Difference between revisions of "Xdscc12"

From XDSwiki
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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> -<abcdeftwrz> FILE_NAME
+
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: also show CC against reference dataset (e.g. Icalc from model)
+
   -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
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   -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.

Revision as of 15:05, 23 November 2018

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 [1], 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 Linux 64bit or Mac.

Usage (this text can be obtained with xdscc12 -h):

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.
mode can be 1 (equal volumes of resolution shells) or 2 (increasing volumes; default).
   -t: total oscillation (degree) to batch fine-sliced frames into
   -r: next parameter: ASCII reference file with lines: h,k,l,Fcalc
 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 identify outliers in XSCALEd data, you should use the -w option. Otherwise, a and b are adjusted 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.

Preparing a reference data set

If the refinement was done with phenix.refine, one could use

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

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

sftools
read mymodel_001.mtz
write temp.hkl format(3i5,2f10.3) col "F-model(+)" "F-model(-)"
y
quit

sftools seems to output only the acentric reflections - but that should be ok since only those have anomalous differences.