 72% 1.712 1120 | |||
4.20 21104 2797 2821 99.1% 3.1% 3.7% 21102 47.24 3.3% 1.7% 72% 1.727 1271 | |||
3.84 23316 3095 3117 99.3% 3.8% 4.0% 23313 42.74 4.1% 2.1% 65% 1.617 1420 | |||
3.55 25693 3345 3366 99.4% 4.4% 4.5% 25693 37.93 4.7% 2.6% 50% 1.411 1548 | |||
3.32 28017 3633 3653 99.5% 5.2% 5.2% 28015 32.89 5.6% 3.6% 40% 1.335 1687 | |||
3.13 30266 3842 3848 99.8% 7.2% 7.2% 30264 25.87 7.7% 4.8% 36% 1.158 1797 | |||
2.97 32595 4114 4118 99.9% 10.4% 10.4% 32594 19.26 11.1% 7.7% 30% 1.068 1925 | |||
2.83 34384 4315 4320 99.9% 14.3% 14.8% 34382 14.88 15.3% 10.3% 20% 0.937 2031 | |||
2.71 35654 4475 4478 99.9% 18.3% 19.1% 35652 12.13 19.5% 13.1% 15% 0.891 2110 | |||
2.61 37307 4705 4710 99.9% 27.5% 28.8% 37304 8.44 29.4% 19.8% 11% 0.834 2224 | |||
2.51 38997 4893 4896 99.9% 35.5% 38.0% 38997 6.78 38.0% 26.0% 10% 0.817 2318 | |||
2.43 40036 5026 5027 100.0% 51.3% 55.1% 40032 4.92 54.8% 38.0% 2% 0.738 2387 | |||
2.35 39975 5180 5222 99.2% 71.3% 68.9% 39967 3.78 76.4% 52.7% 21% 0.887 2446 | |||
2.28 42041 5385 5423 99.3% 93.7% 93.1% 42037 2.90 100.3% 66.7% 11% 0.798 2548 | |||
2.21 43012 5538 5541 99.9% 85.7% 88.3% 43011 2.87 91.8% 58.8% 10% 0.818 2644 | |||
2.16 42610 5701 5703 100.0% 113.6% 120.7% 42607 2.13 122.0% 85.4% 4% 0.722 2724 | |||
2.10 38996 5634 5912 95.3% 146.1% 153.9% 38944 1.50 157.8% 122.7% 3% 0.711 2639 | |||
total 606224 78685 79243 99.3% 6.7% 7.2% 606118 16.88 7.2% 12.0% 29% 1.055 36744 | |||
The anomalous correlation is good at low resolution, though not outstanding. At high resolution it rises again but this is presumably due to the ice rings. | |||