A pilot macromolecular 3D structure determination project - Year 9
Title: A pilot macromolecular 3D structure determination project - Year 9
SNIC Project: SNIC 2021/5-376
Project Type: SNIC Medium Compute
Principal Investigator: Martin Moche <Martin.Moche@ki.se>
Affiliation: Linköpings universitet
Duration: 2021-09-01 – 2022-09-01
Classification: 10203 10601
Homepage: https://www.nsc.liu.se/support/presto/
Keywords:

Abstract

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) Members of this project have access to the PReSTO installation via Swedish National Infrastructure of Computing (SNIC). 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 Aurora, the MAX IV online and offline clusters and the local LiU cluster sigma. The PReSTO homepage is designed for newcomers pointing towards MX software developer manuals, default option batch scripts and slurm configurations for certain MX graphical user interfaces. 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 XDSAPP to work with Eiger detector output format HDF5. 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). In 2021 we will finalize the SX software stack in collaboration with MAX IV staff. For the Swedish cryo-EM community at SciLifeLab we will make PReSTO available at LiU Berzelius to hopefully attract more cryo-EM users towards PReSTO. The collaboration between SNIC, MAX IV and SciLifeLab staff is key to project progress. Swedish researchers with X-ray diffraction data can request remote MX-PReSTO training by contacting project PI. Training in use of cryo-EM and NMR software requires further assistance from these branches of Swedish structural biology. We added instructions to include grant numbers when acknowledging SNIC 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).