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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). | 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 is Wolfgang Kabsch (Wolfgang dot Kabsch at mpimf-heidelberg dot mpg dot de). | 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 . | 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 . | 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). | ||
== Links to XDS papers by Wolfgang Kabsch == | |||
[http:// | # [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 == | == Purpose of the Wiki == | ||
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== Contributing to the Wiki == | == Contributing to the Wiki == | ||
* The MediaWiki software used here works in the same way as the well-known Wikipedia. This means that anyone | * 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]] | * Short introduction to [[creating an article]] | ||
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* [[Topics]] as an attempt to provide a hierarchy of pages | * [[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] | |||