The main documentation for e2refinetorelion3d.py can be found here
This tutorial is designed with 2 assumptions in mind:
1.That the user has installed Relion on their local machine. Though we do not run the relion_refine program on a local machine, several scripts from the Relion installation package are used to prepare the EMAN2 data for a Relion run. Relion can be downloaded here 2.That the user has fully completed an EMAN2 refinement. This program draws from many files in the EMAN2 directory structure and was designed to rely on these files existing.
The first thing to do, assuming you've installed Relion and run an EMAN2 reconstruction is to open up the project manager: