Supported Applications

RELION

Description

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
Usage Notes

SBGrid Usage Info

RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu

CUDA builds of RELION are designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.

RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries.

RELION and MPI versions

RELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. RELION versions in SBGrid include OpenMPI in each version. When called from the SBGrid environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the mpirun.relion executable can be used to ensure the correct version.

RELION versions > 3 use OpenMPI 3.1.6 and include support for SGE and SLURM schedulers. Older releases use OpenMPI 2.1.2.

Notes on RELION versions

Most recent builds
commit e3537c8 - 4.0-beta2_cu11.5
commit a26bd452 - 4.0-beta2_cu11

4.0 Beta2 releases
4.0-beta2_cu11.4.1
4.0-beta2_cu10.2
4.0-beta2_cu9.2

AMD-optimized FFT for beta2
4.0-beta2_cu10.2_amd

Initial version 4.0 beta release
4.0-beta_cu9.2
4.0-beta_cu10.2_amd
4.0-beta_cu10.2

Official Release versions
3.1.3_cu8.0
3.1.3_cu11.4.1
3.1.3_cu10.2

Previous releases
3.1.2_cu9.2_noSAGD
3.1.2_cu9.2
3.1.2_cu8.0
3.1.2_cu11.1
3.1.2
3.1.1_cu9.2
3.1.1
3.1.0_cu8.0_compat
3.1.0
3.0.8_cu9.2
3.0.8_cu8.0
3.0.8
3.0.4_cu9.0
2.1_cu8.0
1.4-randomphase3d
1.4b
1.4

Legacy version/hardware support
Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.
Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library.

Recent Changes

20211020 : Added 4.0 beta2 builds 20220215 : Added 4.0beta2_cu11.5 build
20210305 : Add 3.1.2 RELION release versions
20201111 : Add 3.1.1 RELION release versions
20200703 : Add 3.1.0 RELION release version
20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules.
20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001

Known Issues

20200610 : Empty values in GUI during autopicking can be interpreted as Text instead of Float values.

Deprecated versions

The following verions are deprecated and will be removed in a future SBGrid update, approximately one month from the date listed.

4.0-beta2_cu11.4.1 4.0-beta2_cu10.2

4.0-beta_cu10.2_amd 4.0-beta_cu10.2

3.1.2_cu9.2_noSAGD 3.1.2_cu8.0 3.1.2_cu11.1 3.1.2

(c) Copyright 2022, Structural Biology Grid (www.sbgrid.org)

Last Update to this document

20220215
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install relion
Primary Citation*

S. H. W. Scheres. 2012. A Bayesian View on Cryo-EM Structure Determination. J Mol Biol. 415(2): 406-418.

S. H. W. Scheres. 2012. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 180(3): 519-530.
- *Full citation information available through
Citation Note

If RELION is useful in your work, please use at least one of the primary citations listed. Additional citations can be found here: https://www2.mrc-lmb.cam.ac.uk/groups/scheres/publications.html
Webinars

Topic: New developments in RELION-4.0
Presenter: Prof. Sjors Scheres, MRC Laboratory of Molecular Biology

Host: Jason Key
Recorded on December 7, 2021

Topic: RELION - Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination
Presenter: Dari Kimanius, Ph.D., MRC Laboratory of Molecular Biology

Host: Shaun Rawson
Recorded on June 2, 2020

Topic : RELION-3: new tools for automated high-resolution cryo-EM structure determination
Presenter: Sjors Scheres, Group Leader, MRC Laboratory of Molecular Biology, UK

Host: Jason Key / Shaun Rawson
Recorded: November 6, 2018

Topic: RELION
Presenter: Sjors Scheres, Group Leader
Medical Research Council, The Laboratory of Molecular Biology

Host: Jason Key
Recorded on March 24, 2015