Argonne National Laboratory

GM/CA @ APS

Crystallographic 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)
 

Crystallographic software available at the GM/CA beamlines

A great portion of data processing is now performed by JBluIce automatically via the Analysis tab. You may want to check the following guides to familiarize yourself with the JBluIce data processing capabilities:

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

Serial Crystallography

  


 

Diffraction image viewers

adxv

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

The manual is available at https://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.

 

xdsviewer

	$ xdsviewer [framename]

The information on usage is available at https://xds-viewer.sourceforge.net/

 

 

Data Characterization and Processing software

autoPROC

autoPROC developed by Global Phasing Limited is available for academic users only. For these users autoPROC is automatically run after each data collection. The processing results are accessible from jBluIce Analysis tab. Academic users may also use autoPROC to process their data after data collection through either the jBluIce GUI or a standalone data processing GUI which can be started by typing:

        $ jbluice-process

Power academic users can access full command line interface of autoPROC via mxshell:

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

Parameters from image headers are sufficient for autoPROC to work. Please refer to Global Phasing documentation pages (https://www.globalphasing.com/autoproc/manual/) and wiki pages (https://www.globalphasing.com/autoproc/wiki/) for detailed usage instructions and tips.

 

DIALS

DIALS is available as a part CCP4. A standalone version, that may be newer, can also be launched either as a GUI:

	$ dui
or via mxshell:
	$ mxshell.pl  ==>  then call DIALS from the menu

Documentation is available at https://dials.github.io/documentation/.

 

HKL2000 and HKL3000

	$ HKL2000
and
	$ HKL3000

respectively.

Once the program starts up, please pick the detector which produced your files. The site files for HKL2000 and HKL3000 are the same and can be downloaded here.
Online HKL2000 manual is available at https://www.hkl-xray.com/hkl_web1/hkl/HKL2000manual/index.htm.
Online HKL3000 tutorial is available at https://hkl-xray.com/sites/default/files/HKL-3000_Tutorial.pdf.
A hard copy of the HKL2000 manual is available at the beamline. There is no HKL3000 manual yet.

ATTENTION: The conditions of using HKL2000 and HKL3000 at the GM/CA beamlines are described here. Please read them before use.

 

imosflm/mosflm

	$ imosflm		/GUI version/
or
	$ mosflm		/Command line version/

This program is a part of CCP4 package and it can also be started within ccp4i (ccp4i2).

The imosflm tutorial is available at https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/documentation/tutorial.pdf and the mosflm program guide is available at https://www.mrc-lmb.cam.ac.uk/harry/mosflm/mosflm_user_guide.html.

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".

 

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 (ccp4i2).

 

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

CCP4

	$ ccp4i			/Older interface, being phased out/
or
	$ ccp4i2		/Newer interface/

Information on CCP4 is available at https://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 https://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 https://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 (ccp4i2) GUI and the PHENIX GUI starts the standalone version of Coot with PHENIX extensions. The Coot manual is available at https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/

 

PyMol

	$ pymol

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

 

 

Serial Crystallography

Serial Crystallography programs are NOT available in the default environment, but accessible through mxshell under the name "Serial-X". Users can also run the setup script manually in order to access them:

	source /mnt/software/px/serial-x/serialx-setup.sh

 

Cheetah

	$ mxshell.pl  ==>  then call "Serial-X" from the menu  ==>  then run Cheetah programs
	or
	$ mxshell.pl Serial-X  ==>  then run Cheetah programs

Online information is available at https://www.desy.de/~barty/cheetah/

Both cheetah-cbf (via command line) and cheetah-gui are supported. cheetah-gui works in a similar manner as the SLAC Cheetah. Users are expected to follow certain directory structure. It is recommended that each experiment is located in its own directory. Under the experiment directory, the images are stored in sub-directories named as runXXXX (e.g. run0001 etc).

 

CrystFEL

	$ mxshell.pl  ==>  then call "Serial-X" from the menu  ==>  then run CrystFEL programs
	or
	$ mxshell.pl Serial-X  ==>  then run CrystFEL programs

Online information is available at https://www.desy.de/~twhite/crystfel/

CrystFEL is a set of programs for processing serial crystallography data. External indexing programs available at GMCA include: imosflm, XDS, and dirax.

 

generate_geometry and smx_streamer

	$ mxshell.pl  ==>  then call "Serial-X" from the menu  ==>  then run the scripts
	or
	$ mxshell.pl Serial-X  ==>  then run the scripts

These are locally developed scripts to facilitate usage of Cheetah and CrystFEL programs at GMCA.

The generate_geometry script creates a geometry file of either Pilatus or Eiger detectors. It requires a cbf image as input. The -cheetah option is needed if the geometry file is to be used in cheetah-gui. Gaps between modules and beam shadow are masked.
Usage:

generate_geometry a_cbf_image [-cheetah]

The smx_streamer is a simple GUI for running CrystFEL (indexamajig) automatically. It outputs a merged stream file with indexed reflections.
Usage:

smx_streamer -i image_directory -o output_directory

 

 

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 by Argonne National Laboratory

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