Difference between revisions of "Scripts and interfaces"

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(New page: There is a number of script and graphical interfaces for the XDS package. == XDSi == the first published interface, by Petri Kursula (XDSi: a graphical interface for the data processing ...)
 
 
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== XDSi ==
 
== XDSi ==
  
the first published interface, by Petri Kursula (XDSi: a graphical interface for the data processing program XDS. (2004) J. Appl. Cryst. 37, 347-348). http://cc.oulu.fi/~pkursula/xdsi.html gives 2007 as last modification date.
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the first published interface, by Petri Kursula (XDSi: a graphical interface for the data processing program XDS. (2004) J. Appl. Cryst. 37, 347-348).
 +
 
 +
http://cc.oulu.fi/~pkursula/xdsi.html gives 2007 as last modification date.
  
 
== [[XDSi]] ==
 
== [[XDSi]] ==
  
 
Tcl/Tk interface by Michael Krug (Welte/Diederichs lab). Unfortunately same name. Can process multiple datasets.  
 
Tcl/Tk interface by Michael Krug (Welte/Diederichs lab). Unfortunately same name. Can process multiple datasets.  
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 +
== XDSAPP ==
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python/Qt version of [[XDSi]], developed at [http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/xdsapp/index_en.html BESSY].
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== [[XDSGUI]] ==
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to edit input files and run commands. See its own [[XDSGUI|XDSwiki article]].
  
 
== ixds ==
 
== ixds ==
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== autoxds ==
 
== autoxds ==
  
script in use at SSRL (Stanford) . See [A Quick XDS Tutorial for SSRL http://smb.slac.stanford.edu/facilities/software/xds/]. Download: http://smb.slac.stanford.edu/templates/xds/autoxds ; download http://smb.slac.stanford.edu/templates/xds/mccd_xdsparams.pl , too!
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script in use at SSRL (Stanford) . See [http://smb.slac.stanford.edu/facilities/software/xds/ A Quick XDS Tutorial for SSRL].
 +
 
 +
Download: http://smb.slac.stanford.edu/templates/xds/autoxds ; download http://smb.slac.stanford.edu/templates/xds/mccd_xdsparams.pl , too!
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== autoPROC ==
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software package, not exclusively using XDS, available at http://www.globalphasing.com/autoproc/ (Vonrhein ''et al.'' (2011). Acta Cryst. D67, 293-302)
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== AutoProcess ==
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Pipeline developed by Michel Fodje at Canadian Macromolecular Crystallography Facility (Saskatoon).
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Usage:
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    autoprocess [options] /path/to/set1.img /path/to/set2.img ... /path/to/setn.img
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    options:
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        --mad, -m : Process each set, scale together and generate separate reflection files.
 +
        --screen, -s : Process a few frames from characterize crystal from each set.
 +
        --anom, -a : Process with Friedel's law False
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        --backup, -b : Backup previous output directory if it exists
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        --prefix=p1,p2,p3 : comma separated list of prefixes to use for output files.
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            Default is first part of image name
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            prefix order should correspond to the order of the data sets
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              for example for MAD data, use --prefix=peak,infl,remo
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        --dir=/path : Directory to store processed results. Default is to create a  new one in the current directory.
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        --inputs, -i: generate XDS.INP only and quit
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        --help, -h : display this message
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    Default (no option): Process each set, scale together and merge into one reflection file.
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    Data sets:
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        Each data set can be represented by any frame from that set.
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== xdsme ==
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 +
by Pierre Legrand at SOLEIL (French synchrotron): web address: http://code.google.com/p/xdsme/
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 +
Here's a short description of the program:
 +
 
 +
xdsme is a collection of python scripts made to simplify the processing of crystal
 +
diffraction images with the XDS Program Package. Provided that the diffraction
 +
parameters are well recorded in the diffraction image headers, XDS data processing
 +
can be started with a simple command line like:
 +
 
 +
$ xdsme pos1_1_???.img
 +
 
 +
Supported detector image format include: ADSC, MARCCD, MAR345 + experimental
 +
for PILATUS, SATURN, RAXIS and MAR555.
 +
 
 +
* xdsme (XDS.py), xscale.py and xdsconv.py for data processing, scaling and file conversion.
 +
* XOalign.py for the goniometer setting calculation (to work with different type of goniometer including Kappa, mini-Kappa, Euler...).
 +
* xds2mos.py or xds2dnz.py ... (for conversion of orientation matrices)
 +
 
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== [[generate_XDS.INP]] ==
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 +
is a script for generating a XDS.INP for a given dataset. See its own [[generate_XDS.INP|XDSwiki article]].

Latest revision as of 14:30, 28 June 2020

There is a number of script and graphical interfaces for the XDS package.

XDSi

the first published interface, by Petri Kursula (XDSi: a graphical interface for the data processing program XDS. (2004) J. Appl. Cryst. 37, 347-348).

http://cc.oulu.fi/~pkursula/xdsi.html gives 2007 as last modification date.

XDSi

Tcl/Tk interface by Michael Krug (Welte/Diederichs lab). Unfortunately same name. Can process multiple datasets.

XDSAPP

python/Qt version of XDSi, developed at BESSY.

XDSGUI

to edit input files and run commands. See its own XDSwiki article.

ixds

python script programmed at BESSY.

autoxds

script in use at SSRL (Stanford) . See A Quick XDS Tutorial for SSRL.

Download: http://smb.slac.stanford.edu/templates/xds/autoxds ; download http://smb.slac.stanford.edu/templates/xds/mccd_xdsparams.pl , too!

autoPROC

software package, not exclusively using XDS, available at http://www.globalphasing.com/autoproc/ (Vonrhein et al. (2011). Acta Cryst. D67, 293-302)

AutoProcess

Pipeline developed by Michel Fodje at Canadian Macromolecular Crystallography Facility (Saskatoon).

Usage:

   autoprocess [options] /path/to/set1.img /path/to/set2.img ... /path/to/setn.img
   options:
       --mad, -m : Process each set, scale together and generate separate reflection files.
       --screen, -s : Process a few frames from characterize crystal from each set.
       --anom, -a : Process with Friedel's law False
       --backup, -b : Backup previous output directory if it exists
       --prefix=p1,p2,p3 : comma separated list of prefixes to use for output files. 
           Default is first part of image name
           prefix order should correspond to the order of the data sets
             for example for MAD data, use --prefix=peak,infl,remo
       --dir=/path : Directory to store processed results. Default is to create a  new one in the current directory.
       --inputs, -i: generate XDS.INP only and quit
       --help, -h : display this message
   Default (no option): Process each set, scale together and merge into one reflection file.
   
   Data sets:
       Each data set can be represented by any frame from that set.

xdsme

by Pierre Legrand at SOLEIL (French synchrotron): web address: http://code.google.com/p/xdsme/

Here's a short description of the program:

xdsme is a collection of python scripts made to simplify the processing of crystal diffraction images with the XDS Program Package. Provided that the diffraction parameters are well recorded in the diffraction image headers, XDS data processing can be started with a simple command line like:

$ xdsme pos1_1_???.img

Supported detector image format include: ADSC, MARCCD, MAR345 + experimental for PILATUS, SATURN, RAXIS and MAR555.

  • xdsme (XDS.py), xscale.py and xdsconv.py for data processing, scaling and file conversion.
  • XOalign.py for the goniometer setting calculation (to work with different type of goniometer including Kappa, mini-Kappa, Euler...).
  • xds2mos.py or xds2dnz.py ... (for conversion of orientation matrices)

generate_XDS.INP

is a script for generating a XDS.INP for a given dataset. See its own XDSwiki article.