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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 off:
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  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: no Fisher transformation of delta-CC1/2 values
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   -z: Fisher transformation of delta-CC1/2 values
 
</pre>
 
</pre>
    
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
If xdscc12 is used with XDS_ASCII.HKL, 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); the delta-CC<sub>1/2-ano</sub> may be plotted with e.g. gnuplot after grepping the relevant lines from the output.
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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>. Negative numbers indicate a worsening of the overall signal. 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 list on INPUT_FILEs - the first one provides the best data set, and the last one is the worst one. This XSCALE.INP.rename_me can then be edited (i.e. 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.
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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 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.  
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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.
 
  −
A complete description of how to process serial crystallography data with XDS/XSCALE is given in [[SSX]]. In case of SSX data (which typically have few reflections per data set, compared with complete data sets), we typically use nbin of 1.
  −
 
  −
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]].
      
== 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.
 +
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== 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]].
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