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Xdscc12: Difference between revisions
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XDSCC12 is a program for generating delta-CC<sub>1/2</sub> and delta-CC<sub>1/2</sub>ano 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 delta-CC<sub>1/2</sub> and delta-CC<sub>1/2</sub>ano 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]]. | ||
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Usage (this text can be obtained with <code>xdscc12 -h</code>): | Usage (this text can be obtained with <code>xdscc12 -h</code>): | ||
<pre> | <pre> | ||
xdscc12 KD | 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 | Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst. 49, 1021-1028 | ||
usage: xdscc12 [-dmin <lowres>] [-dmax <highres>] [-nbin <nbin>] [-mode <1 or 2>] [-< | 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 | |||
-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 | FILE_NAME can be XDS or XSCALE reflection file | ||
other options can be combined (e.g. -def), and switch the following off: | 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 | |||
</pre> | </pre> | ||
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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. | ||
Important: to identify outliers in [[XSCALE]]d data, you | Important: to more clearly identify outliers in [[XSCALE]]d 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-CC<sub>1/2</sub> 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 [https://doi.org/10.1107/S1399004713025431 Brehm and Diederichs (2014)] and theory of [https://doi.org/10.1107/S2059798317000699 Diederichs (2017)] is [[xscale_isocluster]]. | 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]]. | ||
== | == 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> | <pre> | ||
mtz2various hklin 2bn3_refine_001.mtz hklout temp.hkl <<eof | mtz2various hklin 2bn3_refine_001.mtz hklout temp.hkl <<eof | ||
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</pre> | </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) | 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.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 | ||
refinement.refine.anomalous_scatterers.group.selection="element S" | |||
and then | and then | ||
<pre> | <pre> | ||
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eof | eof | ||
</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. | ||