Xdscc12: Difference between revisions

26 bytes added ,  13 April 2022
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(→‎See also: remove link to exclude_data_range_from_XDS_ASCII.HKL program; this is no longer needed with recent versions of XDS because CORRECT now also understand EXCLUDE_DATA_RANGE.)
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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.  
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
  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.
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 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.
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. 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.
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 1
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.


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.
== Example output with explanation ==


== Correlation against a reference data set (-r <reference> option) ==
== Correlation against a reference data set (-r <reference> option) ==
2,684

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