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Homepage: https://github.com/OPIC-Oxford/localrec

Localized Reconstruction Notes

Here are some CSSB specific notes on how to run localrec with Relion 3.x. The Scipion 2.0 GUI version has not been tested, but localrec 1.2.1 needs Relion 1.4 but Scipion 2 comes with Relion 3.

Note: Since September 2019 the Scipion Relion plugin can also install older Relion versions, but this has not been tested for localrec yet.

Normally the task is done in 4 steps which can be combined:

  1. Prepare particles
  2. Create subparticles
  3. Extract subparticles
  4. Reconstruct subparticles

In the latest localrec version step 4 cannot be done, since the Relion 3.x star file contains entries not recognized by Relion 1.4 (e.g rlnCtfMaxResolution).

CSSB-specific Quick Start Guide

Create a marker file

Use UCSF Chimera to create your marker file. In the example below it is called marker.cmm.

Create your cluster submission script

Use this template for the DESY maxwell cluster, adapt the command line parameters to your settings and save it as e.g. localrec.sh:

localrec.sh
#!/bin/zsh
#SBATCH --partition cssb
#SBATCH --time 7-00:00
#SBATCH --constraint Gold-6126
#SBATCH --nodes 1
#SBATCH --error localrec.err
#SBATCH --output localrec.out
#SBATCH --job-name localrec
export LD_PRELOAD=""

# run the job
echo "### start : `date`  ###"
echo "### master: `hostname`  ###"
source /etc/profile.d/modules.sh
source /beegfs/cssb/software/anaconda3/etc/profile.d/conda.sh
module use /beegfs/cssb/software/modulefiles/em
module load scipion/2.0
module load cssb/archive
module load relion/1.4

conda activate localrec-1.2

relion_localized_reconstruction.py --prepare_particles \
  --create_subparticles --angpix 1.09 --sym D2 --particle_size 400 --cmm marker.cmm --unique 1 \
  --extract_subparticles --subparticle_size 300 --np 24 \
  --output SubParticles Class3D/job970/run_it025_data.star

# cleanup the relion 1.4 empty folder left behind
rmdir Particles

echo "### end: `date`  ###"

Submit your cluster script

sbatch localrec.sh

Import the extracted information in Relion3

The output directory (from the example above) is called SubParticles.

The Relion import patterns are therefore:

  • SubParticles/*_subparticles.star for the coordinates
  • SubParticles/*_subparticles.mrcs  for the particles

Now do the reconstruction in Relion 3.


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