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RELION

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Utilities for Working with RELION

Opening RELION Jobs

API: cylindra_builtins.relion.open_relion_job

GUI: Plugins > RELION > Open RELION job

After reconstruction of a tomogram in RELION, the next step is usually to pick particles from the tomogram. You may also want to check the distribution of the refined particles in the tomogram. This method provides a convenient way to open a RELION job folder and load the tomograms (and particles) directly into the cylindra batch analyzer.

In this method, you have to specify the path to the RELION job.star file, which contains the description of the job. Currently, following RELION jobs are supported:

  • Reconstruct tomograms
  • Denoise tomograms (predict)
  • Pick tomograms
  • Extract subotomos
  • 3D initial reference
  • 3D auto-refine

Save Pick Results for Import to RELION

API: cylindra_builtins.relion.save_coordinates_for_import

GUI: Plugins > RELION > Save coordinates for import

This method saves the current state of the cylindra batch analyzer, which contains individual tomograms and multiple molecules, as an particle star file. This file can directly be used for the subtomogram extraction job in RELION. To do this, you need to set "OR: use direct entries?" to "Yes".

Low-level File I/O

Import Molecules from RELION

API: cylindra_builtins.relion.load_molecules

GUI: Plugins > RELION > Load molecules

This function read a .star file and add the contents to the viewer as molecules.

Export Molecules for RELION

API: cylindra_builtins.relion.save_molecules

GUI: Plugins > RELION > Save molecules

This function saves the selected molecules as a .star file.

Import Splines from RELION

API: cylindra_builtins.relion.load_splines

GUI: Plugins > RELION > Load splines

The positional coordinates are used for drawing splines. The "rlnHelicalTubeID" column is used to group the coordinates into each splines.

Export Splines for RELION

API: cylindra_builtins.relion.save_splines

GUI: Plugins > RELION > Save splines

Spline objects can be converted into segmented lines. This function saves the splines as segmented lines in a .star file. Following the convention, "rlnHelicalTubeID" are used as the column name for identifying each splines.

Warning

Reading a .star file and saving back to a new .star file does not preserve the original data.