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

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.

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