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Xdscc12: Difference between revisions
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-z: Fisher transformation of delta-CC1/2 values | -z: Fisher transformation of delta-CC1/2 values | ||
</pre> | </pre> | ||
== Example output == | == Example output == | ||
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INPUT_FILE=/scratch/data/JamesHolton_microfocus/2019/wedge0019/xds/XDS_ASCII.HKL | INPUT_FILE=/scratch/data/JamesHolton_microfocus/2019/wedge0019/xds/XDS_ASCII.HKL | ||
</pre> | </pre> | ||
== Explanation of output == | |||
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 <code>-t</code> option; typically <code>-t 1</code>) 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 strongly negative delta-CC<sub>1/2</sub>), and renamed to XSCALE.INP . Only delete the clearly worst data sets, and not more than 10% of the existing ones! This procedure can be iterated, i.e. after another round of XSCALE, XDSCC12 could be run again. | |||
Overall statistics are reported in the lines starting with <code>a</code> and <code>d</code> for | |||
* <b>only</b> those unique reflections that are actually present in the batch of frame / batch / dataset. These values are in columns 3-6. | |||
* <b>all</b> unique reflections of the merged dataset (but a frame / batch / dataset may not have all unique reflections, so the "all" values report the mean influence). These values are in columns 7-10. | |||
Typically, it is sensible to disregard the "all" values, and to base decisions on the "only" values, because the latter are not affected by the number of reflections of the particular frame / batch / dataset. The words "all" and "only" are used in this sense throughout the terminal and file output of XDSCC12. | |||
Statistics for "only" the unique reflections of a frame / batch/ dataset are given in resolution shells for the isomorphous (in lines starting with <code>b</code> and <code>c</code>) and the anomalous signal (in lines starting with <code>d</code> and <code>e</code>). In case of [[SSX]] data (which have few reflections per data set, compared to complete data sets), we typically use <code>-nbin 1</code> as option, to define only a single resolution shell. | |||
To find out about the influence of the ''a'' and ''b'' parameters of the XDS/XSCALE-adjusted error model, you may try the <code>-w</code> 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 <code>-z</code> option. | |||
== Correlation against a reference data set (-r <reference> option) == | == Correlation against a reference data set (-r <reference> option) == | ||