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== What is XDS, and how to obtain it? ==
'''If you want to read about this wiki, go to [[Main Page]], please.'''
XDS is a program written for the "reduction" of 2-dimensional data images ("frames") obtained from crystals irradiated with X-rays.  


The author of the program is Wolfgang Kabsch (Wolfgang.Kabsch@mpimf-heidelberg.mpg.de).  
[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds XDS] is the main program of the [[Main Page|XDS program package]]. Binaries are available for Linux and Mac platforms.  


The program is free for academic use, and can be downloaded from http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/downloading.html .  
XDS reads the user-supplied file [[XDS.INP]] which contains the keywords and parameters for a run of the program. To reduce a dataset, it goes through the steps ("JOB"s)
* [[XYCORR]]  : setup of spatial correction tables if required
* [[INIT]]    : calculate gain of detector and initial background table
* [[COLSPOT]]  : find strong reflections for indexing on one or more frames
* [[IDXREF]]  : index strong reflections in known cell, or supply info about possible cells
* [[DEFPIX]]  : define parts of detector that should be used for intensity integration
* [[INTEGRATE]]: go through dataset and integrate (= calculate intensities of) all reflections
* [[CORRECT]]  : scale symmetry-related reflections and print out statistics (file [[CORRECT.LP]])
(additional, optional JOBs are [[XPLAN]] and [[DIRB]]).


Documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds .
Each step writes a logfile with a name corresponding to the name of the step, with ".LP" appended.


== Links to XDS papers by Wolfgang Kabsch ==
XDS is run simply using
xds
for the single-processor version, and
xds_par
for the parallel version of the program (parallelized using OpenMP). To speed up data reduction even further, several instances of the single or parallel version of the program can be run at the same time on parts of the ''same dataset'' (see MAXIMUM_NUMBER_OF_JOBS= keyword in [[XDS.INP]]).


[http://dx.doi.org/10.1107/S0021889887009737 J. Appl. Cryst. (1988). 21, 67-72. Automatic indexing of rotation diffraction patterns. ]
== See also ==


[http://dx.doi.org/10.1107/S0021889888007903 J. Appl. Cryst. (1988). 21, 916-924. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector]
* [[Special:Allpages|List of all pages]] - to see which pages exist already ...


[http://dx.doi.org/10.1107/S0021889893005588 J. Appl. Cryst. (1993). 26, 795-800. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants]
* [[Topics]] as an attempt to provide a hierarchy of pages


== Purpose of the Wiki ==
* [[Performance]]
The purpose of this Wiki is to supplement the documentation. I (Kay Diederichs) try to keep the Wiki up-to-date with XDS versions and insights. I plan to have [[Tips and Tricks]] for XDS usage, explanations of its output, and recommendations for the parameters in [[XDS.INP]] (if it appears useful to deviate from their defaults).


There is also a [[wishlist]].
* [[FAQ]]
 
== Use of the Wiki ==
The MediaWiki software used here works in the same way as the well-known Wikipedia. This means that any user can edit existing pages, and create new ones. Whether this policy can/will be maintained for the future remains to be seen.
 
To see what's there already, go to http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Special:Allpages . Currently, mostly the file [[XDS.INP]] with its parameters is described.
 
Written by --[[User:Kay|Kay]] 14:53, 8 November 2007 (CET)

Revision as of 14:25, 18 December 2014

If you want to read about this wiki, go to Main Page, please.

XDS is the main program of the XDS program package. Binaries are available for Linux and Mac platforms.

XDS reads the user-supplied file XDS.INP which contains the keywords and parameters for a run of the program. To reduce a dataset, it goes through the steps ("JOB"s)

  • XYCORR  : setup of spatial correction tables if required
  • INIT  : calculate gain of detector and initial background table
  • COLSPOT  : find strong reflections for indexing on one or more frames
  • IDXREF  : index strong reflections in known cell, or supply info about possible cells
  • DEFPIX  : define parts of detector that should be used for intensity integration
  • INTEGRATE: go through dataset and integrate (= calculate intensities of) all reflections
  • CORRECT  : scale symmetry-related reflections and print out statistics (file CORRECT.LP)

(additional, optional JOBs are XPLAN and DIRB).

Each step writes a logfile with a name corresponding to the name of the step, with ".LP" appended.

XDS is run simply using 

xds

for the single-processor version, and 

xds_par

for the parallel version of the program (parallelized using OpenMP). To speed up data reduction even further, several instances of the single or parallel version of the program can be run at the same time on parts of the same dataset (see MAXIMUM_NUMBER_OF_JOBS= keyword in XDS.INP).

See also

  • Topics as an attempt to provide a hierarchy of pages
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