Relion

Relion (for REgularised LIkelihood OptimisatioN, pronounced "rely-on") is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

For more information on version 4.0 and version 5.0

Running Relion

Module	Version
relion	4.0 5.0

To see the available versions when you are logged into eXplor, run the command:

module spider relion

To use Relion, type:

module load relion/<version>

specifying one of the available versions.

Example of Relion GPU Job Script

#!/bin/bash

#SBATCH --account=<group>
#SBATCH --partition=gpu

## GPU Request
#SBATCH --gres=gpu:2

## Resource Request
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=0-10:00:00

# Set the file for output (stdout)
#SBATCH --output=Class3D-%j.out

# Set the file for error log (stderr)
#SBATCH --error=Class3D-%j.err

# Load the modules
module purge
module load relion/4.0

env | grep -i slurm 

echo ""
echo "  JOB started: $(date) "
echo ""

cd $SLURM_SUBMIT_DIR

# Creating temporary directory 
# do not run your JOB in the HOME or $SLURM_SUBMIT_DIR 
WORKDIR="$SCRATCHDIR/job.$SLURM_JOB_ID.$USER"
mkdir -p $WORKDIR

echo ""
echo "  WORKDIR: $WORKDIR"
echo ""

cp $SLURM_SUBMIT_DIR/* $WORKDIR

cd $WORKDIR

#Paste Command here
srun relion_refine_mpi --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --gpu --j 6 --dont_combine_weights_via_disc

cp $WORKDIR/* $SLURM_SUBMIT_DIR

cd $SLURM_SUBMIT_DIR

# removing the $WORKDIR 
rm $WORKDIR/*
rmdir $WORKDIR

echo ""
echo "  JOB finished: $(date) "
echo ""