Skip to content

RELION

REgularised LIkelihood OptimisatioN (RELION) employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryomicroscopy.

RELION is available as a module on Apocrita.

Usage

To run the default installed version of RELION, simply load the relion module:

module load relion

For usage documentation, pass the -h switch to any of the RELION commands, for example: relion_refine -h.

GUI support for RELION

RELION has been compiled with support for the GUI and the binary relion is available on Apocrita, however we suggest to use our OnDemand service for GUI jobs.

Example jobs

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load relion

relion_refine --angpix 1 \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

Parallel job

Here is an example job running on 96 cores across 2 ddy nodes using MPI:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 96
#$ -l infiniband=ddy-i
#$ -l h_rt=240:0:0

module load relion

mpirun -np ${NSLOTS} relion_refine_mpi \
  -x LD_LIBRARY_PATH \
  --angpix 1 \
  --i preprocessed.mrcs \
  --iter 2 \
  --o test

GPU serial job

Here is an example job running on 1 GPU:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 12
#$ -l h_rt=240:0:0
#$ -l h_vmem=7.5G
#$ -l gpu=1

module load relion
relion_refine --angpix 1 \
              --gpu \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

References