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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).  
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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 .  
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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 .
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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].
  
== Links to XDS papers by Wolfgang Kabsch ==
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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.
  
[http://dx.doi.org/10.1107/S0021889887009737 ''J. Appl. Cryst.'' (1988). 21, 67-72. Automatic indexing of rotation diffraction patterns. ]
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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).
  
[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 algorithms employed in the INTEGRATE and CORRECT steps.
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== Links to XDS papers by Wolfgang Kabsch ==
  
[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 is ''the'' reference for the IDXREF step.
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# [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.
 
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# [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://www.iucr.org/iucr-top/comm/commit/volf.html Chapters 11.3 and 25.2.9 in ''International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules''] (don't know the link to PDFs of these)
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# [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'']
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# [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.
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# [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 with a [[Creating an account|userid and password]] can edit existing pages, and create new ones.  
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* 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
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* new articles: [[adxv]], [[SIM_MX]], [[FAQ]], [[Problems]], [[CORRECT]]
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== See also ==
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[http://smb.slac.stanford.edu/facilities/software/xds/ A Quick XDS Tutorial for SSRL]
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[http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_Diederichs_ACA2011.pdf XDS talk given at ACA2011]

Revision as of 14:59, 11 July 2011

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 here.

Since version 30-Jan-2009, the format of the control images written by XDS (and XSCALE) changed. An open-source viewer XDS-Viewer is 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

  1. 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.
  2. 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.
  3. 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.
  4. Chapters 11.3 and 25.2.9 in International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules
  5. Acta Cryst. (2010). D66, 133-144. Integration, scaling, space-group assignment and post-refinement. the definitive reference. Open access.
  6. 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 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 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

  • Topics as an attempt to provide a hierarchy of pages

See also

A Quick XDS Tutorial for SSRL

XDS talk given at ACA2011