Xscale

Simple and advanced usage

XSCALE ist the scaling program of the XDS suite. At the XDS website, there is a short and a long commented example of XSCALE.INP

---

A minimal input file to combine two datasets into one file is:

OUTPUT_FILE=fae-native.ahkl 
INPUT_FILE= ../fae-native/xds_1/XDS_ASCII.HKL
INPUT_FILE= ../fae-native/xds_2/XDS_ASCII.HKL

Several output files can be specified (together with their set of input files) in a single run of XSCALE, simply by concatenation of sections like the above. All output files are then on the same scale - a program feature recommended for MAD data sets:

OUTPUT_FILE=fae-rh.ahkl 
INPUT_FILE= ../fae-rh/xds_1/XDS_ASCII.HKL
FRIEDEL'S_LAW=FALSE   
STRICT_ABSORPTION_CORRECTION=TRUE         ! see XDSwiki:Tips_and_Tricks
INPUT_FILE= ../fae-rh/xds_2/XDS_ASCII.HKL
FRIEDEL'S_LAW=FALSE
STRICT_ABSORPTION_CORRECTION=TRUE

OUTPUT_FILE=fae-ip.ahkl 
INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL
FRIEDEL'S_LAW=FALSE
STRICT_ABSORPTION_CORRECTION=TRUE
INPUT_FILE= ../fae-ip/xds_2/XDS_ASCII.HKL
FRIEDEL'S_LAW=FALSE
STRICT_ABSORPTION_CORRECTION=TRUE

Further keywords

• RESOLUTION_SHELLS=  ! for the printout of R-factors, completeness, ...
• SPACE_GROUP_NUMBER=  ! if not given, picked up from first input reflection file
• UNIT_CELL_CONSTANTS=  ! if not given, picked up from first input reflection file

keywords with the same meaning as in CORRECT

• REIDX=
• REFERENCE_DATA_SET=
• MINIMUM_I/SIGMA=
• REFLECTIONS/CORRECTION_FACTOR=
• FRIEDEL'S_LAW=
• STRICT_ABSORPTION_CORRECTION=
• INCLUDE_RESOLUTION_RANGE=
• MAXIMUM_NUMBER_OF_PROCESSORS=
• CORRECTIONS=

keywords which do not apply to CORRECT

• MERGE=  ! average intensities from all input files, applies to output file
• WEIGHT=  ! applies to input file
• NBATCH=  ! influences number of scale factors
• CRYSTAL_NAME=  ! switch on radiation damage correction
• STARTING_DOSE=  ! (optional for radiation damage correction)
• DOSE_RATE=  ! (optional for radiation damage correction)
• 0-DOSE_SIGNIFICANCE_LEVEL=  ! (optional for radiation damage correction)

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 reduces 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 these parameters are picked up from the header of the first input reflection file.