A pilot macromolecular 3D structure determination project - Year 3
Abstract
In March 2013 Protein Science Facility (PSF) from SciLifeLab in Stockholm and National Supercomputer Centre (NSC) in Linköping started a pilot project to evaluate protein crystallography software applications running at NSC Triolith.
We have installed XDS parallel data processing software used for all protein X-ray diffraction datasets collected today including its graphical user interface (GUI)-scripting derivatives such as XDSGUI/XDSAPP. We also installed SHELX C/D/E, where SHELXD is parallel software, and the SHÈLX-GUI called hkl2map. The two major software packages CCP4 and PHENIX have been installed at Triolith along with Rosetta and the PHENIX-GUI contains a slurm scheduler compatible with NSC Triolith. Project members now have access to supercomputer adapted software such as Arcimboldo (http://chango.ibmb.csic.es/ARCIMBOLDO/) and Shake and Bake (http://www.hwi.buffalo.edu/SnB/SnBHome.htm). The structural biology workflow is further supported by NSC thinlinc software enabling remote graphic applications such as COOT for macromolecular model building and PyMol/VASCo for convenient picture making including protein surface representations. On the pilot project homepage (http://ki.se/en/mbb/get-started-at-national-supercomputer-centre-nsc) users can get access routes and software settings to get started at NSC.
The purpose of this pilot is to build momentum within the protein crystallography community to engage in supporting the PReSTO application headed by NSC. PReSTO stands for rapid protein structure determination in an integrated e-Science environment for structure calculations and data storage. PReSTO is supported by the protein crystallography community via SwedStruct (swedstruct.mbb.ki.se), MaxIV (https://www.maxlab.lu.se/maxiv) and GlobalPhasing (www.globalphasing.com). Gerhard Bricogne, the GlobalPhasing founder, was awarded the Gregori Aminoff prize in 2009 for “development of revolutionary programme systems” by the Royal Swedish Academy of Science. Nine different research groups and PIs mostly from Karolinska Institutet have joined this pilot project and one research group (Jesper Haeggström, Chemistry II, MBB, KI) started their own SNAC medium project.
In 2015 the pilot project aims to:
1. Establish collaboration with Max IV that recently decided to fund part of PReSTO as a MaxIV satellite.
2. Install GlobalPhasing’s leading software packages BUSTER and SHARP at NSC Triolith
3. Develop HPC training sessions for active and upcoming pilot protein crystallography users.
4. Install yet more software and databases such as Crystallography and NMR System called CSN, and potentially the Cambridge Structural Database System (CSDS) for model building of more accurate ligand protein structure complexes.
5. Discuss dedicated Triolith nodes for interactive protein crystallography work where computing and manual model building is altered, i.e. we want to avoid having to alter between computers when doing data processing, phasing, refinement etc. calculations or manual model building, picture making for publications. This requires complete software stack for instance more PyMol plugins and visualization software and motivates a Triolith graphics card update to improve remote graphics experience.
