Scripts and interfaces: Difference between revisions
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== [[generate_XDS.INP]] ==
== [[generate_XDS.INP]] ==
is a script for generating a XDS.INP for a given dataset.
is a script for generating a XDS.INP for a given dataset. .
Revision as of 16:29, 28 June 2020
There is a number of script and graphical interfaces for the XDS package.
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.
Tcl/Tk interface by Michael Krug (Welte/Diederichs lab). Unfortunately same name. Can process multiple datasets.
python/Qt version of XDSi, developed at BESSY.
to edit input files and run commands.
python script programmed at BESSY.
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!
software package, not exclusively using XDS, available at http://www.globalphasing.com/autoproc/ (Vonrhein et al. (2011). Acta Cryst. D67, 293-302)
Pipeline developed by Michel Fodje at Canadian Macromolecular Crystallography Facility (Saskatoon).
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.
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)
is a script for generating a XDS.INP for a given dataset. See its own XDSwiki article.