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:

EMAN2 Project Manager

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.


This opens up three tabs in the viewing window: GUI, Command, and Help. 'GUI' contains the options for, 'Command' is the command that will be executed when the user launches the program, and 'Help' is the help text associated with 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:

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.