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Xdsstat: Difference between revisions
→Tables: explain R_d plot better
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* R-factors as a function of frame number difference (R<math>_d</math> , see [https://www.biologie.uni-konstanz.de/securedl/sdl-eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpYXQiOjE2ODEyNDc2OTgsImV4cCI6MTY4MTkzODg5OCwidXNlciI6MCwiZ3JvdXBzIjpbMCwtMV0sImZpbGUiOiJmaWxlYWRtaW4vYmlvbG9naWUvYWctZGllZGVyaWNocy9wZGZzL0RpZWRlcmljaHMyMDA2X0FjdGFDcnlzdEQucGRmIiwicGFnZSI6ODI4MTV9.qLxfuLL5h1TX0knHEiArN01YRaWbfyVewDl6bv-iHdk/Diederichs2006_ActaCrystD.pdf Diederichs K. (2006) Some aspects of quantitative analysis and correction of radiation damage. Acta Cryst D62, 96-101]). These lines end with " DIFFERENCE" which may be used for "grepping" them from XDSSTAT.LP: | * R-factors as a function of frame number difference (R<math>_d</math> , see [https://www.biologie.uni-konstanz.de/securedl/sdl-eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpYXQiOjE2ODEyNDc2OTgsImV4cCI6MTY4MTkzODg5OCwidXNlciI6MCwiZ3JvdXBzIjpbMCwtMV0sImZpbGUiOiJmaWxlYWRtaW4vYmlvbG9naWUvYWctZGllZGVyaWNocy9wZGZzL0RpZWRlcmljaHMyMDA2X0FjdGFDcnlzdEQucGRmIiwicGFnZSI6ODI4MTV9.qLxfuLL5h1TX0knHEiArN01YRaWbfyVewDl6bv-iHdk/Diederichs2006_ActaCrystD.pdf Diederichs K. (2006) Some aspects of quantitative analysis and correction of radiation damage. Acta Cryst D62, 96-101]). These lines end with " DIFFERENCE" which may be used for "grepping" them from XDSSTAT.LP: | ||
grep DIFFERENCE XDSSTAT.LP > D | grep DIFFERENCE XDSSTAT.LP > D | ||
The red line is a fit to the data, and the green line marks sqrt(2)*(R_d at zero dose). At a dose (frame number) where R_d is sqrt(2) times higher than at the beginning (i.e. where the red line intersects the green line), radiation damage is the dominant source of error. It appears sensible to discard frames beyond this point. | |||
* R_meas as a function of the percentage of expected profile available for [[INTEGRATE|integration]] ("PEAK"), and logarithm of intensity. This table is only available for reflection files written by XDS; the information needed for the table is not in the files written by XSCALE. This table is most relevant for high-mosaicity datasets, and for datasets with few frames. <br> A bit more explanation: the number PEAK is the same as partiality. For example, reflections with PEAK of 75 are "3/4 fullies". These are "scaled up" by CORRECT, for example reflections with PEAK=75 are simply multiplied by 4/3 to recover the "full" intensity (which is written to XDS_ASCII.HKL after scaling). The same scaling-up is done for the sigmas of the reflections.<br> Of course, the PEAK value is itself a bit uncertain, and this uncertainty should in principle be taken into account when scaling-up the sigmas. This is not done since the uncertainty of PEAK is unknown.<br> The table gives (by rows), for values of PEAK from MINPK to 100, the R_meas of the reflections with that value of PEAK. Weak reflections are in the leftmost columns, and the strongest reflections are in the rightmost colums. From column to column the cutoff rises by a factor of 2. The next line then reports the number of reflections of that PEAK and intensity.<br> The idea is that e.g. if you see that strong reflections at PEAK=75 give bad R_meas values, but reflections of the same intensity (same column) give good R_meas values starting at PEAK=80, then you should/can raise MINPK to 80. | * R_meas as a function of the percentage of expected profile available for [[INTEGRATE|integration]] ("PEAK"), and logarithm of intensity. This table is only available for reflection files written by XDS; the information needed for the table is not in the files written by XSCALE. This table is most relevant for high-mosaicity datasets, and for datasets with few frames. <br> A bit more explanation: the number PEAK is the same as partiality. For example, reflections with PEAK of 75 are "3/4 fullies". These are "scaled up" by CORRECT, for example reflections with PEAK=75 are simply multiplied by 4/3 to recover the "full" intensity (which is written to XDS_ASCII.HKL after scaling). The same scaling-up is done for the sigmas of the reflections.<br> Of course, the PEAK value is itself a bit uncertain, and this uncertainty should in principle be taken into account when scaling-up the sigmas. This is not done since the uncertainty of PEAK is unknown.<br> The table gives (by rows), for values of PEAK from MINPK to 100, the R_meas of the reflections with that value of PEAK. Weak reflections are in the leftmost columns, and the strongest reflections are in the rightmost colums. From column to column the cutoff rises by a factor of 2. The next line then reports the number of reflections of that PEAK and intensity.<br> The idea is that e.g. if you see that strong reflections at PEAK=75 give bad R_meas values, but reflections of the same intensity (same column) give good R_meas values starting at PEAK=80, then you should/can raise MINPK to 80. | ||