Difference between revisions of "Xdscc12"

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XDSCC12 is a program for generating delta-CC<sub>1/2</sub> values. It implements the method described in Greta Assmann, Wolfgang Brehm and Kay 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], but instead of for individual datasets, it does it for individual frames, or groups of frames, from a single dataset collected with the rotation method and processed by [[XDS]].
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XDSCC12 is a program for generating delta-CC<sub>1/2</sub> values for XDS_ASCII.HKL, or for XSCALE.HKL containing several files of type XDS_ASCII.HKL after scaling in XSCALE (with MERGE=FALSE).  
  
The program can be downloaded for Linux 64bit[ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64] or Mac[ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac].
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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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The program can be downloaded for [ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12.rhel6.64 Linux 64bit] or [ftp://turn5.biologie.uni-konstanz.de/pub/xdscc12-mac Mac].
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Usage (this text can be obtained with xdscc12 -h):
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<pre>
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usage: deltacc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -<abcdeftwz> FILE_NAME
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dmax (default 999A), dmin (default 1A) and nbin (default 10) have the usual meanings.
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mode can be 1 (equal volumes of resolution shells) or 2 (increasing volumes; default).
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  -t: total oscillation (degree) to batch fine-sliced frames into
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other options can be combined (e.g. -def), and switch the following off:
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  -a: individual isomorphous summary values
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  -b: individual (Fisher-transformed) delta-CC1/2 values
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  -c: individual delta-CC1/2 reflection numbers
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  -d: individual anomalous summary values
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  -e: individual (Fisher-transformed) delta-CC1/2ano values
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  -f: individual delta-CC1/2ano reflection numbers
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  -w: weighting of intensities with their sigmas
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  -z: Fisher transformation of delta-CC1/2 values
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</pre>
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The program output is terse but supposed to be self-explanatory. Part of it is most easily visualized via XDSGUI, however, that currently deals with the isomorphous signal of a batch of frames (width chosen with the -t option) relative to all data.
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For multiple datasets, the output lines show the contribution of each dataset toward the total CC<sub>1/2</sub>. Negative numbers indicate a worsening of the overall signal.
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All statistics are given for the isomorphous and the anomalous signal.

Revision as of 11:44, 14 December 2016

XDSCC12 is a program for generating delta-CC1/2 values for XDS_ASCII.HKL, 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):

usage: deltacc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -<abcdeftwz> 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
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: Fisher transformation of delta-CC1/2 values

The program output is terse but supposed to be self-explanatory. Part of it is most easily visualized via XDSGUI, however, that currently deals with the isomorphous signal of a batch of frames (width chosen with the -t option) relative to all data.

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.

All statistics are given for the isomorphous and the anomalous signal.