Xdscc12: Difference between revisions
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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]. | 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]. | ||
Usage (this text can be obtained with xdscc12 -h): | Usage (this text can be obtained with <code>xdscc12 -h</code>): | ||
<pre> | <pre> | ||
usage: | usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -<abcdeftwrz> 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) | |||
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 | -a: individual isomorphous summary values | ||
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</pre> | </pre> | ||
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. | The program output is terse but supposed to be self-explanatory. Part of it is most easily visualized via XDSGUI, however, that currently only 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 CC<sub>1/2</sub>. Negative numbers indicate a worsening of the overall signal. | 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. | ||
Statistics are given (in resolution shells) for the isomorphous and the anomalous signal. | |||
Revision as of 19:21, 14 December 2016
XDSCC12 is a program for generating delta-CC1/2 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):
usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -<abcdeftwrz> 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: also show CC against reference dataset (e.g. Icalc from model) 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 only 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.
Statistics are given (in resolution shells) for the isomorphous and the anomalous signal.