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== 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) , and [[XDSCONV]] (for conversion of a reflection output file to other formats). Additional auxiliary programs are [[cellparm]], [[2cbf]] and [[merge2cbf]]. [[XDS-viewer]], for visualizing frames, can be downloaded separately (see [[Installation]]). | |||
The author of the program package is Wolfgang Kabsch (Wolfgang dot Kabsch at mpimf-heidelberg dot mpg dot de); since 2007 I contribute code, handle and fix bugs and teach XDS usage. | |||
The program is free for academic use, and can be downloaded from http://xds.mpimf-heidelberg.mpg.de/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://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html or [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/index.html here]. | |||
An open-source viewer [[XDS-Viewer]] is [http://xds-viewer.sourceforge.net available] for visualization of the control images written by [[XDS]] (and [[XSCALE]]). 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). Yet another program that produces frame-wise (for XDS_ASCII.HKL) or dataset-wise (for XSCALE.HKL) CC<sub>1/2</sub> statistics is [[XDSCC12]]. | |||
[[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]]. | |||
* Short introduction to [[creating an article]] | * Short introduction to [[creating an article]] | ||
* [[Special:Allpages|List of all pages]] - to see which | == 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: [[SSX]], [[Xscale_isocluster]], [[LIB]] | |||
== News == | |||
[[xds_nonisomorphism]] | |||
[[xscale_isocluster]] | |||
== See also == | |||
[ftp://turn5.biologie.uni-konstanz.de/pub/XDS_Yamashita_ACA2014.pdf Keitaro Yamashita's talk about XDS processing given at ACA2014]. | |||
[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. ] | |||
[http://www.helmholtz-berlin.de/forschung/oe/funkma/soft-matter/forschung/bessy-mx/xdsapp/index_en.html XDSAPP, a graphical user interface for automatic data processing with XDS] | |||
[[Installation]] | |||