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XDSCC12 is a program for generating delta-CC<sub>1/2</sub> values for XDS_ASCII.HKL (written by XDS), or for XSCALE.HKL containing several files of type XDS_ASCII.HKL after scaling in XSCALE (with MERGE=FALSE). | 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 containing several files of type XDS_ASCII.HKL after scaling in [[XSCALE]] (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 [ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12 | The program can be downloaded for [ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin/xdscc12 Linux] or [ftp://turn5.biologie.uni-konstanz.de/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>): | ||
<pre> | <pre> | ||
usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -< | xdscc12 KD 2019-04-30. Academic use only; no redistribution. -h option shows options. | ||
Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst. 49, 1021-1028 | |||
running 'xdscc12 -h' on 20190502 at 16:11:46 +0200 | |||
usage: xdscc12 [-dmin <lowres>] [-dmax <highres>] [-nbin <nbin>] [-mode <1 or 2>] [-<abcdefstwz>] [-r <ref>] FILE_NAME | |||
dmin (default 999A), dmax (default 1A) and nbin (default 10) have the usual meanings. | |||
mode can be 1 (equal volumes of resolution shells) or 2 (increasing volumes; default). | mode can be 1 (equal volumes of resolution shells) or 2 (increasing volumes; default). | ||
-r: next parameter: ASCII reference file with lines: h,k,l,Fcalc or h,k,l,Fcalc+,Fcalc- | |||
this allows calculation of CC of isomorphous signal with reference | |||
other options can be combined (e.g. -def), and switch the following | -s: read two columns from reference: Fcalc(+), Fcalc(-). | ||
this allows calculation of CC of anomalous signal with that of reference | |||
-t: total oscillation (degree) to batch fine-sliced frames into | |||
FILE_NAME can be XDS or XSCALE reflection file | |||
other options can be combined (e.g. -def), and switch the following OFF: | |||
-a: individual isomorphous summary values | |||
-b: individual (Fisher-transformed) delta-CC1/2 values | |||
-c: individual delta-CC1/2 reflection numbers | |||
-d: individual anomalous summary values | |||
-e: individual (Fisher-transformed) delta-CC1/2ano values | |||
-f: individual delta-CC1/2ano reflection numbers | |||
-w: weighting of intensities with their sigmas | |||
-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 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. A program that implements the method of [https://doi.org/10.1107/S1399004713025431 Brehm and Diederichs (2014)] | == Correlation against a reference data set (-r <reference> option) == | ||
The correlation of the experimental data set against the user-supplied reference data is shown in the lines starting with r. | |||
To prepare a reference data set if the refinement was done with phenix.refine, one could use e.g. | |||
<pre> | |||
mtz2various hklin 2bn3_refine_001.mtz hklout temp.hkl <<eof | |||
OUTPUT USER * | |||
LABIN FC=F-model PHIC=PHIF-model | |||
END | |||
eof | |||
</pre> | |||
- the column corresponding to PHIC will not be used by xdscc12. Alternatively, | |||
<pre> | |||
sftools | |||
read mymodel_001.mtz | |||
write temp.hkl format(3i5,f10.3) col F-model | |||
y | |||
quit | |||
</pre> | |||
=== Reference data with anomalous signal (additional -s option) === | |||
The correlation of the anomalous difference of the experimental data set against the anomalous signal of the user-supplied reference data is shown in the lines starting with s. | |||
A simple way to obtain Fcalc(+) and Fcalc(-) is to run <code>phenix.refine</code> with options (in case of S as anomalous scatterer) | |||
refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-),merged" refinement.refine.anomalous_scatterers.group.selection="element S" strategy=individual_sites+individual_adp+group_anomalous+occupancies | |||
and then | |||
<pre> | |||
sftools <<eof | |||
read mymodel_001.mtz | |||
write anom-reference.hkl format(3i5,2f10.3) col "F-model(+)" "F-model(-)" | |||
y | |||
quit | |||
eof | |||
</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. | |||
== 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]]. | |||