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Xdscc12: Difference between revisions
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XDSCC12 is a program for generating [[CC1/2|delta-CC<sub>1/2</sub>]] and delta-CC<sub>1/2</sub> | XDSCC12 is a program for generating [[CC1/2|delta-CC<sub>1/2</sub>]] and delta-CC<sub>1/2-ano</sub> values for XDS_ASCII.HKL (written by [[XDS]]), or for XSCALE.HKL (written by [[XSCALE]]) containing data from several files of type XDS_ASCII.HKL after scaling (with MERGE=FALSE). | ||
It implements the method described in Assmann, Brehm and Diederichs (2016) Identification of rogue datasets in serial crystallography. J. Appl. Cryst. 49, 1021 [http://journals.iucr.org/j/issues/2016/03/00/zw5005/zw5005.pdf], and it does this not only for the individual datasets in XSCALE.HKL, but also for individual frames, or groups of frames, of a single dataset collected with the rotation method and processed by [[XDS]]. | It implements the method described in Assmann, Brehm and Diederichs (2016) Identification of rogue datasets in serial crystallography. J. Appl. Cryst. 49, 1021 [http://journals.iucr.org/j/issues/2016/03/00/zw5005/zw5005.pdf], and it does this not only for the individual datasets in XSCALE.HKL, but also for individual frames, or groups of frames, of a single dataset collected with the rotation method and processed by [[XDS]]. | ||
The program can be downloaded for [ | The program can be downloaded for [https://{{SERVERNAME}}/pub/linux_bin/xdscc12 Linux] or [https://{{SERVERNAME}}/pub/mac_bin/xdscc12 Mac]. | ||
Usage (this text can be obtained with <code>xdscc12 -h</code>): | Usage (this text can be obtained with <code>xdscc12 -h</code>): | ||
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-t: total oscillation (degree) to batch fine-sliced frames into | -t: total oscillation (degree) to batch fine-sliced frames into | ||
FILE_NAME can be XDS or XSCALE reflection file | FILE_NAME can be XDS or XSCALE reflection file | ||
other options can be combined (e.g. -def), and switch the following | other options can be combined (e.g. -def), and switch the following OFF: | ||
-a: individual isomorphous summary values | -a: individual isomorphous summary values | ||
-b: individual (Fisher-transformed) delta-CC1/2 values | -b: individual (Fisher-transformed) delta-CC1/2 values | ||
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-f: individual delta-CC1/2ano reflection numbers | -f: individual delta-CC1/2ano reflection numbers | ||
-w: weighting of intensities with their sigmas | -w: weighting of intensities with their sigmas | ||
-z: | -z: Fisher transformation of delta-CC1/2 values | ||
</pre> | </pre> | ||
The program output is terse but supposed to be self-explanatory. | The program output in the terminal window is terse but supposed to be self-explanatory; it can (and most often should) be saved or re-directed to a file. | ||
xdscc12 ... > xdscc12.log # or xdscc12 ... | tee xdscc12.log | |||
All statistics (tables) produced by xdscc12 may be visualized with e.g. gnuplot, after grepping the relevant lines from the output. | |||
If xdscc12 is used with a XDS_ASCII.HKL reflection file (from XDS), the isomorphous delta-CC<sub>1/2</sub> of a batch of frames (width chosen with the -t option) relative to all data is most easily visualized via [[XDSGUI]] (Statistics tab). Negative numbers indicate a worsening of the overall signal. | |||
If xdscc12 is used with a XSCALE.HKL generated from multiple datasets, the output lines show the contribution of each dataset toward the total CC<sub>1/2</sub>. In this case, the program writes a file called XSCALE.INP.rename_me which shows statistics of delta-CC<sub>1/2</sub> and delta-CC<sub>1/2-ano</sub> values, and has a sorted enumeration of the INPUT_FILEs - the first of these provides the best data set, and the last one is the worst one. This XSCALE.INP.rename_me can then be edited (i.e. for deleting a few data sets with very negative delta-CC<sub>1/2</sub>), and renamed to XSCALE.INP. | |||
Statistics are given (in resolution shells) for the isomorphous and the anomalous signal. | Statistics are given (in resolution shells) for the isomorphous and the anomalous signal. In case of [[SSX]] data (which have few reflections per data set, compared to complete data sets), we typically use nbin of 1 in xdscc12. | ||
To find | To find out about the influence of the ''a'' and ''b'' parameters of the XDS/XSCALE-adjusted error model, you may try the -w option; this assigns the same sigma to all reflections. Likewise, the [https://en.wikipedia.org/wiki/Fisher_transformation Fisher transformation], which serves to make changes in CC<sub>1/2</sub> comparable across resolution ranges, may be switched off for testing purposes, with the -z option. | ||
== Correlation against a reference data set (-r <reference> option) == | == Correlation against a reference data set (-r <reference> option) == | ||
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</pre> | </pre> | ||
in which case <code>sftools</code> outputs only the acentric reflections - only those have anomalous differences. <code>XDSCC12</code> then has to be run with the <code>-s -r anom-reference.hkl</code> option. | in which case <code>sftools</code> outputs only the acentric reflections - only those have anomalous differences. <code>XDSCC12</code> then has to be run with the <code>-s -r anom-reference.hkl</code> option. | ||
== See also == | |||
A complete description of how to process serial crystallography data with XDS/XSCALE is given in [[SSX]]. | |||
A program that implements the method of [https://doi.org/10.1107/S1399004713025431 Brehm and Diederichs (2014)] and theory of [https://doi.org/10.1107/S2059798317000699 Diederichs (2017)] is [[xscale_isocluster]]. | |||
To remove bad frames from a XDS_ASCII.HKL file, you can use the program [[exclude_data_range_from_XDS_ASCII.HKL]], or re-INTEGRATE with the keyword [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#EXCLUDE_DATA_RANGE= EXCLUDE_DATA_RANGE] in [[XDS.INP]]. | |||