A pilot macromolecular 3D structure determination project - Year 5


SNIC 2017/1-199


SNAC Medium

Principal Investigator:

Martin Moche


Linköpings universitet

Start Date:


End Date:


Primary Classification:

10203: Bioinformatik (beräkningsbiologi) (tillämpningar under 10610)

Secondary Classification:

10601: Strukturbiologi





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 NSC Triolith. Supported by positive feedback from the Swedish MX community, the Swedish light source MAX IV decided to fund a pilot extension called PReSTO (https://www.nsc.liu.se/support/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 pilot and PReSTO installation is via Swedish Network of Infrastructure Computing (SNIC) being a collaboration of Swedish HPC centres funded by the Swedish research council (www.snic.vr.se). The integrated structural biology workflow is supported by NSC thinlinc software enabling remote graphic applications such as coot/chimera/ccp4mg/pymol/vasco for model building, calculation and visualization of protein surface properties and structures. The pilot MX installation is a standard HPC installation while for PReSTO the same MX software has been installed using easybuild (https://easybuild.readthedocs.io/en/latest/). The easybuild HPC MX installation has several advantages to standard HPC such as A) it can be easily shared with other Swedish HPC centres such as Lunarc Aurora B) software environment can be send to compute nodes C) software dependencies are made visible in easyconfigs used by easybuild. PReSTO for MX is now available with no known issues at NSC Triolith while at Lunarc Aurora a test install and demo session at MAX IV on 22 March 2017 revealed some phenix software wizards need an update to write correct output PDB files at the Lustre filesystem. For 2017 we now want to share the easybuild HPC MX installation developed at NSC Triolith with Lunarc Aurora and make Lunarc Aurora available to pilot members. Lunarc Aurora is equipped 230 nodes having with 20 cores per node and the dynamic read cache lustre filesystem making XDS and its derivatives running very efficient on a single node. PReSTO homepage is currently written towards NSC Triolith usage (https://www.nsc.liu.se/support/presto/) however a clone with almost identical guidance will be made available to Lunarc Aurora users. During 2016 a desktop PReSTO menu have been developed that A) start MX software at login or compute node B) enable user to select number of cores and compute time C) enable user to select output directory for software such as hkl2map. We also kindly ask structural biology researchers to acknowledge access to SNIC resources when possible as done here(1-3) www.snic.vr.se/apply-for-resources/template-for-acknowledgements-for-the-convenience-of-snic-users References 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).