PEET is a set of programs, separate from but typically used in conjunction with IMOD, to align and average particles / subvolumes extracted from 3D volumes.

References:

• PEET was developed at the University of Colorado, Boulder. PEET was first applied for averaging axonemes and its methods were described in Nicastro et al 2006. Many new features have since been added, including clustering / classification as described in Heumann et al 2011. Please cite these papers if you use PEET in your research. /li>

• PEET Manual

• Module Name: PEET (see the modules page for more information)
• Used in conjunction with IMOD
• Environment variables set
  • PARTICLE_DIR

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load PEET

[user@cn3144 ~]$   averageAll
Starting averageAll_mce ...
This is PEET Version 1.12.0 5-March-2018.
Copyright 2000-2018 The Regents of the University of Colorado.
MATLAB. Copyright 1984-2018 The Mathworks, Inc.
[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. PEET.sh). For example:

#!/bin/bash
set -e
module load PEET
PEET < PEET.in > PEET.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PEET.sh

Create a swarmfile (e.g. PEET.swarm). For example:

PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out
PEET < PEET.in > PEET.out

Submit this job using the swarm command.

swarm -f PEET.swarm [-g #] [-t #] --module PEET