Difference between revisions of "Xdscc12"

From XDSwiki
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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: deltacc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -<abcdeftwz> FILE_NAME
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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.
  
All statistics are given for the isomorphous and the anomalous signal.
+
Statistics are given (in resolution shells) for the isomorphous and the anomalous signal.

Revision as of 17:21, 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.