XDS Package

XDS Program Package

 Version: December 2003  Release_Notes

X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. 

Documentation of the package, including references, could be accessed from here by activating xds_doc.

XDS is free of charge for non-commercial applications; a license is required for industrial usage (e-mail enquiry : Wolfgang Kabsch)

To use XDS, executables and documentation must both be downloaded and installed. Input file templates that simplify the use of the programs are provided as part of the documentation.

 

Executables

(Expiration date: January 31, 2005)

of the program package are collected in a single compressed tar-file. Dependent on the computer platform the package comes in two flavours, for a single processor and for running in parallel mode making use of up to 32 cpu's. For downloading select the name of the tar-file appropriate for your computer and operating system. Parallel versions of the programs are not available for computers marked '1 cpu' .

name of tar-file for downloading computer operating system
XDS-IRIX_R5000.tar.Z SGI R5000, 1 cpu IRIX6.5
XDS-IRIX_R10000.tar.Z SGI R10000 IRIX6.5
XDS-Tru64_V5.1A.tar.Z Compaq alpha, 1 cpu Tru64 V5.1A
XDS-Tru64_V5.1F.tar.Z Compaq alpha Tru64 V5.1F
XDS-linux_ifc_Intel+AMD.tar.Z Pentium, AthlonXP Linux
XDS-OSX.tar.Z Mac G4, 1 cpu Mac OS X
XDS-aix.tar.Z IBM POWER-4 (Regatta), 1 cpu AIX

Uncompress and untar the downloaded file. This will create a directory on your machine, say XDS-IRIX_R10000 when you selected the XDS-package for your R10000 (Origin). In this directory you will find the executables mentioned in the table below. For convenient access, copy the executables to your private bin/ directory or ask your system administrator to copy the files to /usr/local/bin/ for general availability.

xds Main data processing program for rotation images (single processor version).
xds_par Multiprocessor version of xds for up to 32 cpu's.
xscale Scaling program for XDS-produced data sets (single processor version).
xscale_par Multiprocessor version of xscale for up to 32 cpu's.
xdsconv Converts reflection intensities determined by XDS to amplitudes in a format suitable for various structure solution program packages.
VIEW Program to look at images (Author W.Gebhard).
cellparm Computes mean cell constants from a number of XDS-runs.

Remarks

  1. The memory needed is about proportional to the number of processors employed by xds_par and may well amount to one gigabyte.
  2. For the SGI platform running under IRIX, it may be necessary to issue the shell command limit stacksize 65536 before calling xds_par. Whether this is necessary or not depends on the defaults set by the system's administrator. You could include this command in your .login file to prevent xds_par from crashing with wild system error messages.
  3. The version for the Mac G4 under the Mac OS X operating system requires X11 for running the VIEW program of XDS.

 

Documentation

of the package comes as a single compressed tar-file, named XDS_html_doc.tar.Z, for downloading to your machine. Uncompress and untar the downloaded file. This will create a directory, named XDS_html_doc, that contains all documentation in html format. The documents could then be accessed locally by a web browser at location XDS_html_doc/XDS.html.

For a more convenient access to the document by the command xds_doc, add the line
alias xds_doc "netscape location_of/XDS_html_doc/XDS.html"
to your .cshrc file, or ask your system administrator to include the alias in /etc/cshrc for general availability. Here, location_of denotes the full path name to the directory that should be made generally accessible.

 

How to start data processing with XDS

To maintain a tidy organization of files being generated in the course of data processing, the following procedure is recommended.

  1. Make a new directory using a name that is related to your crystal so that you could always retrieve the exact conditions for crystal growth, buffer, etc.
  2. Move to the new directory and plant a symbolic link to the directory which contains your rotation data images; for example,
    ln -s path_to_image_directory images abbreviates a possibly long path name by "images".
  3. Make a subdirectory to collect the results of processing your images with XDS. Usually, the name of the subdirectory bears some relationship to the subset of images you are going to process now; for example you could name it xds_high if the subdirectory will contain the results of processing your high resolution images.
  4. Now move to this subdirectory, then type xds_doc to post the XDS documentation on screen. As an alternative in case the documentation is not installed at your data collection site, you could access it from here by activating xds_doc.
  5. Activate Getting started and follow the instructions.

 

Wolfgang Kabsch
page last updated: December 3, 2003