XSCALE

 

• puts one or more files obtained from data processing with xds on a common scale,
• determines correction factors that partially compensate for absorption effects and radiation damage,
• discards user-specified reflections that do not obey Wilson statistics,
• reports completeness and quality of the scaled data as well as the intensity distribution of the data set,
• offers the choice to either merge symmetry-equivalent observations or to save the scaled but unmerged observations on the output file,
• allows for several output files all on the same scale - a feature that is recommended for MAD data sets taken from the same crystal at different wavelengths,
• can correct reflections individually for radiation damage (for reference on this subject, see the article by Diederichs, McSweeney & Ravelli).

The program uses three files with a fixed name.

XSCALE.INP

contains the parameter values that control the action of XSCALE. This file is mandatory and must reside in the current directory from which XSCALE is called. For a detailed discussion see XSCALE Input Parameters.

XSCALE.LP

is generated by XSCALE and contains the results, statistical summaries, and diagnostics of the input and output data sets.

REMOVE.HKL

is an optional file that may contain up to 10000 reflections which specify outliers that are not wanted in the scaled data set. Reflections not obeying Wilson's statistic (i.e. from ice rings) are listed near the end of the output file XSCALE.LP. These can be edited/inspected and copied/appended to a file named REMOVE.HKL in the currect directory. To omit these outliers from the scaled data set, just repeat XSCALE. If the file REMOVE.HKL does not exist, XSCALE will not suppress any reflections from the input data files.

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Example for XSCALE.INP

RESOLUTION_SHELLS= 10 6 5 4 3 2.7 2.6 2.5
SPACE_GROUP_NUMBER=5
UNIT_CELL_CONSTANTS=228.4 69.9 113.6 90.0 97.57 90.0

! Defines first scaled data set (at minimum of f')
OUTPUT_FILE=ip.ahkl  FRIEDEL'S_LAW=FALSE !TRUE
!file-name, type, resolution range, (WEIGHT=),(DELFRM=),(NBATCH=)
INPUT_FILE= ../ip/xds/XDS_ASCII.HKL  XDS_ASCII 20 2.5
CRYSTAL_NAME=Seleno1

! Defines second scaled data set (at maximum of f'')
OUTPUT_FILE=pk.ahkl  FRIEDEL'S_LAW=FALSE !TRUE
INPUT_FILE= ../pk/xds/XDS_ASCII.HKL  XDS_ASCII 20 2.5
CRYSTAL_NAME= Seleno1

! Defines third scaled data set (remote from absorption edge)
OUTPUT_FILE=rm.ahkl  FRIEDEL'S_LAW=FALSE !TRUE
INPUT_FILE=*../rm/xds/XDS_ASCII.HKL  XDS_ASCII 20 2.5
CRYSTAL_NAME= Seleno1

Puts the data sets collected from the same selenomethionyl protein crystal, named Seleno1, at three different wavelengths on a common, approximately absolute scale and corrects reflections individually for radiation damage. The '*' preceeding the name of the third data set (taken at a wavelength remote from the K-absorption edge of selenium) marks it as a reference that defines the fall-off with respect to resolution for all output data sets. Note, that FRIEDEL'S_LAW=FALSE for all output files as anomalous effects are expected to be present due to the selenium atoms.

The three separate output files (ip.ahkl, pk.ahkl, rm.ahkl) thus obtained from XSCALE contain reflection intensities that can be converted to structure factors by the program xdsconv. The converted files may then be used directly as input files, for example to the structure solution and refinement program package CNS (CNS input file "merge.inp").

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Wolfgang Kabsch 
page last updated: November 18, 2003