Created by Frank Schluenzen, last modified on Feb 01, 2022 18:08


Summary

Source: http://xds.mpimf-heidelberg.mpg.de/

License: XDS is free of charge for non-commercial applications

Documentation: http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html

Path:  /opt/xray/xds  and various other places

XDS is a program package written for the "reduction" of 2-dimensional data images ("frames") obtained from crystals irradiated with monochromatic X-rays.

Using XDS

To initialize the environment use the module command:

xwhich xds_par

 Provided by module(s)
  ... module load maxwell crystfel/0.10.0                      which xds_par: /software/crystfel/0.10.0/bin/xds_par 
  ... module load maxwell crystfel/0.8.0                       which xds_par: /software/crystfel/0.8.0/bin/xds_par 
  ... module load maxwell crystfel/0.9.1                       which xds_par: /software/crystfel/0.9.1/bin/xds_par 
  ... module load maxwell crystfel/0.7.0                       which xds_par: /software/crystfel/0.8.0/bin/xds_par 
  ... module load maxwell crystfel/0.9.0                       which xds_par: /software/crystfel/0.9.0/bin/xds_par 
  ... module load maxwell crystfel/0-devel                     which xds_par: /software/crystfel/devel/bin/xds_par 
  ... module load xray                                         which xds_par: /opt/xray/xds/xds_par 
  ... module load ccp4/6.4                                     which xds_par: /opt/xray/xds/xds_par 
  ... module load ccp4/6.5                                     which xds_par: /opt/xray/xds/xds_par 
  ... module load ccp4/7.0                                     which xds_par: /opt/xray/xds/xds_par 
  ... module load ccp4/7.1                                     which xds_par: /opt/xray/xds/xds_par


Helper Utilities

XDS is a pure command line application. It's however supplemented by a number of utilities including GUI applications, all of them also initialized with the xray or ccp4 modules:

  • xdsapp - an XDS GUI developed at HZB
  • xds-viewer - an open source XDS gui replacing the now obsolete VIEW program
  • xdsGUI - a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users
  • xdsstat - prints various statistics (that are not available from XDS itself), available from within xdsGUI


Running the helper applications
[elx]% module avail
[elx]% module load xray              # sets the environment for xds and the helper application

[elx]% which xdsGUI                  # start is as xdsGUI from the command-line or with the full PATH
/opt/xray/xds/xdsGUI

[elx]% module load phenix            # if you need the phenix bindings in xdsAPP
[elx]% which xdsapp                  # start is as xdsapp from the command-line or with the full PATH
/opt/xray/xdsapp/xdsapp
 
[elx]% which xds-viewer              # start is as xds-viewer from the command-line or with the full PATH
/opt/xray/xds/xds-viewer

[elx]% which xdsstat                 # start is as xdsstat from the command-line or with the full PATH. It's also used inside xdsAPP and xdsGUI
/opt/xray/bin/xdsstat