XSCALE: Files

The files used or generated by XSCALE are either ASCII files that can be inspected and modified by using a text editor, or binary, compressed image files in the CBF format, a byte-offset variant of the CBFlib format that can be looked at using the XDS-Viewer program. Such files are indicated by the file name extension ".cbf" and represent two-dimensional control images of the correction factors determined by XSCALE.

All files have fixed names defined by XSCALE, which makes it mandatory to run the program in a newly created directory to avoid name clashes. Clearly, one should not run more than one XSCALE-job simultaneously in the same directory. Also, when rerunning XSCALE, files from a previous run should first be given another name if their original contents are meant to be saved.


XSCALE.INP

This file contains the input parameters you have to provide to run XSCALE.

Each parameter name consists of a string of characters without intervening blanks or exclamation marks and includes an equal sign as its last character. The parameter value must directly follow the parameter name and be on the same line. The parameter names cannot be abbreviated; they are case sensitive, too. The parameters may be given in arbitrary order. Characters in a line to the right of an exclamation mark are comment.


XSCALE.LP

This self-explanatory ASCII-file is generated by XSCALE for inspection by the user and contains the results of scaling, statistical summaries and diagnostics of the input and output data sets.


REMOVE.HKL

XSCALE checks for the presence of a file named REMOVE.HKL in the current directory. A file of this name can be provided by the user to specify the indices of reflections that should be excluded from the scaled output file. Each record of REMOVE.HKL consists of the reflection indices h, k, l and possibly other information that will be ignored. Up to 10000 reflections can be specified.

Reflections that do not obey Wilson's statistic often arise from ice rings in the data images. These outliers are reported in the file XSCALE.LP. To suppress the unwanted reflections from the final output file(s), the user copies them to a file named REMOVE.HKL in the current directory and repeats XSCALE. If the file REMOVE.HKL does not exist, XSCALE will not suppress any reflections from the input data files.


ABSORP_???.cbf

This file contains an image of the correction factors applied to the reflection intensities as function of image number (horizontally) and identifying number of the nearest region on the detector surface where the reflection is recorded (vertically). The detector surface is subdivided into 13 fixed regions of about equal area. The ??? enumerate the input data sets in the order they were defined in XSCALE.INP. The correction factors are multiplied by 1000 and saved in the file ABSORP_???.cbf as a byte-offset compressed INTEGER array(IX+NX*(IY-1)), with NX "fast" pixels (IX=1,NX; along image numbers) running from left to right and NY "slow" pixels (IY=1,NY; enumerating the detector regions) pointing upwards. This file is meant to be inspected by the user with the XDS-Viewer program.


DECAY_???.cbf

This file contains an image of the correction factors applied to the reflection intensities as function of image number (horizontally) and resolution of the reflection (vertically). The ??? enumerate the input data sets in the order they were defined in XSCALE.INP. The correction factors are multiplied by 1000 and saved in the file DECAY_???.cbf as a byte-offset compressed INTEGER array(IX+NX*(IY-1)), with NX "fast" pixels (IX=1,NX; along image numbers) running from left to right and NY "slow" pixels (IY=1,NY; along (2*sin(theta)/lamda)^2) pointing upwards. This file is meant to be inspected by the user with the XDS-Viewer program.


MODPIX_???.cbf

This file contains an image of the correction factors applied to the reflection intensities as function of the detector coordinates of their recorded Bragg peaks. The ??? enumerate the input data sets in the order they were defined in XSCALE.INP. The correction factors are multiplied by 1000 and saved in the file MODPIX.cbf as a byte-offset compressed INTEGER array(IX+NX*(IY-1)), with NX "fast" pixels (IX=1,NX; along the detector's X-direction) running from left to right and NY "slow" pixels (IY=1,NY; along the detector's Y-direction) pointing upwards. This file is meant to be inspected by the user with the XDS-Viewer program.


© 2009, MPI for Medical Research, Heidelberg Imprint.
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: January 30, 2009