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Xdsstat: Difference between revisions
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* R-factors as a function of frame number difference (R<math>_d</math> , see [http://strucbio.biologie.uni-konstanz.de/strucbio/files/Diederichs_ActaD62_96.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 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/Diederichs_ActaD62_96.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 | ||
* R_meas as a function of the percentage of expected profile available for [[INTEGRATE|integration]] ("PEAK"), and logarithm of intensity. | * 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. | ||
The first two of these tables may be visualized with [http://www.ccp4.ac.uk/html/loggraph.html loggraph]. | |||
=== Images === | === Images === | ||
The following quantities mapped onto the detector surface: | The following quantities mapped onto the detector surface: | ||
* misfits.pck: outliers identified in CORRECT. Useful e.g. to identify [[ice rings]]. | * misfits.pck: outliers identified in CORRECT. Useful e.g. to identify [[ice rings]]. | ||
* corr.pck: correlation with standard profiles | |||
* peaks.pck: completeness of profiles | |||
* rf.pck: R-factor (very interesting) | * rf.pck: R-factor (very interesting) | ||
* anom.pck: anomalous signal (very interesting) | * anom.pck: anomalous signal (very interesting) | ||
* scales.pck: | * scales.pck: intensity ratios between symmetry-related reflections, after scaling (very interesting) | ||
* nobs.pck: observed reflections (not very interesting) | * nobs.pck: observed reflections (not very interesting) | ||
* rlps.pck: reciprocal lorentz factor (not very interesting) | * rlps.pck: reciprocal lorentz factor (not very interesting) | ||
These images are in the .pck format and may be visualized | These images are in the .pck format and may be visualized with the (obsolete) [[VIEW]] program; it should also be possible to use [[XDS-Viewer]]. | ||
N.B.: Images are currently only produced for reflection files coming from XDS, ''not'' for those from XSCALE. The reason is that the latter lack a line like | N.B.: Images are currently only produced for reflection files coming from XDS, ''not'' for those from XSCALE. The reason is that the latter lack a line like | ||
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== Availability == | == Availability == | ||
[https://{{SERVERNAME}}/pub/linux_bin/xdsstat Linux] and [https://{{SERVERNAME}}/pub/mac_bin/xdsstat Mac] binaries are available. | |||
I (Kay dot Diederichs at uni-konstanz dot de) appreciate feedback. | I (Kay dot Diederichs at uni-konstanz dot de) appreciate feedback. | ||
The source code is in Fortran90 and requires a Fortran90-compiled CCP4 library, so few people are currently in a position to compile and link the program. | |||
The source code is in Fortran90 and requires a Fortran90-compiled CCP4 library, so few people are currently in a position to compile and link the program | |||