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RELION

Description

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

How to Use

There are multiple versions of RELION available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail RELION

To select a module, type

module load RELION/[ver]

where [ver] is the version of choice.

RELION can be used in both command-line mode and in GUI mode. For the GUI, you will need an X-Windows connection.

GUI

To use the GUI, on the Biowulf login node, type

module load RELION

Change directory to where your input files are and type:

relion &

This will create a window with lots of options. Set the options as appropriate. In order to launch jobs onto the cluster, you will need to set options in the 'Running' tab to specific values:

Running Tab

Most importantly, the number of MPI procs must equal the number of processors made available by the qsub command. For example, if the qsub command is qsub -l nodes=2:c16, then the number of procs is 32.

If doing a step other than Preprocessing, then set 'Number of MPI procs' to the number of nodes allocated, and 'Number of threads' to the number of processors available on each of the nodes. For example,

Running Tab 2

The 'Queue name' is irrelevant, since the qsub template will not use queues. If a specific queue is needed, then the 'Queue submit command' should be modified to include the queue. For example, qsub -l nodes=4 -q ccr will submit the RELION job to the ccr queue.

Qsub Script

Create a qsub script with the specific commands required:

#!/bin/bash
# This file is runRELION.sh

#PBS -N RELION
#PBS -e RELION.err
#PBS -o RELION.out

module load RELION
cd $PBS_O_WORKDIR
mpiexec --bynode -n 4 relion_refine_mpi --o Class2D/run1 \
  --i ./particles.star --particle_diameter 360 \
  --angpix 7.08 --iter 25 --tau2_fudge 2 --flatten_solvent \
  --zero_mask --ctf --K 50 --oversampling 1 --psi_step 10 \
  --offset_range 5 --offset_step 2 --norm --scale   --j 16
echo "Done!"

In this case, we are running a 2D refinement run on 4 c16 nodes:

qsub -l nodes=4:c16 runRELION.sh

Documentation