A pilot macromolecular 3D structure determination project - Year 11
Title: A pilot macromolecular 3D structure determination project - Year 11
DNr: NAISS 2023/22-811
Project Type: NAISS Small Compute
Principal Investigator: Martin Moche <Martin.Moche@ki.se>
Affiliation: Linköpings universitet
Duration: 2023-09-01 – 2024-09-01
Classification: 10203
Homepage: https://www.nsc.liu.se/support/presto/


In 2013, Protein Science Facility from Karolinska Institutet in Stockholm and National Supercomputer Centre (NSC) in Linköping started a pilot project to evaluate Macromolecular X-ray crystallography (MX) applications performance at NSC Triolith. In 2015, the Swedish light source MAX IV decided to fund an extension called PReSTO for MX, Nuclear Magnetic Resonance (NMR) and cryo-electron microscopy (cryo-EM). In 2018, the Swedish Research Council granted funds to this project (dnr. 2018-06479) Access to PReSTO installation goes via National Academic Infrastructure for Supercomputing in Sweden (NAISS). Thinlinc software from Cendio supports the structural biology workflow by enabling remote graphic applications such as coot/chimera/ccp4mg/pymol for interactive model building and visualization of protein structure and surface properties. Since 2017, we use easybuild when installing PReSTO with several advantages to a standard HPC installation such as A) software environments can be send to compute nodes B) software build and runtime dependencies are made explicit in easyconfigs and easyblocks C) the version controlled software stack can be moved into new hardware with minor effort. PReSTO is now available at NSC Tetralith, LUNARC Cosmos, the MAX IV cluster, and the local NSC cluster Berzelius. The PReSTO homepage is designed for newcomers pointing towards structural biology software developer manuals, default option batch scripts and slurm configurations for a few GUIs with inherent slurm scheduler. We also developed a PReSTO menu that enable users to A) launch MX software at login or compute nodes where appropriate B) select compute node time and core number C) select output directory for some software such as hkl2map. Code optimization are made to adapt the forkxds script of popular XDS package to slurm, and XDSAPP3 to set local parameters according to slurm allocation. In 2020, MAX IV developed a fragment screening web application on top of the stable PReSTO installation(1) and PReSTO were acknowledged for making Serial X-ray crystallography software available to Swedish researchers(2) doing time resolved diffraction experiments using X-ray Free Electron Lasers (XFEL). During 2022 we transfer the PReSTO installation to LiU local NSC Berzelius cluster using easybuild. We had a first installation of Scipion, Relion, EMAN2, CisTEM, Gctf, Gautomatch, MotionCor2, and CTFFIND at Tetralith and added CryoSPARC when transfer to NSC Berzelius. Today users may collect cryo-EM data at SciLifeLab Umeå site and perform live data processing using “CryoSPARC live” at NSC Berzelius. We added instructions to include grant numbers when acknowledging NAISS and PReSTO on our homepage. 1. G. M. A. Lima et al., FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. ActaD 77, 799-808 (2021). 2. V. Srinivas et al., High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. JACS 142, 14249-14266 (2020).