Notes:


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

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.

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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:

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 boolean options in this section. Check the ctfcorrect box if you want Relion to perform CTF correction on the particles. The second box, dataphaseflipped, should be checked if your data has been phase flipped already. The final option, ignoretofirstpeak, should be checked if you want CTF-amplitude correction to be performed from the first peak onward.

Optimisation Options

Two important (and required) options are in this section as well as another optional input. lowpass is the value to which Relion will lowpass filter the reference map. If set to 0, Relion will perform no lowpass filtering on the reference map. imagemaskd is the diameter of a soft circular mask that Relion will apply to your particles. If you specify a diameter too large, you will include a lot of noise from outside the particle. If you use a value too small, you run the risk of masking out part of the particle. The final option in this section is the solventmask. If you wish to provide a Spider/mrc map containing a (soft) mask with the same dimensions as the reference(s), and values between 0 and 1, with 1 being 100% protein and 0 being 100% solvent, the reconstructed reference map will be multiplied by this mask.

Sampling Options