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/