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Scripts and interfaces: Difference between revisions
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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. | 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. | ||
== XDSAPP == | |||
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]. | |||
== [[XDSGUI]] == | |||
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 [ | 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! | |||
== 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 == | == xdsme == | ||
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* XOalign.py for the goniometer setting calculation (to work with different type of goniometer including Kappa, mini-Kappa, Euler...). | * 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) | * 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 [[generate_XDS.INP|XDSwiki article]]. | |||