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Xdscc12

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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 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]].
The program can be downloaded for [ftphttps://turn5.biologie.uni-konstanz.de{{SERVERNAME}}/pub/linux_bin/xdscc12.rhel6.64 Linux 64bit] or [ftphttps://turn5.biologie.uni-konstanz.de{{SERVERNAME}}/pub/mac_bin/xdscc12-mac Mac].
Usage (this text can be obtained with <code>xdscc12 -h</code>):
<pre>
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, 1021-1028running 'xdscc12 -h' on 20190502 at 16:11:46 +0200usage: xdscc12 [-dmin <lowres> ] [-dmax <highres> ] [-nbin <nbin> ] [-mode <1 or 2> ] [-<abcdeftwrzabcdefstwz> ] [-r <ref>] FILE_NAMEdmax dmin (default 999A), dmin 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).
-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 -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 -r: also show CC against reference dataset (e.g. Icalc from model) FILE_NAME can be XDS or XSCALE reflection file other options can be combined (e.g. -def), and switch the following offOFF: -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>
The program output in the terminal window is terse but supposed to be self-explanatory. Part of ; it is can (and most easily often should) be saved or re-directed to a file. xdscc12 ... > xdscc12.log # or xdscc12 ... | tee xdscc12.logAll statistics (tables) produced by xdscc12 may be visualized via XDSGUIwith e.g. gnuplot, howeverafter grepping the relevant lines from the output.If xdscc12 is used with a XDS_ASCII.HKL reflection file (from XDS), that currently only deals with the isomorphous signal delta-CC<sub>1/2</sub> of a batch of frames (width chosen with the -t option) relative to all datais most easily visualized via [[XDSGUI]] (Statistics tab). Negative numbers indicate a worsening of the overall signal.
For 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 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 worsening sorted enumeration of the overall signalINPUT_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.
ImportantTo 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 identify outliers 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) ==The correlation of the experimental data set against the user-supplied reference data is shown in [[XSCALE]]d the lines starting with r.To prepare a reference dataset if the refinement was done with phenix.refine, you should one could use e.g.<pre>mtz2various hklin 2bn3_refine_001.mtz hklout temp.hkl <<eofOUTPUT USER *LABIN FC=F-model PHIC=PHIF-modelENDeof</pre>- the column corresponding to PHIC will not be used by xdscc12. Alternatively,<pre>sftoolsread mymodel_001.mtzwrite temp.hkl format(3i5,f10.3) col F-w modelyquit</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. OtherwiseA 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(+), a SIGF(+),F(-),SIGF(-),merged" refinement.refine.anomalous_scatterers.group.selection="element S" strategy=individual_sites+individual_adp+group_anomalous+occupanciesand b are adjusted such then<pre>sftools <<eofread mymodel_001.mtzwrite anom-reference.hkl format(3i5,2f10.3) col "F-model(+)" "F-model(-)"yquiteof</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 sigmas are very highprogram [[exclude_data_range_from_XDS_ASCII.HKL]], which reduces or re-INTEGRATE with the signal in deltakeyword [http://xds.mpimf-CC1heidelberg.mpg.de/html_doc/2xds_parameters.html#EXCLUDE_DATA_RANGE= EXCLUDE_DATA_RANGE] in [[XDS.INP]].
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