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2013-12-05T12:43:37Z

Fulvio.saccoccia: /* See also */

== What is XDS, and how to obtain it? ==
XDS is a program package written for the "reduction" of 2-dimensional data images ("frames") obtained from crystals irradiated with monochromatic X-rays. The package mainly consists of the programs [[XDS]] (which processes a single dataset), [[XSCALE]] (for scaling of several datasets) , [[XDSCONV]] (for conversion of output file to other formats) and [[VIEW]] (for visualizing).

The author of the program package is Wolfgang Kabsch (Wolfgang dot Kabsch at mpimf-heidelberg dot mpg dot de).

The program is free for academic use, and can be downloaded from http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/downloading.html (if the download from that site fails, there's a copy at ftp://turn5.biologie.uni-konstanz.de/xds ).

Documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds or [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/index.html here].

Since version 30-Jan-2009, the format of the control images written by [[XDS]] (and [[XSCALE]]) [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/Release_Notes.html changed]. An open-source viewer [[XDS-Viewer]] is [http://xds-viewer.sourceforge.net available]. Latest versions of [[Adxv]] can also visualize XDS output files.

There is another program available, which serves to produce additional output of tables and plots. This is not part of the official XDS package; its name is [[XDSSTAT]] (written and distributed by Kay Diederichs).

[[XDSgui]], a graphical user interface, serves to help using XDS.

== Links to XDS papers by Wolfgang Kabsch ==

# [http://dx.doi.org/10.1107/S0021889887009737 ''J. Appl. Cryst.'' (1988). 21, 67-72. Automatic indexing of rotation diffraction patterns.] explaining the diffraction geometry as used in XDS, the local-indexing method used in IDXREF and the refinement of diffraction geometry parameters.
# [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]. This is ''the'' reference for the integration and scaling algorithms employed in the INTEGRATE and CORRECT steps.
# [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]. This builds upon publication 1. and gives further important details of the IDXREF step, in particular about space-group determination.
# [http://it.iucr.org/Fa/contents/ Chapters 11.3 and 25.2.9 in ''International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules'']
# [http://dx.doi.org/10.1107/S0907444909047374 ''Acta Cryst.'' (2010). '''D66''', 133-144. Integration, scaling, space-group assignment and post-refinement.] the definitive reference. Open access.
# [http://dx.doi.org/10.1107/S0907444909047337 ''Acta Cryst.'' (2010). '''D66''', 125-132. XDS] the definitive reference. Open access.

== Purpose of the Wiki ==
The purpose of this Wiki is to provide an accurate resource for XDS users, and to provide explanations and hints for the successful use of XDS. I (Kay Diederichs) try to keep the Wiki up-to-date with XDS versions and insights. I collect [[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).

To see what's there already, go to [[Special:Allpages|List of all pages]]. A good starting point is the article about [[XDS.INP]] where the keywords and parameters for running XDS are described. There is also a [[wishlist]], and [[Known Bugs]], and [[Quality Control]] (under construction).

== Contributing to the Wiki ==
* The MediaWiki software used here works in the same way as the well-known Wikipedia. This means that anyone can read articles, but for editing existing pages, and creating new ones (this happens automatically when you click on a [[red link]]), you need a [[Creating an account|userid and password]]. Due to the amount of spam created by abuse of Google mail accounts, we are no longer allowing account creation for @gmail.com email addresses.
* Short introduction to [[creating an article]]

== Wiki contents ==

* [[Special:Allpages|List of all pages]] - to see which pages exist already ...

* [[Topics]] as an attempt to provide a hierarchy of pages

* new articles: [[adxv]], [[SIM_MX]], [[FAQ]], [[Problems]], [[CORRECT]]

== See also ==
[http://smb.slac.stanford.edu/facilities/software/xds/ A Quick XDS Tutorial for SSRL]

[http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_Diederichs_ACA2011.pdf XDS talk given at ACA2011]

[https://www.researchgate.net/publication/236032099_Practical_use_of_XDS_%28for_data_reduction%29._Presented_in_April_4th_2013_Dept._of_Biochemical_Sciences_Sapienza_University_of_Rome?ev=prf_pub Practical use of XDS (for data reduction) - by Fulvio Saccoccia, Presented in April, 4th 2013; Dept. of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti - Sapienza University of Rome. ]

XDSwiki - User contributions [en]

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