Software
State of the art software programs for Data Collection and Data Processing are available on the Macromolecular Crystallography (MC) computers. The beamline control GUI Blu-Ice and Web-Ice provide an interface for data collection, screening, image viewing, strategy calculations and data processing. Other supported software programs include Phasing, Refinement, Model Building and Graphics Display.
Several 3rd party software programs have SSRL-specific manuals available as noted in the tables below. In addition, extensive documentation provided by the author(s) is available on their respective websites.
Running Software Processing Programs
A directory for storing data images and a directory containing software template files are automatically created the first time you log in to a SSRL MC computer. These directories are accessible from all beamline computers.
/data/account_name
This directory is used to store the diffraction images and should also be used for data processing.
Recommendation: Create subdirectories for each data set collected.
Template Files
/data/account_name/templates
This directory contains SSRL-specific data processing input and shell files for many of the data processing programs.
Auto-processing
/data/account_name/data_collection_directory/auto-processing-file_name
This directory contains data processing results that automatically run in the background, providing quick feedback on the quality of your data. Auto-indexing and integration are carried out with LABELIT and XDS. The data are analyzed with POINTLESS and XTRIAGE, scaled and merged with AIMLESS, and transformed to amplitudes with TRUNCATE. A free R-set is also generated using 5% of the reflections. All programs use default settings with no resolution or I/sig(I) cutoffs. The input files can be modified and each step can be rerun using the run.csh scripts located in each program subdirectory.
Processing Computers
Use the dedicated pxproc09 - pxproc32 computers to run data processing software. From any beamline computer, click on the "SSRL Icon" on the Xfce Panel to bring up a list of processing computers (Fig. 1).
Figure 1. A list of dedicated data processing computers (pxproc) is displayed using the Xfce Panel on any beamline computer. (Click-on to Enlarge)
Clicking on Select Least Loaded displays information about the pxproc computers (Fig. 2). Choose the computer that is least loaded to run software.
Figure 2. Display window that shows CPU loads and memory usage for the pxproc computers.
Command Line Execution
All 3rd party programs can be executed on the command line using the program name.
[account_name@smbnxs2 ~/data/account_name/raddose43d_test] $ raddose3d -i raddose3d.in --o raddose3d.out
Data Collection Programs
| Program | Current Version | Program Description | SSRL Manual | Software Development Website |
|---|---|---|---|---|
| ADXV | 1.9.13 | Powerful GUI interface for analyzing diffraction images. | https://www.scripps.edu/tainer/arvai/adxv.html | |
| BEST | 3.4.4a | Data collection strategy | http://www.embl-hamburg.de/BEST/ | |
| Blu-Ice | 5.0 | Experimental contol and graphical user interface | Blu-Ice Manual | https://www-ssrl.slac.stanford.edu/smb-mc/content/documentation/manuals/developm… |
| ELVES | 1.2.5 | Automated data collection strategy, data processing, and structure solution | https://bl831.als.lbl.gov/~jamesh/elves/ | |
| RADDOSE3D | ||||
| Web-Ice | 4.5 | Data collection, strategy, and auto-processing | Web-Ice Manual |
Data Processing Programs
| Program | Current Version | Program Description | SSRL Manual | Software Development Website |
|---|---|---|---|---|
| autoPROC | 20200506 | Indexing, integration, scaling and merging of diffraction data | http://www.globalphasing.com/autoproc/ | |
| CCP4 | 7.0.078 | Full crystallography software suite | http://www.ccp4.ac.uk/ | |
| ELVES | 1.2.5 | Automated data collection strategy, data processing, and structure solution | https://bl831.als.lbl.gov/~jamesh/elves/ | |
| HKL-2000 | 715 | Indexing and integration of raw diffraction images | HKL-2000 at SSRL | http://www.hkl-xray.com/ |
| iMOSFLM | 7.2.2 | Indexing and integration of raw diffraction images | MOSFLM and SCALA at SSRL | http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ |
| IOTA | 1.1.033 | Indexing and integration of raw serial diffraction images | http://viper.lbl.gov/cctbx.xfel/index.php/IOTA | |
| MAD Scripts | 1.57 | Scripts for rapid data processing of SAD and MAD data sets. | MAD Scripts Manual | https://www-ssrl.slac.stanford.edu/smb-mc/node/2242 |
| nXDS/nXSCALE | 201901 | Indexing, integration, scaling and merging of serial diffraction data | http://nxds.mpimf-heidelberg.mpg.de/html_doc/nXDS.html | |
| PHENIX | 1.13-2889 | Full crystallography software suite | http://www.phenix-online.org/ | |
| SCALA | 3.3.22 | Scaling, post-refinement, and merging of integrated diffraction images | MOSFLM and SCALA at SSRL | http://www.ccp4.ac.uk |
| Uppsala Software Factory | A vast set of tools for data, map, and structure tinkering | http://xray.bmc.uu.se/usf/ | ||
| Web-Ice | 4.5 | Data collection, strategy, and auto-processing | Web-Ice Manual | |
| XDS / XSCALE | Mar 15, 2019 BUILT=20191015 | Indexing, integration, scaling and merging of diffraction data | XDS at SSRL | http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html |
Phasing Programs
| Program | Current Version | Program Description | SSRL Manual | Software Development Website |
|---|---|---|---|---|
| autoSHARP | 20200206 | Phasing, density modification, map-making | http://www.globalphasing.com/sharp/ | |
| CCP4 | 7.0.078 | Full crystallography software suite | http://www.ccp4.ac.uk/ | |
| CNS | 1.3 | Full crystallography software suite | http://cns-online.org/v1.3/ | |
| ELVES | 1.2.5 | Automated data collection strategy, data processing, and structure solution | https://bl831.als.lbl.gov/~jamesh/elves/ | |
| MAD Scripts | 1.57 | Scripts for rapid data processing of SAD and MAD data sets. | MAD Scripts Manual | https://www-ssrl.slac.stanford.edu/smb-mc/node/2242 |
| Phaser | 2.8.1 | Molecular replacement | http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software | |
| PHENIX | 1.13-2889 | Full crystallography software suite | http://www.phenix-online.org/ | |
| SHELX | 2019_1 | Phasing, density modification, refinement | http://shelx.uni-ac.gwdg.de/SHELX/ | |
| Solve / Resolve | 2.13 | Phasing, density modification, and automatic model-building | https://solve.lanl.gov/ | |
| Uppsala Software Factory | A vast set of tools for data, map, and structure tinkering | http://xray.bmc.uu.se/usf/ |
Refinement Programs
| Program | Current Version | Program Description | SSRL Manual | Software Development Website |
|---|---|---|---|---|
| BUSTER | 20200206 | Structure refinement, automated model building | http://www.globalphasing.com/buster/ | |
| CCP4 | 7.0.078 | Full crystallography software suite | http://www.ccp4.ac.uk/ | |
| CNS | 1.3 | Full crystallography software suite | http://cns-online.org/v1.3/ | |
| PHENIX | 1.13-2889 | Full crystallography software suite | http://www.phenix-online.org/ | |
| Refmac5 | 5.8.0222 | Structure refinement | http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac.html | |
| SHELX | 2019_1 | Phasing, density modification, refinement | http://shelx.uni-ac.gwdg.de/SHELX/ | |
| Uppsala Software Factory | A vast set of tools for data, map, and structure tinkering | http://xray.bmc.uu.se/usf/ |
Modeling and Graphics Programs
| Program | Current Version | Program Description | SSRL Manual | Software Development Website |
|---|---|---|---|---|
| ADXV | 1.9.13 | Powerful GUI interface for analyzing diffraction images. | https://www.scripps.edu/tainer/arvai/adxv.html | |
| ARP/wARP | 7.6 | Automated model building | http://www.embl-hamburg.de/ARP/ | |
| BUSTER | 20200206 | Structure refinement, automated model building | http://www.globalphasing.com/buster/ | |
| CCP4 | 7.0.078 | Full crystallography software suite | http://www.ccp4.ac.uk/ | |
| CNS | 1.3 | Full crystallography software suite | http://cns-online.org/v1.3/ | |
| COOT | 0.8.9.1 (CCP4) | Model building, visualization, real-space refinement, validation and analysis | COOT at SSRL | http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ |
| JCSG Software Toolkit | Ligand Search, QC Check and Xpleo for missing resudues | https://www-ssrl.slac.stanford.edu/smb-mc/content/jcsg-software-toolkit | ||
| O | 12.0 | Model building | http://xray.bmc.uu.se/~alwyn/ | |
| PHENIX | 1.13-2889 | Full crystallography software suite | http://www.phenix-online.org/ | |
| PyMOL | 1.7.5.0 | Model building, visualization, and analysis | http://www.pymol.org/ | |
| pymolsnips | Templates for writing PyMOL scripts | pymolsnips: PyMOL Script Writing with Code Templates | https://github.com/MooersLab/pymolsnips | |
| Solve / Resolve | 2.13 | Phasing, density modification, and automatic model-building | https://solve.lanl.gov/ | |
| Uppsala Software Factory | A vast set of tools for data, map, and structure tinkering | http://xray.bmc.uu.se/usf/ |