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> | ||
xdscc12 KD | xdscc12 KD 2023-01-08. 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 | ||
running 'xdscc12 | running 'xdscc12' on 20240403 at 16:49:03 +0200 | ||
usage: xdscc12 [-dmin <lowres>] [-dmax <highres>] [-nbin <nbin>] [-mode <1 or 2>] [-<abcdefstwz>] [-r <ref>] FILE_NAME | usage: xdscc12 [-dmin <lowres>] [-dmax <highres>] [-nbin <nbin>] [-mode <1 or 2>] [-<abcdefstwz>] [-r|-R <ref>] FILE_NAME | ||
dmin (default 999A), dmax (default 1A) and nbin (default 10) have the usual meanings. | 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: | -r: <ref> is ASCII reference file with lines: h,k,l,Fref or h,k,l,Fref+,Fref- | ||
-R: <ref> is ASCII reference file with lines: h,k,l,Iref or h,k,l,Iref+,Iref- | |||
-s: read two columns from reference: | -r and -R allow calculation of CC of isomorphous signal with reference | ||
-s: read two columns from reference: Fref+, Fref- or Iref+, Iref-. | |||
this allows calculation of CC of anomalous signal with that of reference | this allows calculation of CC of anomalous signal with that of reference | ||
-A: sort INPUT_FILEs in XSCALE.INP.rename_me by anomalous instead of isomorphous delta-CC1/2 | |||
-t: total oscillation (degree) to batch fine-sliced frames into | -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 | ||
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-w: weighting of intensities with their sigmas | -w: weighting of intensities with their sigmas | ||
-z: Fisher transformation of delta-CC1/2 values | -z: Fisher transformation of delta-CC1/2 values | ||
The program writes a commented XSCALE.INP.rename_me that is sorted on delta-CC1/2 | |||
</pre> | </pre> | ||
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== Explanation of output == | == Explanation of output == | ||
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. | 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 FILE_FROM_XSCALE > xdscc12.log # or xdscc12 FILE_FROM_XSCALE | tee xdscc12.log | ||
All statistics (tables) produced by XDSCC12 may be visualized with e.g. gnuplot, after grepping the relevant lines from the output. | 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 <code>-t</code> option; typically <code>-t 1</code>) 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 XDS_ASCII.HKL reflection file (from XDS), the isomorphous delta-CC<sub>1/2</sub> of a batch of frames (width chosen with the <code>-t</code> option; typically <code>-t 1</code>) relative to all data is most easily visualized via [[XDSGUI]] (Statistics tab). Negative numbers indicate a worsening of the overall signal. | ||
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To prepare a reference data set if the refinement was done with phenix.refine, one could use e.g. | 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 | mtz2various hklin 2bn3_refine_001.mtz hklout reference.hkl <<eof | ||
OUTPUT USER * | OUTPUT USER * | ||
LABIN FC=F-model PHIC=PHIF-model | LABIN FC=F-model PHIC=PHIF-model | ||
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sftools | sftools | ||
read mymodel_001.mtz | read mymodel_001.mtz | ||
write | write reference.hkl format(3i5,f10.3) col F-model | ||
y | y | ||
quit | quit | ||
</pre> | </pre> | ||
For a Refmac-written MTZ file, you would use "col FC_ALL" instead of "col F-model". | |||
=== Reference data with anomalous signal (additional -s option) === | === Reference data with anomalous signal (additional -s option) === | ||