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Relion 3.1 offers the execution of external jobs inside the Relion user interface.

Therfore I made a wrapper script, which

  • setup's the proper directory structure for a crYOLO run and the correct Relion paths for later import of the particle coordinates
  • generates a DESY Maxwell crYOLO cluster submission script
  • submits this script to the cluster
  • when finished Relion detects that the job is done
  • prints the import pattern for Relion Import to the output log and to the job's note.txt

Currently only the latest generic models from crYOLO are supported and used.

Quickstart Guide

  1. Start any 3.1 version of Relion in a new terminal, because the generated crYOLO submission script uses its own environment without interference.
  2. Go to External at the bottom
  3. As external executable enter relion_ext_cryolo_gmodel.sh
  4. As input micrographs use a Motioncorr job result file like corrected_micrographs.star
  5. At the Running tab disable cluster submission. Otherwise Relion will use the Relion template instead of the generated crYOLO script.
  6. Press Run and watch the logfiles until its finished. The wrapper script sends the crYOLO run to P100 or V100 GPUs on the Maxwell cluster.

The script currently supports the additional crYOLO parameter threshold. If you need to change this you can add in the Params tab otherwise the default value of 0.3 is used:

When the script is done look at the relion log window for something like below and use this as input file pattern in the Relion Import tab.

#####################################
import in relion: External/job019/Movies/*.star
### end: Fri Apr 24 14:55:18 MEST 2020  ###

So use the import pattern like:

External/job019/Movies/*.star

Finally choose the used micrographs and imported particles for particle extraction.

Verify the picking-results in Relion

To verify the picking results you can use:

  • the cryolo_boxmanager.py in the External/job??? folder as described in the crYOLO manual
  • the Relion handpicking job with the script lines below

For Relion you first have to create a Manual picking job, choose your micrographs_ctf.star file, press the Run button, select one particle on a micrograph and save it. Now Relion has created the necessary folder structure. You can got into the directory, delete the file with the one selected particle and copy the imported crYOLO star files into it and rename them properly as in the following bash commandline examples:

cd ManualPick/job014/Movies
rm *_manualpick.star
cp ../../../Import/cryolo_picks/Movies/*.star .
for i in $(/usr/bin/ls -1 *.star); do mv $i ${i%.star}_manualpick.star; done

Now use the Continue button in the Relion GUI to restart your handpicking job and look at the results. You can select/unselect picked particles and save it in Relion.

For the particle extraction use then the coordinates from the handpicking job.


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