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== What is XDS, and how to obtain it? == | == 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 [[ | 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 | The program is free for academic use, and can be downloaded from https://xds.mr.mpg.de/html_doc/XDS.html (if the download from that site fails, there's a copy at https://{{SERVERNAME}}/xds ). | ||
Documentation is at http://xds.mr.mpg.de/html_doc/XDS.html ; possibly old documentation is [https://{{SERVERNAME}}/pub/xds/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]]). E.g. [[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 == | == Links to XDS papers by Wolfgang Kabsch == | ||
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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://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://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 can read articles, but for editing existing pages, and creating new ones (this happens automatically when you click on a [[red link]]), | * 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]]), we need to a create an account for you - send us a personal email (kay.diederichs@uni-konstanz.de, or karsten.schaefer@uni-konstanz.de). | ||
* Short introduction to [[creating an article]] | * Short introduction to [[creating an article]] | ||
| Line 34: | Line 39: | ||
* [[Topics]] as an attempt to provide a hierarchy of pages | * [[Topics]] as an attempt to provide a hierarchy of pages | ||
* new articles: [[ | * new articles: [[SSX]], [[Xscale_isocluster]], [[LIB]] | ||
== News == | |||
New version of XDSGUI May 2023 - see [[Installation]] | |||
[https://www.youtube.com/watch?v=3WU9NrILECo XDS and XDSGUI. SBGrid Webinar by Kay Diederichs, May 2020] [https://strucbio.biologie.uni-konstanz.de/pub/Crystallographic_data_processing_with_XDS_using_XDSGUI.pdf slides of the talk] | |||
[[xdscc12]] | |||
[[xscale_isocluster]] | |||
Our [https://doi.org/10.1107/S2059798320006348 July 2020 paper] about selection and scaling in multi-data-set crystallography | |||
== See also == | |||
[https://{{SERVERNAME}}/pub/MWhitley_CSHL-2018_XDS-Tutorial.pdf Matthew J. Whitley's excellent tutorial] about XDS processing with [[XDSGUI]], from the 2018 Cold Spring Harbor X-Ray Methods in Structural Biology Course. | |||
[https://{{SERVERNAME}}/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. | |||
[[XDSGUI]], a graphical user interface for data processing with XDS developed by Wolfgang Brehm and Kay Diederichs | |||
[http://www.helmholtz-berlin.de/xdsapp XDSAPP3], a graphical user interface for automatic data processing with XDS | |||
[[Installation]] | |||
Latest revision as of 10:27, 20 June 2023
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 https://xds.mr.mpg.de/html_doc/XDS.html (if the download from that site fails, there's a copy at https://wiki.uni-konstanz.de/xds ).
Documentation is at http://xds.mr.mpg.de/html_doc/XDS.html ; possibly old documentation is here.
An open-source viewer XDS-Viewer is available for visualization of the control images written by XDS (and XSCALE). E.g. 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) CC1/2 statistics is XDSCC12.
XDSGUI, a graphical user interface, serves to help using XDS.
Links to XDS papers by Wolfgang Kabsch
- 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.
- 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.
- 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.
- Chapters 11.3 and 25.2.9 in International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules
- Acta Cryst. (2010). D66, 133-144. Integration, scaling, space-group assignment and post-refinement. the definitive reference. Open access.
- 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), we need to a create an account for you - send us a personal email (kay.diederichs@uni-konstanz.de, or karsten.schaefer@uni-konstanz.de).
- Short introduction to creating an article
Wiki contents
- 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
New version of XDSGUI May 2023 - see Installation
XDS and XDSGUI. SBGrid Webinar by Kay Diederichs, May 2020 slides of the talk
Our July 2020 paper about selection and scaling in multi-data-set crystallography
See also
Matthew J. Whitley's excellent tutorial about XDS processing with XDSGUI, from the 2018 Cold Spring Harbor X-Ray Methods in Structural Biology Course.
Keitaro Yamashita's talk about XDS processing given at ACA2014.
XDS talk given at ACA2011.
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.
XDSGUI, a graphical user interface for data processing with XDS developed by Wolfgang Brehm and Kay Diederichs
XDSAPP3, a graphical user interface for automatic data processing with XDS