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Xdscc12: Difference between revisions
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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> | ||
usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -< | xdscc12 KD 2018-9-6. Academic use only; no redistribution. -h option shows options. | ||
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>] [-<abcdeftwz>] [-r <ref>] FILE_NAME | |||
dmax (default 999A), dmin (default 1A) and nbin (default 10) have the usual meanings. | dmax (default 999A), dmin (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). | ||
-t: total oscillation (degree) to batch fine-sliced frames into | -t: total oscillation (degree) to batch fine-sliced frames into | ||
-r: | -r: next parameter: ASCII reference file with lines: h,k,l,Fcalc | ||
other options can be combined (e.g. -def), and switch the following off: | 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 | -a: individual isomorphous summary values | ||
-b: individual (Fisher-transformed) delta-CC1/2 values | -b: individual (Fisher-transformed) delta-CC1/2 values | ||
| Line 20: | Line 23: | ||
-f: individual delta-CC1/2ano reflection numbers | -f: individual delta-CC1/2ano reflection numbers | ||
-w: weighting of intensities with their sigmas | -w: weighting of intensities with their sigmas | ||
-z: Fisher transformation of delta-CC1/2 values | -z: no Fisher transformation of delta-CC1/2 values | ||
</pre> | </pre> | ||
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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]]. | ||
== Preparing a reference data set == | |||
If the refinement was done with phenix.refine, one could use | |||
<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> | |||
== Anomalous Fcalc as reference (under development) == | |||
The easiest way 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 | |||
and then | |||
<pre> | |||
sftools | |||
read mymodel_001.mtz | |||
write temp.hkl format(3i5,2f10.3) col "F-model(+)" "F-model(-)" | |||
y | |||
quit | |||
</pre> | |||
sftools seems to output only the acentric reflections - but that should be ok since only those have anomalous differences. | |||