Using the Main Script

Note that the preferred way is to run the method from Scipion GUI. These instructions refer to using the script from command line.

The main input to the script is a STAR file from Relion 3D classification or 3D refinement. Normally the script is run in four steps:

1. Prepare particles. (Optionally part of the signal is subtracted from the particle images.)
2. Create subparticles. (Subparticle coordinates and orientations are calculated.)
3. Extract subparticles. (Subparticles are extracted from particle images.)
4. Reconstruct subparticles. (A reconstruction of the subparticle is calculated.)

After these steps have been executed, the subparticle STAR file and 3D reconstruction can be used as inputs for 3D classification or 3D refinement of subparticles in Relion.

A simple example

Example to run steps 1-3 simultaneously:

scipion run relion_localized_reconstruction.py --prepare_particles --create_subparticles --extract_subparticles --sym C6 --vector 1,0,0 --length 50 --angpix 1.0 --particle_size 128 --subparticle_size 40 --output example particles.star

Continuation to run step 4:

scipion run relion_localized_reconstruction.py --reconstruct_subparticles --subsym C1 --maxres 15 --output example