Xdsstat: Difference between revisions
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=== Tables === | === Tables === | ||
* statistics ( | * 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. | * 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 | * rf.pck: R-factor (very interesting) | ||
* anom.pck: anomalous signal | * anom.pck: anomalous signal (very interesting) | ||
* scales.pck: scale factors between symmetry-related reflections | * 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. | 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. | ||
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 20:41, 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]\displaystyle{ _meas }[/math] and # reflections used for R[math]\displaystyle{ _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]\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").
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.