Notes:
The main documentation for e2refinetorelion3d.py can be found here
- This tutorial is designed with 2 assumptions in mind:
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
- 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.
e2refinetorelion3d Tutorial
Getting Started
The first thing to do, assuming you've installed Relion and run an EMAN2 reconstruction is to open up the Project Manager:
e2projectmanager.py
Once you open up the project manager, select the plus (+) next to the 3D refinement tab and you will see several new options appear. The option we want to select is the "Relion 3D Refinement" option.
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This opens up three tabs in the viewing window: GUI, Command, and Help. 'GUI' contains the options for e2refinetorelion3d.py, 'Command' is the command that will be executed when the user launches the program, and 'Help' is the help text associated with e2refinetorelion3d.py. Along the right side, you will see 7 option buttons with various shapes. (More information about the project manager can be found here) The Three buttons that are directly impacted by this program are:
The Wiki Button. This button will open the wiki page for e2refinetorelion3d.py 
The Wizard Button. This button will open up a step-by-step wizard for new users. It will lead you through entering the program options one at a time with help information. 
The Expert Button. This button opens up more options in the GUI that are optional and for more expert users.
In the 'GUI' window, there are several sections of options. The first set options you will see are the I/O options.
I/O Options
set_name: This is the name of the particle set that will be used as input to Relion. By clicking 'Browse', you will open the EMAN2 browser and be able select the set by browsing to it.
refmap: This is the 3D map that will be used as a reference map by Relion. It should have the same dimensions as your particles. Typically you should use an EMAN2 completed reconstruction as input.
randomizemodel: This is an option that can be used to randomize the phases of the initial model to a particular resolution (In Angstroms) greyscale: Is the reference map on greyscale? symmgroup: What symmetry group does the particle belong to? Options are C,D, T, O, and I. symmnumber: What symmetry number does this particle have?
Once you have these options entered, you can move further down to the CTF options section.
CTF Options
There are three options in this section. The first, ctfcorrect, is a boolean checkbox. Check this box if you want Relion to perform CTF correction on the particles.