Difference between revisions of "Xdscc12"
Revision as of 08:15, 5 July 2019
XDSCC12 is a program for generating delta-CC1/2 and delta-CC1/2ano 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 , 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.
Usage (this text can be obtained with
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). -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 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: no Fisher transformation of delta-CC1/2 values
The program output is terse but supposed to be self-explanatory. The isomorphous delta-CC1/2 of a batch of frames (width chosen with the -t option) relative to all data is most easily visualized via XDSGUI (Statistics tab); the anomalous delta-CC1/2 may be plotted with e.g. gnuplot after grepping the relevant lines from the output.
For multiple datasets, the output lines show the contribution of each dataset toward the total CC1/2. Negative numbers indicate a worsening of the overall signal.
Statistics are given (in resolution shells) for the isomorphous and the anomalous signal.
Important: to more clearly identify outliers in XSCALEd data, you may want use the -w option. This can be helpful since the a and b parameters of the error model are adjusted by XSCALE such that the sigmas are very high, which reduces the delta-CC1/2 signal.
A complete description of how to process serial crystallography data with XDS/XSCALE is given in SSX. A program that implements the method of Brehm and Diederichs (2014) and theory of Diederichs (2017) is xscale_isocluster.
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.
mtz2various hklin 2bn3_refine_001.mtz hklout temp.hkl <<eof OUTPUT USER * LABIN FC=F-model PHIC=PHIF-model END eof
- the column corresponding to PHIC will not be used by xdscc12. Alternatively,
sftools read mymodel_001.mtz write temp.hkl format(3i5,f10.3) col F-model y quit
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
phenix.refine 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
sftools <<eof read mymodel_001.mtz write anom-reference.hkl format(3i5,2f10.3) col "F-model(+)" "F-model(-)" y quit eof
in which case
sftools outputs only the acentric reflections - only those have anomalous differences.
XDSCC12 then has to be run with the
-s -r anom-reference.hkl option.