Difference between revisions of "Xdsstat"

From XDSwiki
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=== Tables ===
 
=== Tables ===
 
   
 
   
* statistics (R-factors, misfits, unique reflections, correlation ...) for each frame. These lines end with " L" which may be used for "grepping" them from XDSSTAT.LP.
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* statistics: for each frame: # reflections, # misfits, <I>, <sigma(I)>, <I/sigma(I)>, <fraction of reflections observed>, <correlation with standard profiles>, R<math>_meas</math> and # reflections used for R<math>_meas</math>, # 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>_d</math> , see [http://strucbio.biologie.uni-konstanz.de/strucbio/files/Diederichs_ActaD62_96.pdf 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.
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* R-factors as a function of frame number difference (R<math>_d</math> , see [http://strucbio.biologie.uni-konstanz.de/strucbio/files/Diederichs_ActaD62_96.pdf 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").
  
 
=== Images ===
 
=== Images ===
 
The following quantities mapped onto the detector surface:  
 
The following quantities mapped onto the detector surface:  
 
* misfits.pck: outliers identified in CORRECT. Useful e.g. to identify [[ice rings]].  
 
* misfits.pck: outliers identified in CORRECT. Useful e.g. to identify [[ice rings]].  
* rf.pck: R-factor
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* rf.pck: R-factor (very interesting)
* anom.pck: anomalous signal
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* anom.pck: anomalous signal (very interesting)
* scales.pck: scale factors between symmetry-related reflections
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* scales.pck: scale factors between symmetry-related reflections (very interesting)
 
* nobs.pck: observed reflections (not very interesting)
 
* nobs.pck: observed reflections (not very interesting)
 
* rlps.pck: reciprocal lorentz factor (not very interesting)
 
* rlps.pck: reciprocal lorentz factor (not very interesting)
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== Availability ==
 
== Availability ==
  
The binary program is at [ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat.bz2]; a statically linked version is [ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat.static.bz2]. I (Kay dot Diederichs at uni-konstanz dot de) appreciate feedback.
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The binary program is at [ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat.bz2]; a statically linked version is [ftp://turn5.biologie.uni-konstanz.de/pub/xdsstat.static.bz2]. Before using the program, you have to set up a CCP4 environment, because it uses the CCP4 routines and files.
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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.
 
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.

Revision as of 19:41, 7 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).

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, , <sigma(I)>, , <fraction of reflections observed>, <correlation with standard profiles>, R[math]_meas[/math] and # reflections used for R[math]_meas[/math], # 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]_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").

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.

Availability

The binary program is at [1]; a statically linked version is [2]. Before using the program, you have to set up a CCP4 environment, because it uses the CCP4 routines and files.

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.