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GM/CA @ APS

Software

Department of Energy Office of Science
GM/CA @ APS Sponsors:
National Institute of General Medical Sciences (NIGMS) and National Cancer Institute (NCI) of the National Institutes of Health (NIH)
 

User Program - While at the Beamline - Data Processing

Crystallographic software available at the GM/CA beamlines

This page describes crystallography-related software packages that are installed at GM/CA computers. Best effort is made to keep the commonly used programs and packages, such as HKL2000, CCP4, PHENIX, 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 most of the software, just start using. A few programs which require conflicting environments needs to run via mxshell (see below).

Diffraction image viewers

Data Characterization and Processing Software

Structure determination and Refinement

Model Building and Refinement

  


 

Diffraction image viewers

adxv

       $ adxv [-marccd] [mardatafile|cbfdatafile|hdfdatafile]

The manual is available at http://www.scripps.edu/tainer/arvai/adxv.html. You can also run "adxv -HELP" to find all available keywords. Please note that when viewing HDF5 files (*.h5), by default the frame advance buttons load next or previous HDF5-file. If you want to browse through frames, you need to check the "+Slabs" box. Opening HDF5 master file does not display any images, just the content of the HDF5 tree.

 

albula

       $ albula [cbfdatafile|hdfdatafile]

Check built-in help pages. Please note that Albula is heavily dependent on OpenGL and therefore in many cases may not work during remote operations.

 

marView

	$ marView [mardatafile|cbfdatafile]

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

autoPROC

autoPROC is available for academic users only via mxshell. Documentation is available at https://www.globalphasing.com/autoproc/manual/.

	$ mxshell.pl  ==>  then call autoPROC from the menu

 

CCTBX

CCTBX (Computational Crystallography Toolbox) is available as a part of PHENIX and DIALS. A standalone version, which may be newer, can also be launched via mxshell. Documentation is available at https://cctbx.github.io/.

	$ mxshell.pl  ==>  then call CCTBX from the menu

 

DIALS

DIALS is available as a part CCP4. A standalone version, that may be newer, can also be launched via mxshell. Documentation is available at https://dials.github.io/documentation/.

	$ mxshell.pl  ==>  then call DIALS from the menu

 

HKL2000

	$ HKL2000

Once the program starts up, please pick the detector which produced your files. 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.
NOTE: although HKL2000 can load the HDF5 files produced by the Eiger-16m detector at 23IDB, the operations on them are slow. Therefore, we recommend running the program on CBF files which are automatically generated from HDF5 during data collection.
ATTENTION: The conditions of using HKL2000 and HKL3000 at the GM/CA beamlines are described here. Please read them before use.

 

HKL3000

	$ HKL3000

Once the program starts up, please pick the detector which produced your files. The site files for HKL3000 are the same as for HKL2000 and they can be downloaded here. Online tutorial is available at http://hkl-xray.com/sites/default/files/HKL-3000_Tutorial.pdf.
There is no manual yet.
NOTE: although HKL3000 can load the HDF5 files produced by the Eiger-16m detector at 23IDB, the operations on them are slow. Therefore, we recommend running the program on CBF files which are automatically generated from HDF5 during data collection.
ATTENTION: The conditions of using HKL2000 and HKL3000 at the GM/CA beamlines are described here. Please read them before use.

 

Labelit

Labelit commands are available within PHENIX, which needs to be started via mxshell.

	$ labelit.distl [framename1] [framename2]
	$ labelit.index [framename]

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://cci.lbl.gov/labelit/

 

imosflm

	$ imosflm

This program is a part of CCP4 package and it can also be started within ccp4i. The tutorial is available at http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/documentation/tutorial.pdf.

Please note: if a single CPU is used, imosflm may be quite slow (>2 sec per image or >30 minutes per 1000 images). However, if the parallel mode is chosen (e.g. using 16 CPUs on ws6, which is the default data processing workstation), one can integrate 1000 images in a few minutes. To choose parallel integration mode in imosflm, go to the integration tab, choose the down triangle arrow next to the "Process" button (NB: not the "Process" the button itself), and select "Parallel".

 

mosflm/ipmosflm

	$ mosflm
or
	$ ipmosflm

This program is a part of CCP4 package and it can also be started within ccp4i. 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 is an automated data reduction system. Information is available at https://xia2.github.io/. This program is a part of CCP4 package and it can also be started within ccp4i.

 

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

Online information available at http://cns-online.org/

 

CCP4

	$ ccp4i

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://webapps.embl-hamburg.de/hkl2map/

 

PHENIX

	$ mxshell.pl  ==>  then call phenix from the menu

PHENIX is a software suite for the automated determination of macromolecular structures. The documentation is available at http://www.phenix-online.org/documentation/. You need to start programs via mxshell.

 

SHELX

	$ shelx c/d/e..

All executables of shelx are available within CCP4. The manual is available at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E

 

 

Model Building

Coot

	$ coot

The above command starts a standalone version of Coot, which will likely be the latest. In addition, you can also start a CCP4 version of coot from the ccp4i GUI and the PHENIX GUI starts the standalone version of Coot with PHENIX extensions. The Coot manual available at http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/

 

PyMol

	$ pymol

The manual is available at http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners

 

 

Running programs via mxshell

These days many crystallographic packages include the same software components, which may have different versions and thus conflict with each other. Good examples are CCP4 and PHENIX. Another example is when one wants to use the latest version of DIALS, but DIALS is also included with CCP4. To avoid possible conflicts, we make available by default (i.e. included in the system PATH) only CCP4 as the most comprehensive suit and any packages that do not conflict with the others (e.g. HKL2000 and HKL3000). Everything else needs to be started in special shells opened from the mxshell GUI:

mxshell

Please note that the buttons on the GUI may change since we add or update some packages for each APS run.

To start mxshell, type:

	$ mxshell.pl

... or click on the crystal image in the EPICS controls toolbar:

23ID-epics

GM/CA @ APS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Argonne National Laboratory

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