Journal: Elife / Year: 2016 Title: Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Authors: Dari Kimanius / Björn O Forsberg / Sjors Hw Scheres / Erik Lindahl / Abstract: By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large ...By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.
History
Deposition
Sep 21, 2016
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Header (metadata) release
Oct 5, 2016
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Map release
Oct 5, 2016
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Update
Jul 29, 2020
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Current status
Jul 29, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Number classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) Details: Standard RELION post-processing, i.e. convolution effects of the solvent mask are corrected for using phase-randomisation. Number images used: 108209
Initial angle assignment
Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) / Details: Standard RELION 3D auto-refine
Final angle assignment
Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) / Details: Standard RELION 3D auto-refine
Final 3D classification
Number classes: 8 / Software - Name: RELION (ver. 2.0) Details: Selected 7 out of 8 3D classes. Also 2D classification was performed to select suitable particles.
FSC plot (resolution estimation)
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