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 MaxIV 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.
In november 2015, MaxIV and NSC formally decided to develop a HPC platform for MX in support of Swedish MaxIV users giving the PReSTO project the status of a MaxIV satellite. The MX installation made by NSC below is meant to be shared across Swedish HPC centers that want to participate in PReSTO and we therefore select to install all software at NSC Triolith using Easybuild for later move into with LUNARC Aurora. The Aurora installation of PReSTO will start early April 2017.
Swedish structural biologists can access the PReSTO project today by requesting membership in its predessesor pilot project (SNIC 2017/1-199) according to:
The pilot installation is a standard HPC installation, while the PReSTO installation has been performed by Easybuild for rapid sharing with other Swedish HPC centers coordinated by SNIC. The PReSTO installation also enable software launching from the Linux menu for my own Linux computer look and feel. Easybuild also enable transfer of environment variables to the compute nodes as been shown important to MX software that depend on Perl such as pipedream from GlobalPhasing.
This homepage contains startup instructions for the Easybuild installation of MX software that we call PReSTO. We attempt to guide HPC beginners in using the PReSTO environment and simply share links to excellent MX software guides and tutorials generated by MX software developers.
explain basic HPC commands
login, compute nodes and OpenGL acceleration
links to MX sw manuals and references
forkxds enable multi-node XDS
convenient GUI launching at single compute/login node
Information on how to start Phenix jobs in HPC slurm environment
Aurora vs Triolith & H5ToXDS vs dectris-neggia
Launch MX sw script at single compute node