Xds: Difference between revisions

From XDSwiki
Jump to navigation Jump to search
mNo edit summary
mNo edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
== What is XDS, and how to obtain it? ==
'''If you want to read about this wiki, go to [[Main Page]], please.'''
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).  
[http://xds.mpimf-heidelberg.mpg.de/ XDS] is the main program of the [[Main Page|XDS program package]]. Binaries are available for Linux and Mac platforms.  


The program is free for academic use, and can be downloaded from http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/downloading.html .  
XDS reads the user-supplied file [[XDS.INP]] which contains the keywords and parameters for a run of the program. To reduce a dataset, it goes through the steps ("JOB"s)
* [[XYCORR]]  : setup of spatial correction tables if required
* [[INIT]]    : calculate gain of detector and initial background table
* [[COLSPOT]]  : find strong reflections for indexing on one or more frames
* [[IDXREF]]  : index strong reflections in known cell, or supply info about possible cells
* [[DEFPIX]]  : define parts of detector that should be used for intensity integration
* [[INTEGRATE]]: go through dataset and integrate (= calculate intensities of) all reflections
* [[CORRECT]]  : scale symmetry-related reflections and print out statistics (file [[CORRECT.LP]])
(additional, optional JOBs are [[XPLAN]] and [[DIRB]]).


Documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds .
Each step writes a logfile with a name corresponding to the name of the step, with ".LP" appended.


== Links to XDS papers by Wolfgang Kabsch ==
XDS is run simply using
xds
for the single-processor version, and
xds_par
for the parallel version of the program (parallelized using OpenMP). To speed up data reduction even further, several instances of the single or parallel version of the program can be run at the same time on parts of the ''same dataset'' (see MAXIMUM_NUMBER_OF_JOBS= keyword in [[XDS.INP]]).


[http://dx.doi.org/10.1107/S0021889887009737 ''J. Appl. Cryst.'' (1988). 21, 67-72. Automatic indexing of rotation diffraction patterns. ]
== See also ==


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


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


[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)
* [[Performance]]


== Purpose of the Wiki ==
* [[FAQ]]
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 with a userid and password can edit existing pages, and create new ones. I might enable or disable account creation as it appears suitable. If you would like to get an account, and "create login" does not appear at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Special:Userlogin, email me, Kay dot Diederichs at uni-konstanz dot de, to have me enable it temporarily. I ask you to choose the user name such that your real name may be recognized.
 
== Wiki contents ==
 
* [[Special:Allpages|List of all pages]] - to see which pages exist already ...
 
* [[Topics]] as an attempt to provide a hierarchy of pages

Latest revision as of 14:27, 22 October 2019

If you want to read about this wiki, go to Main Page, please.

XDS is the main program of the XDS program package. Binaries are available for Linux and Mac platforms.

XDS reads the user-supplied file XDS.INP which contains the keywords and parameters for a run of the program. To reduce a dataset, it goes through the steps ("JOB"s)

  • XYCORR  : setup of spatial correction tables if required
  • INIT  : calculate gain of detector and initial background table
  • COLSPOT  : find strong reflections for indexing on one or more frames
  • IDXREF  : index strong reflections in known cell, or supply info about possible cells
  • DEFPIX  : define parts of detector that should be used for intensity integration
  • INTEGRATE: go through dataset and integrate (= calculate intensities of) all reflections
  • CORRECT  : scale symmetry-related reflections and print out statistics (file CORRECT.LP)

(additional, optional JOBs are XPLAN and DIRB).

Each step writes a logfile with a name corresponding to the name of the step, with ".LP" appended.

XDS is run simply using 

xds

for the single-processor version, and 

xds_par

for the parallel version of the program (parallelized using OpenMP). To speed up data reduction even further, several instances of the single or parallel version of the program can be run at the same time on parts of the same dataset (see MAXIMUM_NUMBER_OF_JOBS= keyword in XDS.INP).

See also

  • Topics as an attempt to provide a hierarchy of pages
Retrieved from "https://wiki.uni-konstanz.de/xds/index.php?title=Xds&oldid=3986"