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(New page: A useful Unix command for evaluating the overall quality of an experimental setup is awk '/CORRECTION PARAMETERS/{for (i=0;i<9;++i) getline;print 1/($1*$2)^0.5}' CORRECT.LP Why? Because t...) |
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CORRECT is the scaling step of XDS. | |||
==Assessing the overall quality of an experimental setup== | |||
A useful Unix command for evaluating the overall quality of an experimental setup is | A useful Unix command for evaluating the overall quality of an experimental setup is | ||
awk '/CORRECTION PARAMETERS/{for (i=0;i<9;++i) getline;print 1/($1*$2)^0.5}' CORRECT.LP | awk '/CORRECTION PARAMETERS/{for (i=0;i<9;++i) getline;print 1/($1*$2)^0.5}' CORRECT.LP | ||
Why? Because this will give you the maximum value of I/sigma(I) for any reflection in your dataset, no matter how good your crystal is. | Why? Because this will give you the best (maximum) value of I/sigma(I) for any reflection in your dataset - even if your crystal is great, all reflections are bound to be worse than that. | ||
Why does the command give you such a useful value? It just finds the line "CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES", skips the next 9 lines, and grabs the values of "a" and "b" from [[CORRECT.LP]]. These values appear in the formula v(I)=a*(v0(I)+b*I^2) which is used by CORRECT to adjust the variances of the intensities, to match their experimental spread. For strong and well-measured reflections, the variance is dominated by the systematic error that is introduced by any beam or detector instability. For weak reflections, v0(I), the variance from counting statistics, dominates. The minimum value for v(I) this formula gives | |||
If your crystal is badly split or broken, then of course a and b will be strongly influenced by the crystal. If your crystal is good (and no matter how good your crystal is!), then a and b will reflect the quality of the beamline. | |||
I personally have seen values lower than 20 for good crystals at bad beamlines. On the bright side, I have also seen a value of 87 for Z. Dauter's 0.98A Proteinase K sulfur-SAD data from J. Holton's APS/22-ID beamline. | |||