Xscale: Difference between revisions
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[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_parameters.html XSCALE] ist the scaling program of the XDS suite. | [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_parameters.html XSCALE] ist the scaling program of the XDS suite. At the XDS website, there is a short a long commented example of [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/INPUT_templates/XSCALE.INP XSCALE.INP] | ||
A minimal input file to combine two datasets into one file is: | A minimal input file to combine two datasets into one file is: | ||
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INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL | INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL | ||
To | == Radiation damage correction == | ||
To "switch on" radiation damage correction ([http://dx.doi.org/10.1107/S0907444903006516 K. Diederichs, S. McSweeney and R. B. G. Ravelli (2003) Zero-dose extrapolation as part of macromolecular synchrotron data reduction. ''Acta Cryst.'' '''D59''', 903-909]) it suffices to use the CRYSTAL_NAME keyword. '''The CRYSTAL_NAME parameters of different datasets do not have to be different'''. If they are different, this results in more degrees of freedom (namely, the slopes of the reflection intensity as a function of dose) for the program to fit the observed changes of intensities which are induced by radiation damage. However, if the datasets are based on the same crystal, or the datasets are based on crystals from the same drop, it is reasonable to assume that the slopes are the same. | |||
Example: | Example: | ||
OUTPUT_FILE=fae-merge.ahkl | OUTPUT_FILE=fae-merge.ahkl | ||
INPUT_FILE= ../fae-ip/xds_1/XDS_ASCII.HKL ! | |||
CRYSTAL_NAME=ip | |||
INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL ! same crystal, but translated along z | |||
CRYSTAL_NAME= | CRYSTAL_NAME=ip | ||
This is the recommended way as it avoids overfitting. | |||
If, however, the crystals represent different heavy atom soaks, it is advisable to give a different CRYSTAL_NAME to each dataset. Example: | |||
OUTPUT_FILE=hg.ahkl | |||
INPUT_FILE= ../xds-hg/XDS_ASCII.HKL ! a mercury soak | |||
CRYSTAL_NAME=Hg | |||
OUTPUT_FILE=pt.ahkl | |||
INPUT_FILE= ../xds-pt/XDS_ASCII.HKL ! a platinum soak | |||
CRYSTAL_NAME=Pt | |||
== A hint for long-time XSCALE users == | |||
The latest versions do not require | |||
SPACE_GROUP_NUMBER= | |||
UNIT_CELL_PARAMETERS= | |||
in XSCALE.INP because they pick these parameters up from the header of the first input reflection file. | |||
Revision as of 17:47, 20 December 2007
XSCALE ist the scaling program of the XDS suite. At the XDS website, there is a short a long commented example of XSCALE.INP
A minimal input file to combine two datasets into one file is:
OUTPUT_FILE=fae-merge.ahkl INPUT_FILE= ../fae-ip/xds_1/XDS_ASCII.HKL INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL
Radiation damage correction
To "switch on" radiation damage correction (K. Diederichs, S. McSweeney and R. B. G. Ravelli (2003) Zero-dose extrapolation as part of macromolecular synchrotron data reduction. Acta Cryst. D59, 903-909) it suffices to use the CRYSTAL_NAME keyword. The CRYSTAL_NAME parameters of different datasets do not have to be different. If they are different, this results in more degrees of freedom (namely, the slopes of the reflection intensity as a function of dose) for the program to fit the observed changes of intensities which are induced by radiation damage. However, if the datasets are based on the same crystal, or the datasets are based on crystals from the same drop, it is reasonable to assume that the slopes are the same. Example:
OUTPUT_FILE=fae-merge.ahkl INPUT_FILE= ../fae-ip/xds_1/XDS_ASCII.HKL ! CRYSTAL_NAME=ip INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL ! same crystal, but translated along z CRYSTAL_NAME=ip
This is the recommended way as it avoids overfitting.
If, however, the crystals represent different heavy atom soaks, it is advisable to give a different CRYSTAL_NAME to each dataset. Example:
OUTPUT_FILE=hg.ahkl INPUT_FILE= ../xds-hg/XDS_ASCII.HKL ! a mercury soak CRYSTAL_NAME=Hg OUTPUT_FILE=pt.ahkl INPUT_FILE= ../xds-pt/XDS_ASCII.HKL ! a platinum soak CRYSTAL_NAME=Pt
A hint for long-time XSCALE users
The latest versions do not require
SPACE_GROUP_NUMBER= UNIT_CELL_PARAMETERS=
in XSCALE.INP because they pick these parameters up from the header of the first input reflection file.