A great portion of data processing is now performed by JBluIce/PyBluIce automatically via the Analysis tab. You may want to check the following guides to familiarize yourself with the JBluIce/PyBluIce 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 HKL3000, 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 the CCP4 software, XDS and common viewers, just start using. A few programs which require conflicting environments needs to run via mxshell (see below). Alternatively, these programs are also managed by Environment Modules, and can be loaded or unloaded as needed. To list available modules, type:
$module availTo load enviroment for a package, e.g. phenix, type
$ module load phenixTo unload it:
$ module unload phenixIf the module command is not available, type:
$ source /etc/profile.d/modules.sh
$ adxv [-marccd] [mardatafile|cbfdatafile|hdfdatafile]
The manual is available here. 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 [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 [framename]
The information on usage is available here.
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 the jBluIce/PyBluIce Analysis tab. Academic users may also use autoPROC to process their data after data collection through either the jBluIce/PyBluIce GUI or a standalone data processing GUI which can be started by typing:
$ bluice-process
Power academic users can access full command line interface of autoPROC via mxshell:
$ mxshell.pl
Then call autoPROC from the menu displayed by the mxshell.pl script.
Parameters from image headers are sufficient for autoPROC to work. Please refer the Global Phasing documentation pages and wiki pages for detailed usage instructions and tips.
DIALS is available as a part CCP4 by default. A standalone version, usually newer, can also be access through module:
$ module load dials $ duior via mxshell:
$ mxshell.pl ==> then call DIALS from the menu
Documentation is available here.
$ HKL
Only run it on ws5 or ws6. Once the program starts up, please pick the detector which produced your files.
The site files for HKL3000 are the same and can be downloaded
here.
Online HKL3000 tutorial is available
here.
A hard copy of the HKL2000 manual is available at the beamline. There is
no HKL3000 manual yet.
ATTENTION: The conditions of using HKL software at the GM/CA beamlines are described here. Please read them before use.
$ 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 here and the mosflm program guide is available here.
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".
$ xdsgui or $ xds_par
For manual processing, we recommend using xdsgui. The environment variable NEGGIA_PATH is pre-defined in the user's environment to enable loading of Dectris HDF5 files. If xds or xds_par is used, XDS.INP file is expected in the current directory where xds or xds_par is being invoked. XDS.INP can be generated using the following command:
$ generate_XDS.INP "hdf_master_file_full_path"The xds manual is available here.
$ xia2
xia2 is an automated data reduction system. Information is available here. This program is a part of CCP4 package and it can also be started within ccp4i (ccp4i2).
$ ccp4i /Older interface, obsolete/ or $ ccp4i2 /Newer interface/
Information on CCP4 is available here.
$ mxshell.pl ==> then call phenix from the menu
PHENIX is a software suite for the automated determination of macromolecular structures. The documentation is available here. You need to start programs via mxshell.
$ shelx c/d/e..
All executables of shelx are available within CCP4. The manual is available here.
$ xprep
A data analysis software developed by George Sheldrick that is more versatile than SHELXC. Information on the program xprep is available here.
$ coot /older version/ or $ coot1 /coot 1.0 branch, new version/ or $ Moorhen /Web-based interactive model viewing and building/
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 here.
$ pymol
The manual is available here.
$ chimerax
UCSF ChimeraX package. The manual is available here.
$ module load crystfel $ crystfel
Online information is available here.
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
These are locally developed scripts to facilitate usage of CrystFEL programs at GMCA.
The generate_geometry script creates a geometry file of either
Pilatus or Eiger detectors. It requires a cbf image or hdf5 master file as input. Gaps between modules and beam shadow are masked.
Usage:
$ generate_geometry cbfdatafile | hdf5masterfile
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
$ module load nxds $ nxds_par etc
XDS-based package for processing serial crystallography data. Online information is available here.
$ module load emc $ emc.sh
The Expand-Maximize-Compress (EMC) algorithm is an iterative reconstruction method designed to reconstruct reciprocal space models from noisy and sparse diffraction data. Please consult with GMCA staff if you wish to process your data using this method.
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. HKL3000). Everything else needs to be started in special shells opened from the mxshell GUI:
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:
GM/CA @ APS
