User Program - While at the Beamline - Data Processing
Crystallographic software available at the GM/CA beamlines
This page describes crystallography-releated software packages that are
installed at GM/CA computers. Best effort is made to keep the supported programs
and packages, such as HKL2000, CCP4, Mosflm, O, and Coot regularly updated
and thoroughly tested in the beamline computer environment. Some other
programs, while made available to the users, are not guaranteed to be up to
date or that local expertise exists for these programs.
Environment is already setup for all of the software, just start using.
Diffraction image viewers
Data Characterization and Processing Software
Structure determination and Refinement
Model Building and Refinement
Diffraction image viewers
adxv
$ adxv [-marccd] [framename]
The manual is available at
http://www.scripps.edu/~arvai/adxv.html
marView
$ marView [framename]
The manual is available at
http://www.marresearch.com/man/marView.htm
xdsviewer
$ xdsviewer [framename]
The information on usage is available at
http://xds-viewer.sourceforge.net/
Data Characterization and Processing software
distl
$ labelit.distl [framename]
A related journal article is available at
http://scripts.iucr.org/cgi-bin/paper?ea5046
HKL2000
$ HKL2000
Use MAR300 as the detector. The site files for HKL2000
can be downloaded here. A hard
copy of the manual is available at the beamline. Online manual is available at
http://www.hkl-xray.com/hkl_web1/hkl/HKL2000manual/index.htm.
ATTENTION:: The conditions of using HKL2000 and HKL3000 at
the GM/CA beamlines are described here.
Please read them before use.
HKL3000
$ HKL3000
Use MAR300 as the detector. HKL3000 is only available on WS1 at each beamline.
There is no manual yet, but the interface is similar to that of HKL2000.
ATTENTION:: The conditions of using HKL2000 and HKL3000 at
the GM/CA beamlines are described here.
Please read them before use.
Labelit
$ labelit [framename1] [framename2]
labelit can work with just one frame, but works better with two frames,
which are at least more than 5 degrees apart. Labelit manual is available at
http://adder.lbl.gov/labelit/
imosflm
$ imosflm
This is a GUI version of mosflm version 1.0.7 (64-bit). The tutorial is available at
http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver107/documentation/tutorial.pdf
mosflm/ipmosflm
$ mosflm
or
$ ipmosflm
This is an older version of mosflm version 7.0.9 (64-bit). User's guide is available at
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/mosflm_user_guide.html
XDS
$ xds
or
$ xds_par
XDS.INP file is expected in the current directory where xds or xds_par is being invoked.
The xds manual is available at
http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html
xia2
$ xia2
xia2 (Version 0.3.4.0) is an automated data reduction system. Information is available at
http://www.ccp4.ac.uk/xia/
xprep
$ xprep
A data analysis software developed by George Sheldrick that is more
versatile than SHELXC. Information on the program xprep is available at
http://shelx.uni-ac.gwdg.de/tutorial/english/xprep.htm
Structure determination and Refinement
CNS
$ cns_solve
cns version 1.3 is provided. Online information available at
http://cns-online.org/v1.3/
CCP4i
$ ccp4i
ccp4 version 6.3.0 (64-bit) is provided. Information on ccp4 is available at
http://www.ccp4.ac.uk/
hkl2map
$ hkl2map
HKL2MAP is a graphical user interface for macromolecular phasing. It connects
several programs from the SHELX-suite. Usage information is available at
http://schneider.group.ifom-ieo-campus.it/hkl2map/
PHENIX
$ phenix
PHENIX is a software suite for the automated determination of macromolecular
structures. The documentation is available at
http://www.phenix-online.org/documentation/
SHELX
$ shelx c/d/e..
All stand alone executables of shelx are also available. The manual is available at
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E
Model Building
Coot
$ coot
coot is installed at version 0.6.2 (64-bit). The manual available at
http://biop.ox.ac.uk/coot/docs.html
O
$ ono
O is installed at version 13.0.0. The manual is available at
http://www.doe-mbi.ucla.edu/Software/o_man/manual.html
PyMol
$ pymol
PyMol is installed at version 1.5. The manual is available at
http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners
xtalview
$ xtalmgr
or
$ xfit
Xtalview is a complete package for solving a macromolecular crystal
structure by isomorphous replacement, including model building that was
developed by Duncan McRee. Xtalview has not been supported by the author
since 2003, but is made available for old timers. Manual pages for XtalView
version 4.0 is available at
http://www.sdsc.edu/CCMS/Packages/XTALVIEW/XV1TOC.html#manpage
MIFit
$ MIFit
MIFit was created by Duncan McRee as a successor to the XtalView/Xfit
program. MIFit manual is available at
http://www.msg.ucsf.edu/local/programs/MIFit/MIFitManual.pdf
Main
$ Main
Main crystallography was developed by Dusan Turk and his group. The
program is intended for high as well as low throughput crystal structure
determination. Information on Main Crystallography is available at http://www-bmb.ijs.si/
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