Difference between revisions of "Xdsstat"

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N.B.: Images are currently only produced for reflection files coming from XDS, ''not'' for those from XSCALE. The reason is that the latter lack a line like
 
N.B.: Images are currently only produced for reflection files coming from XDS, ''not'' for those from XSCALE. The reason is that the latter lack a line like
 
  !NX=  2048  NY=  2048    QX=  0.079090  QY=  0.079090
 
  !NX=  2048  NY=  2048    QX=  0.079090  QY=  0.079090
which is used to tell the program how big the detector is. If you want image output for XSCALE reflection files, just copy this line into it.
+
which is used to tell the program how big the detector is (only NX and NY are actually required). If you want image output for XSCALE reflection files, just copy this line into it.
  
 
== Availability ==
 
== Availability ==

Revision as of 13:28, 20 February 2008

XDSSTAT is a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.

Usage

The program reads from a file written by CORRECT or XSCALE (default: XDS_ASCII.HKL). Before using the program, you have to set up a CCP4 environment, because it uses the CCP4 routines and files.

As the output is long, it should be called as

xdsstat > XDSSTAT.LP

This will probably soon be changed to the XDS style.

The program may be called with two parameters which define the resolution range of data to be read:

xdsstat 20 3 > XDSSTAT.LP

Features

Tables

  • statistics: for each frame: # reflections, # misfits, I, sigma(I), I/sigma(I), fraction of reflections observed, correlation with standard profiles, R_meas and # reflections used for R_meas, # unique reflections which only occur on this frame and would thus be lost if this frame were deleted from the dataset. These lines end with " L" which may be used for "grepping" them from XDSSTAT.LP:
grep ' L$' XDSSTAT.LP > L
grep DIFFERENCE XDSSTAT.LP > D

Images

The following quantities mapped onto the detector surface:

  • misfits.pck: outliers identified in CORRECT. Useful e.g. to identify ice rings.
  • rf.pck: R-factor (very interesting)
  • anom.pck: anomalous signal (very interesting)
  • scales.pck: scale factors between symmetry-related reflections (very interesting)
  • nobs.pck: observed reflections (not very interesting)
  • rlps.pck: reciprocal lorentz factor (not very interesting)

These images are in the .pck format and may be visualized by VIEW.

N.B.: Images are currently only produced for reflection files coming from XDS, not for those from XSCALE. The reason is that the latter lack a line like

!NX=  2048  NY=  2048    QX=  0.079090  QY=  0.079090

which is used to tell the program how big the detector is (only NX and NY are actually required). If you want image output for XSCALE reflection files, just copy this line into it.

Availability

A Linux binary is at [1].

I (Kay dot Diederichs at uni-konstanz dot de) appreciate feedback.

The source code is in Fortran90 and requires a Fortran90-compiled CCP4 library, so few people are currently in a position to compile and link the program. I might opensource it someday, but preferably as part of the XDS distribution.