Xdsstat
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 (default: XDS_ASCII.HKL) written by CORRECT or XSCALE (MERGE=FALSE). 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 might eventually 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
Visualization of part of the tabular output (tables 1 and 2) may be done with the CCP4 program loggraph.
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
- R-factors as a function of frame number difference (R[math]\displaystyle{ _d }[/math] , see Diederichs K. (2006) Some aspects of quantitative analysis and correction of radiation damage. Acta Cryst D62, 96-101). These lines end with " DIFFERENCE" which may be used for "grepping" them from XDSSTAT.LP:
grep DIFFERENCE XDSSTAT.LP > D
- R_meas as a function of the percentage of expected profile available for integration ("PEAK"), and logarithm of intensity. This table is only available for reflection files written by XDS; the information needed for the table is not in the files written by XSCALE.
The first two of these tables may be visualized with loggraph.
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]. Mac binaries are at [2] and [3] (thanks to Graeme Winter for compiling those!). The latest version is of 2008-04-29.
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.