XDSwiki - User contributions [en]

Main Page

2010-12-17T13:41:56Z

Michael: /* 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 [[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 .

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://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]]

== 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: [[adxv]], [[SIM_MX]], [[FAQ]], [[Problems]], [[CORRECT]]

== See also ==
[http://smb.slac.stanford.edu/facilities/software/xds/ A Quick XDS Tutorial for SSRL]

XDSi

2010-02-03T12:11:18Z

Michael: /* XDSi */

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still beta, but
*:* it should work reasonably well for PILATUS datasets
*:* it works for MAR-CCD datasets at the SLS using 5 digits (*?????.img) for bzip2ed or raw images
*:* it works for the ADSC Quantum Q315r of the ESRF for bzip2ed or raw images

* Here you can see some screenshots of XDSi: [[XDSi screenshots]]

* To be able to use XDSi you must have installed
*:* wish
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:*:* depending on your installation you may have to change globally xdsviewer to xds-viewer
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

File:Xdsi4.jpg

2009-07-24T15:26:48Z

Michael: uploaded a new version of "Image:Xdsi4.jpg"

File:Xdsi4.jpg

2009-07-24T15:23:27Z

Michael: uploaded a new version of "Image:Xdsi4.jpg"

XDSi screenshots

2009-07-24T09:13:34Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the infobox displaying information about datasets that have already finished processing during an XDS Fullauto run.

[[Image:infobox.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).
*:* A green line indicates the threshold below which are 80% of all frames.
*:* The fraction of frames excessing the threshold for each intervall of 100 frames is given and the 10 frames with highest <math>R_{meas}</math> are labeled.

[[Image:xdsi5.jpg]]

* This screenshot shows the lengthrefinement of the "c" axis during each integration cycle

[[Image:xdsi8.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

File:Infobox.jpg

2009-07-24T09:11:43Z

Michael:

XDSi screenshots

2009-07-24T09:11:07Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the infobox during an XDS Fullauto run.

[[Image:infobox.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).
*:* A green line indicates the threshold below which are 80% of all frames.
*:* The fraction of frames excessing the threshold for each intervall of 100 frames is given and the 10 frames with highest <math>R_{meas}</math> are labeled.

[[Image:xdsi5.jpg]]

* This screenshot shows the lengthrefinement of the "c" axis during each integration cycle

[[Image:xdsi8.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

XDSi screenshots

2009-07-23T18:53:55Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).
*:* A green line indicates the threshold below which are 80% of all frames.
*:* The fraction of frames excessing the threshold for each intervall of 100 frames is given and the 10 frames with highest <math>R_{meas}</math> are labeled.

[[Image:xdsi5.jpg]]

* This screenshot shows the lengthrefinement of the "c" axis during each integration cycle

[[Image:xdsi8.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

File:Xdsi5.jpg

2009-07-23T18:49:02Z

Michael: uploaded a new version of "Image:Xdsi5.jpg"

Main Page

2009-06-29T10:57:17Z

Michael: /* 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 [[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 .

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).

A graphical interface (beta) to XDS is available, that allows processing of multiple datasets with minimum user effort. It is called
XDSi and you can download it here: [[XDSi]]

== 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'']

== 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]]

== 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: [[adxv]], [[SIM_MX]]

File:Xdsi8.jpg

2009-06-29T10:55:44Z

Michael:

XDSi screenshots

2009-06-29T10:55:25Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).

[[Image:xdsi5.jpg]]

* This screenshot shows the lengthrefinement of the "c" axis during each integration cycle

[[Image:xdsi8.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

XDSi

2009-06-29T10:17:45Z

Michael: /* XDSi */

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still beta, but
*:* it should work reasonably well for PILATUS datasets
*:* it may work for MAR-CCD datasets if the frames are bzip2ed

* Here you can see some screenshots of XDSi: [[XDSi screenshots]]

* To be able to use XDSi you must have installed
*:* wish
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

XDSi screenshots

2009-06-29T10:16:14Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T10:15:32Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T10:15:03Z

Michael:

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).

[[Image:xdsi5.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the "select datasets" dialogue

[[Image:xdsi7.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

XDSi screenshots

2009-06-29T10:13:00Z

Michael: /* XDSi screenshots */

File:Xdsi7.jpg

2009-06-29T10:12:20Z

Michael: uploaded a new version of "Image:Xdsi7.jpg"

File:Xdsi7.jpg

2009-06-29T10:11:37Z

Michael:

XDSi screenshots

2009-06-29T10:09:56Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the datasets that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and shows the Rmeas values per frame (taken from XDSSTAT.LP).

[[Image:xdsi5.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the "select datasets" dialogue

[[Image:xdsi7.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

XDSi screenshots

2009-06-29T10:07:57Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T10:07:23Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T10:06:44Z

Michael: /* XDSi screenshots */

File:Xdsi6.jpg

2009-06-29T10:05:43Z

Michael: uploaded a new version of "Image:Xdsi6.jpg"

File:Xdsi5.jpg

2009-06-29T10:05:11Z

Michael: uploaded a new version of "Image:Xdsi5.jpg"

File:Xdsi3.jpg

2009-06-29T10:04:45Z

Michael: uploaded a new version of "Image:Xdsi3.jpg"

XDSi screenshots

2009-06-29T10:02:48Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T10:01:42Z

Michael: /* XDSi screenshots */

== XDSi screenshots ==

* This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the datasets that is currently being processed and about the dataset that have already finished processing. The blue infobox displays a summary of IDXREF.LP for the dataset that is currently being processed.

[[Image:xdsi2.jpg]]

* This screenshot shows the first plot of the file plots.pdf that is generated for each dataset. It shows the scalefactors per frame and gives information about the dataset. The a- and b- values of the function <math>v(I)=a(v_0 (I) + b I^2)</math> are also given.

[[Image:xdsi3.jpg]]

* This screenshot is also taken from the file plots.pdf and show the Rmeas values per frame (taken from XDSSTAT.LP).

[[Image:xdsi5.jpg]]

* This screenshot shows the "You know what you do dialogue"

[[Image:xdsi4.jpg]]

* This screenshot shows the first plot of the file compall.pdf that is generated after XDS Fullauto has finished. It compares the Rmeas of all the datasets that have been processed.

[[Image:xdsi6.jpg]]

File:Xdsi2.jpg

2009-06-29T10:00:58Z

Michael: uploaded a new version of "Image:Xdsi2.jpg"

File:Xdsi6.jpg

2009-06-29T09:59:54Z

Michael:

XDSi screenshots

2009-06-29T09:59:40Z

Michael: /* XDSi screenshots */

XDSi screenshots

2009-06-29T09:58:49Z

Michael: /* XDSi screenshots */

File:Xdsi4.jpg

2009-06-29T09:57:05Z

Michael:

File:Xdsi5.jpg

2009-06-29T09:56:37Z

Michael:

File:Xdsi3.jpg

2009-06-29T09:55:45Z

Michael:

File:Xdsi2.jpg

2009-06-29T09:53:50Z

Michael: uploaded a new version of "Image:Xdsi2.jpg"

File:Xdsi2.jpg

2009-06-29T09:53:04Z

Michael: uploaded a new version of "Image:Xdsi2.jpg"

File:Xdsi2.jpg

2009-06-29T09:47:49Z

Michael:

XDSi screenshots

2009-06-29T09:47:17Z

Michael: New page: == XDSi screenshots == * This screenshot shows XDSi during an XDS Fullauto run. The yellow infobox displays information about the dataset that is currently being processed and about the d...

XDSi

2009-06-29T09:45:41Z

Michael: /* XDSi */

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still beta, but
*:* it should work reasonably well for PILATUS datasets
*:* it may work for MAR-CCD datasets if the frames are bzip2ed

* To be able to use XDSi you must have installed
*:* wish
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

Main Page

2009-06-29T09:45:21Z

Michael: /* 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 [[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 .

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).

A graphical interface (beta) to XDS is available, that allows processing of multiple datasets with minimum user effort. It is called
XDSi and you may find it here: [[XDSi]]

== 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'']

== 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]]

== 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: [[adxv]], [[SIM_MX]]

XDSi

2009-06-25T11:47:50Z

Michael: /* XDSi */

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still alpha, but
*:* it should work reasonably well for PILATUS datasets
*:* it may work for MAR-CCD datasets if the frames are bzip2ed

* To be able to use XDSi you must have installed
*:* wish
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

Main Page

2009-06-25T11:44:50Z

Michael: /* 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 [[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 .

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).

A graphical interface (alpha) to XDS is available, that allows processing of multiple datasets with minimum user effort. It is called
XDSi and you may find it here: [[XDSi]]

== 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'']

== 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]]

== 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: [[adxv]], [[SIM_MX]]

Xdsi

2009-06-25T11:44:14Z

Michael: Xdsi moved to XDSi: looks better

#REDIRECT [[XDSi]]

XDSi

2009-06-25T11:44:14Z

Michael: Xdsi moved to XDSi: looks better

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still alpha, but
*:* it should work reasonably well for PILATUS datasets
*:* it may work for MAR-CCD datasets if the frames are bzip2ed

* To be able to use XDSi you must have installed
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

Main Page

2009-06-25T11:30:15Z

Michael: /* 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 [[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 .

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).

A graphical interface (alpha) to XDS is available, that allows processing of multiple datasets with minimum user effort. It is called
XDSi and you may find it here: [[Xdsi]]

== 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'']

== 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]]

== 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: [[adxv]], [[SIM_MX]]

XDSi

2009-06-25T11:21:55Z

Michael: New page: == XDSi == * XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''. *:* You just have to provide it with a resultdirectory and ...

== XDSi ==

* XDSi offers you the possibility to process '''all your datasets''' in a given directory with '''minimum effort'''.
*:* You just have to provide it with a resultdirectory and the directory where your frames are stored.
*:* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed.
*:* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package
*:* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset
*:* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated
*:* You can also generate plots for datasets that have been processed using XDS without XDSi

* XDSi is still alpha, but
*:* it should work reasonably well for PILATUS datasets
*:* it may work for MAR-CCD datasets if the frames are bzip2ed

* To be able to use XDSi you must have installed
*:* xds_par
*:* xdsstat
*:* xdsviewer
*:* pointless
*:* gnuplot >= Version 4.0
*:* convert (part of ImageMagick)
*:* kpdf

* To install XDSi
*:* Download xdsi.tar.gz at [ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/ XDSi]
*:* tar -zxf xdsi.tar.gz; you get the files xdsi, xdsi_doc.pdf and the folder templates
*:* open the ﬁle xdsi with a texteditor and change
*:*:* set Templates “/mydir/templates” to the correct path
*:*:* set initial “/mydir/SLS-2009” to the path where your synchrotron data are stored
*:* put the ﬁle xdsi somewhere in your $PATH (e.g.: /usr/local/bin), chmod 755 xdsi and source ~/.cshrc
*:* You should now be able to start XDSi via the command xdsi

If it works well, enjoy!

I (michaelkrug at uni-konstanz dot de) appreciate feedback.

XDS.INP

2007-11-13T13:37:36Z

Michael:

XDS.INP is a user-provided file that is read by [[XDS]]. Each line consists of one or more <keyword>=<parameter(s)> pairs.

Complete documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html .

Templates for various detectors are at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html .

== Required keywords ==

These keywords have no default parameters and must be given with the correct values.

The values may be obtained from logfiles of the beamline software, your notes, or (for many types of frames) from the headers of the frames (using 'strings <filename>|more'). A good way to retrieve them is by using MOSFLM.

A minimal XDS.INP needs at least these keywords and their parameters:

* Keywords that describe the detector:

DETECTOR NX NY QX QY - for a list of supported detectors and possible geometries, see [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#Table%20of%20supported%20detectors Table of supported detectors]

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_X-AXIS= DIRECTION_OF_DETECTOR_X-AXIS] - often 1 0 0

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DIRECTION_OF_DETECTOR_Y-AXIS= DIRECTION_OF_DETECTOR_Y-AXIS] - often 0 1 0

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCIDENT_BEAM_DIRECTION= INCIDENT_BEAM_DIRECTION] - often 0 0 1

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ROTATION_AXIS= ROTATION_AXIS] - often 1 0 0 at a synchrotron

* Keywords that describe your particular dataset:

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#ORGX= ORGX ORGY] - in pixels '''The most critical parameters for a successful data reduction''' . See [[Obtaining ORGX ORGY]]

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DETECTOR_DISTANCE= DETECTOR_DISTANCE] - in millimeters

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE] - in degrees

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#X-RAY_WAVELENGTH= X-RAY_WAVELENGTH] - in Angstrom

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= NAME_TEMPLATE_OF_DATA_FRAMES] - path and name of frames, with wildcards for numbers

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DATA_RANGE= DATA_RANGE] - numbers of frames to be reduced

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#BACKGROUND_RANGE= BACKGROUND_RANGE] - numbers of frames to be used for initial background estimation, "1 5" is usually enough, and "1 20" should be ample.

== Keywords that additionally describe your experiment ==

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#FRACTION_OF_POLARIZATION= FRACTION_OF_POLARIZATION] and [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#POLARIZATION_PLANE_NORMAL= POLARIZATION_PLANE_NORMAL] should be specified for detectors at synchrotron sites. If they are not specified, their effect will mostly be absorbed by the scale factors determined in [[CORRECT]].

== Keywords for space group assignment ==

* If you know the space group and unit cell parameters of your crystal in advance you just need these two keywords:

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SPACE_GROUP_NUMBER= SPACE_GROUP_NUMBER] - a mapping of space group names against their numbers is near the end of [[IDXREF.LP]].

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#UNIT_CELL_PARAMETERS= UNIT_CELL_PARAMETERS] - unit cell parameters need to respect the constraints of the Laue group, e.g. all angles must be exactly 90.0 for orthorhombic and tetragonal space groups, a and b must be equal for trigonal and tetragonal, and so on.

* If you want to assign a space group and unit cell parameters to a crystal you most probably need this keyword as well:

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REINDEX= REINDEX] - 12 numbers, 9 of which are used as a re-indexing matrix. The other 3 are normally 0. These 12 numbers can be obtained from [[IDXREF.LP]].

The way how to determine a space group (and unit cell parameters) is described in [[space_group_determination|space group determination]].

== Keywords which affect which detector pixels will be used ==

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#INCLUDE_RESOLUTION_RANGE= INCLUDE_RESOLUTION_RANGE] - the default is "20.0 0.0" but it would be good to change this to sensible values for your data set, e.g. 50.0 for the lower resolution limit and the limiting resolution, where the average signal-to-noise ratio drops below 1, for the upper limit (the latter number could be obtained from [[CORRECT.LP]]).

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS] - the default is "7000. 30000." but the first number is probably on the low side. See [[Determining_VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS]].

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MINIMUM_ZETA= MINIMUM_ZETA] - the default of 0.15 is rather on the safe side. A lower value increases completeness. See [[MINIMUM_ZETA]].

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#TRUSTED_REGION= TRUSTED_REGION] - The default is "0.00 1.05" but if you have a square detector, and their are reflections visible in the corners, you may go as high as "0. 1.4142". Depending on the symmetry of your crystal, this may give you useful high-resolution data.

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#EXCLUDE_RESOLUTION_RANGE= EXCLUDE_RESOLUTION_RANGE] - to exclude ice rings. Whether ice rings are a problem should be obvious by looking at frames, FRAME.pck and the "alien" statistics at the end of [[CORRECT.LP]]. Please note that there are five more "high-resolution" ice ring resolution ranges (given at the end of [[CORRECT.LP]]), in addition to the five ranges already supplied in templates of XDS.INP.

== Keywords which affect aspects of geometry parameter refinement ==

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(IDXREF)= REFINE(IDXREF)] - The defaults (REFINE(IDXREF)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK, but '''only if''' COLSPOT has seen '''all''' (or rather, a significant fraction of the) frames. If only a small SPOT_RANGE was used (which is not the best way, but possible), one should use REFINE(IDXREF)= AXIS BEAM ORIENTATION CELL . (The next thing to omit would be AXIS)

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)] - The defaults (REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL) could be modified by omitting DISTANCE, because one should assume that the distance is constant. Furthermore, by fixing the distance one can better see from the results of the refinement whether the cell parameters are stable, or whether they change due to radiation damage. There are situations when one wants to reduce the number of parameters to be refined even more, see [[Optimization]].

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(CORRECT)= REFINE(CORRECT)] - The defaults (REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS i.e. refine everything) are OK

== Keywords which affect whether indexing will succeed ==

In addition to [[Obtaining ORGX ORGY]], I recommend to look at:

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#STRONG_PIXEL= STRONG_PIXEL] - the default is 3, but 6 is usually more appropriate.

== Keywords which affect the speed of data reduction ==

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] - speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine.

[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS] - speeds up XDS by chopping the DATA_RANGE into pieces, and feeding each piece to a new process. That process may run on the local machine, or a different one (but this needs to be configured by the system administrator). Unless specifically set up for a given computer environment (e.g., at a synchrotron site), don't set ''both'' MAXIMUM_NUMBER_OF_PROCESSORS ''and'' MAXIMUM_NUMBER_OF_JOBS to values >1!

== What can go wrong with this file? ==

The most important possible pitfalls are:

* Lines longer than 80 characters are not allowed. This happens most often with the NAME_TEMPLATE_OF_DATA_FRAMES keyword line, because the path to the directory with the frames may be long. Fix: use a symlink to the directory with the frames.

* Error due to omitting the "=" directly after the keyword (i.e. having an intervening blank).

* There may be decoding errors in the parameter which may lead to obscure error messages. E.g., see what happens if you provide only one cell parameter instead of six!

Written by --[[User:Kay|Kay]] 14:44, 8 November 2007 (CET)