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Built-in External Jobs

General-Purpose Jobs

Symmetry Expansion

This job uses relion_particle_symmetry_expand to create a new particle star file with expanded particles.

Helical Symmetry Expansion

This job uses relion_particle_symmetry_expand to create a new particle star file with helical symmetry expanded particles.

Shift Map

This job uses the relion_star_handler and a custom-built function to create a shifted particles, map and mask. If you make a 3D reconstruction using the shifted particles, the resulting map will be similar to the shifted map.

Common usage of this job will be:

  • Re-center particles to the region of interest after 3D classification.
  • Re-center particles to the subunits after symmetry expansion.

Tomography-specific Jobs

Find Beads 3D

This job uses the findbeads3d program from IMOD to locate fiducial gold beads in tomograms. The output files are IMOD .mod files. You can check the results in the job widget.

Erase Gold

This job uses the output of the "Find Beads 3D" job to erase the gold beads in the un-aligned tilt series. Therefore, subsequent denoising and particle reconstruction using output tilt series from this job will not be affected by the strong contrast of the gold beads.

Inspect Particles

This job simply creates a "optimisation_set.star" file from the inputs. The main purpose of this job will be to inspect the filtered particle file after any of the "Select" jobs.