A pilot macromolecular 3D structure determination project - Year 6

SNIC 2018/3-251


SNAC Medium Compute

Principal Investigator:

Martin Moche


Linköpings universitet

Start Date:


End Date:


Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Secondary Classification:

10601: Structural Biology



In March 2013 Protein Science Facility (PSF) from Karolinska Institutet in Stockholm and National Supercomputer Centre (NSC) in Linköping started a pilot project to evaluate macromolecular crystallography (MX) software applications running at the HPC environment of NSC Triolith. In 2015 the Swedish light source MAX IV decided to fund a pilot extension called PReSTO(, that aim to support integrated structural biology calculations including macromolecular crystallography (MX), Nuclear Magnetic Resonance (NMR) and cryo-electron microscopy (cryo-EM). Access to the PReSTO installation is via Swedish Network of Infrastructure Computing (SNIC) being a collaboration of Swedish HPC centres funded by the Swedish research council ( Thinlinc software from cendio supports the integrated structural biology workflow by enabling remote graphic applications such as coot/chimera/ccp4mg/pymol for model building, calculation and visualization of protein structure and surface properties. In PReSTO the HPC-MX installation has been made using easybuild ( with several advantages to a standard HPC installation. For instance A) the installation itself can be easily shared with other HPC computers such as LUNARC Aurora or the MAX IV cluster B) software environments can be send to compute nodes C) software dependencies are visible in easyconfigs. PReSTO for MX is now available at NSC Triolith, LUNARC Aurora and the MAX IV cluster and used on a daily basis by its members and by a crystallography course hosted by Swedish Agricultural University (SLU) and MAX IV in April 2018. The PReSTO homepage ( intended for HPC-MX newcomers point towards MX software developer manuals. To adapt users to the HPC-MX workflow we also developed a PReSTO menu that A) start MX software at login or compute node with graphics support when appropriate B) enable user to select number of cores and runtime at compute nodes C) enable user to select output directory for software such as hkl2map. In late 2018 we want to share easybuild daily operations including support and upgrades with local HPC administrators and install PReSTO at the new Tetralith ( We also want to improve HPC-MX training for crystallographers and in late 2018 more Swedish researchers will access BioMAX and some MX-HPC training will come from using the MAX IV cluster during beamtime. Regular after beamtime training sessions with users own data/questions will be available at protein science facility, Karolinska Institutet and PReSTO get started seminar/workshop can also be requested by other Swedish Universities by contacting project PI (Martin Moche) as done by Uppsala University in 2015 and SLU in 2018. Please acknowledge access to SNIC resources as done here(1-3) see: 1. M. Anandapadamanaban et al., Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression. Structure 24, 1311-1321 (2016). 2. A. Janfalk Carlsson et al., Laboratory-Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis. Chembiochem, (2016). 3. J. S. Brock et al., A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase. Proceedings of the National Academy of Sciences of the United States of America 113, 972-977 (2016).