Structural biologists use Macromolecular X-ray crystallography (MX), Nuclear Magnetic Resonance (NMR) and cryo Electron Microscopy (cryo-EM) to determine 3D structures of macromolecules such as proteins, DNA and RNA. To address complex research questions structural biologists is now stretching towards cellular length scales with techniques such as cryo-EM tomography and X-ray imaging while capturing dynamics via correlative microscopy and molecular dynamics (MD) simulations. The multi-purpose and multi-technique approach to characterize how macromolecules and their assemblies interact with virus and other pathogens in space and time is known as integrated structural biology. Today structural biologists experience an increasing amount of experimental raw data being collected by modern photon counting detectors at national and international facilities. Swedish structural biology research groups using the Swedish MAX IV light source for macromolecular X-ray crystallography and the cryo-EM facilities at Science For Life laboratories are generated large amounts of raw data that require supportive and research driven computational and storage solutions.
PReSTO is available at NSC computer Tetralith, LUNARC computer Aurora and the MAX IV cluster. The NSC and LUNARC installations are available through SNIC, while the MAX IV cluster is accessible when having MX beamtime at BioMAX.
Swedish structural biologists can access and use PReSTO by requesting membership in compute project (SNIC 2020/5-368):
We are indepted to all MX software authors that kindly share their software for academic use in an HPC environment. We list all MX software currently in PReSTO installation with links to software home page and citations. Specifically we want to mention Gérhard Bricogne and Claus Flensburg from GlobalPhasing supporting the PReSTO project since its very beginning and shared all their MX software for academic HPC use including autoPROC with Staraniso for convenient elliptical scaling of diffraction datasets. We also want to mention the developers behind XDSAPP version 2.99 (Karine Röwer, Uwe Müller and Manfred Weiss) sharing a pre-release that can process Eiger data containers directly and Graeme Winter from the DIALS development team sharing a BioMAX specific software patch for DIALS.
Beside MX software authors, the Swedish National Infrastructure for Computing (SNIC) also require acknowledgements upon publishing. Perhaps use
Computations were performed at NSC Tetralith/LUNARC Aurora provided by the Swedish National Infrastructure for Computing (SNIC) and PReSTO funded by the Swedish Research Council through grant agreement no. 2018-05973 (SNIC) and 2018-06479 (PReSTO)or adapt on online SNIC acknowledgement template
We attempt to provide get started instructions to the PReSTO environment and simply share links to excellent MX software guides and tutorials generated by MX software developers.
BioMAX data processing scripts/settings/keywords
login, compute nodes and OpenGL acceleration
List of issues
Support sessions for newcomers
Triolith is exchanged for Tetralith
convenient GUI launching at single compute/login node
PReSTO version control and releases
Links to home, citations and licences
sending parallel jobs to the queue