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

• adxv
• marView
• xdsviewer

Data Characterization and Processing Software

• distl
• HKL2000
• HKL3000 (available on WS1 only)
• Labelit
• imosflm (GUI version)
• mosflm/ipmosflm (older version)
• XDS
• xia2
• xprep

Structure determination and Refinement

• CNS
• CCP4i
• HKL3000 (available on WS1 only)
• hkl2map
• PHENIX
• SHELX

Model Building and Refinement

• Coot
• O
• PyMol
• xtalview
• MIFit
• Main

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/