Software

State-of-the-art software for beam line control and data collection is developed and supported by SSRL-SMB. Further, to simplify data processing and structural analysis, a software toolkit is maintained with detailed user manuals.

Beamline Control and Automation Software

Blu-Ice/DCS, the beamline control software and graphical user interface, installed at all the beamlines, allows the users to control every aspect of their experiments, from moving the detector and adjusting the beam size to screening crystals from a cassette, to collecting data in several regimes. The many features of Blu-Ice/DCS are described in detail in the extensive user manual. Blu-Ice/DCS continues to be under active development with new features added and updated frequently in order to respond to the evolving needs of our user base.

All diffraction data collected is automatically processed with the results available in the same directory as the diffraction data. Furthermore, to evaluate a fast-moving experiment in real time, a strip chart placed in the Collect tab, provides information on diffraction quality. This new data monitoring system makes use of AI to perform real-time analysis of diffraction images.

Supported Macromolecular Crystallography Software

Most of the major crystallographic software packages can be used on the SMB-PX processing cluster. These include processing programs such as xia2, XDS, and mosflm, aggregate suites and pipelines such as Phenix and CCP4, and graphics packages such as COOT and PyMOL. Most of these packages are fully supported by SSRL staff, regularly updated (usually within 2-3 months of the version release) and thoroughly tested in the beamline and processing environment. Some unsupported, deprecated, and niche packages are also available (or can be made available upon request); however we do not guarantee timely updates, configuration, testing, etc.

Older and more recent versions of some programs may be available. To find out which versions are available, use the module command:

  • module list (list the currently active version of the programs).
  • module avail (list all available versions of the programs).
  • module switch -f "default-version" "another-version" (changes the current default version of the program with the desired version).
Nightly builds and other mid-release versions of certain software packages can be installed upon request, but will not be set as default versions that load when an environment is accessed. Use the module switch -f command to switch to the version you have requested. That command can also be used to switch between suites of software that have conflicting components and cannot be loaded at the same time, e.g. Phenix and DIALS.

The table below lists the software packages that are available to users through our processing cluster.

Program SSRL Manual Program Website Program Manual Current Version Last update Expiration date License contact/Download site User Support
Data Collection Strategy and Monitoring
Blu-Ice/DCS Blu-Ice/DCS manual Blui-Ice/DCS development website N/A N/A N/A none email Scott McPhillips (scottm@slac.stanford.edu) yes
Data Monitoring Not available Data monitoring website ResoNet AI guide
Interceptor guide 		Interceptor v. 0.33.3 Jan 2024 none ResoNet AI repository
Interceptor repository 		yes
RADDOSE-3D Not available RADDOSE-3D website Manual 4.0.head N/A none GitHub no
ADXV Not available ADXV website Manual (PDF) N/A N/A none Download from website yes
Data Processing and Strategy
xia2 xia2 tutorial xia2 website Manual 3.13.0 (DIALS version) March 2023 none Download options yes
autoPROC Not available autoPROC website Documentation 1.0.5 Jul 2023 Jul 2024 Download from GlobalPhasing site no
autoXDS autoXDS manual N/A N/A N/A N/A N/A Under Construction yes
XDS/XSCALE XDS tutorial XDS website Manual Jun 30, 2023 BUILT=20230630 Jun 30, 2023 Aug 31, 2024 Download yes
cctbx.xfel Not available cctbx.xfel website cctbx.xfel manual N/A Oct 6, 2022 none Installation instructions yes
mosflm iMosflm Strategy and Processing manual mosflm website Manual 7.4.0 (current CCP4 dist.) Feb 2024 none Download from MOSFLM site
Distributed w/ CCP4		 yes
HKL-3000 Not available HKL-3000 website HKL-3000 tutorial 723 Apr 2023 none Contact Iwona Minor at HKL yes
ELVES Not available ELVES website Manual 1.2.5 June 2009 none Download no
Scala Mosflm-Scala tutorial Scala website Manual 3.3.22 (current CCP4 dist.) July 2013 none Distributed w/ CCP4 yes
Phasing and Refinement
CCP4 Not available CCP4 website Manual 8.0.0717 Feb 9, 2024 none Download yes
Phenix Not available Phenix website Manual 1.21-5207 (dev versions available via module command) Feb 9, 2024 none Download no
Refmac5 Not available Refmac5 website Manual 5.8.0425 (current CCP4 dist.) Feb 9, 2024 none Download no
Solve/Resolve Not available Solve/Resolve website Solve Manual
Resolve Manual		 2.13 April 2010 N/A Download yes
SHELX Not available SHELX website SHELX Wikis and Manuals shelxc-2016/1 shelxd-2013/2 shelxe-2023/1 shelxl-2019/3 Jan 2023 None Download yes
autoSHARP Not available autoSHARP website Documentation 20191129 November 2019 November 2019 Download from GlobalPhasing site no
BUSTER Not available BUSTER website Documentation 1.3.3 Jul 2023 Jul 2024 Download from GlobalPhasing site no
ARP/wARP Not available ARP/wARP website Manual 8.0 Aug 2019 none Distributed w/ CCP4 no
CNS Not available CNS website Manual 1.3 Mar 2011 none Download no
Phaser Not available Phaser website Manual 2.8.3 (CCP4), 2.8.3(?) (Phenix) As per CCP4/Phenix none Download no
Model Building and Molecular Graphics
COOT Coot tutorial Coot website Manual 0.9.8.92 EL (CCP4 dist.) As per CCP4 none Download yes
PyMOL Not available PyMOL website PyMOL Wiki 2.5.2 Jan 2022 none Download no

Helpful Scripts and Tools

The SSRL staff as well as our user community have created a number of useful scripts and other tools that make a crystallographer's life easier. These are listed in the table below.
Name Purpose Website Download Manual
AlphaFold coloring Color AlphaFold Protein Structure Database predictive models by per-residue confidence score (pLDDT) AlphaFold coloring repository Implementation instructions Usage instructions
pymolsnips PyMOL macro language templates pymolsnips repository Installation instructions Manual
pymolshortcuts Aliased PyMOL shortcuts for non-coders pymolshortcuts repository Installation instructions Manual