Using Relion for data processing - cianfrocco-lab/Old-school-processing GitHub Wiki

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Relion is a power program that can provide users with particle picking, CTF estimation, and analysis tools.

In order to use Relion, you must make sure that you set up your directories in a way that Relion expects. Namely, that your current working directory has the following directories:

$ ls
Class2D       Micrographs       Refine3D
Class3D       Particles

Therefore, as the first step in processing, make sure to copy all of your micrograph files into the Micrographs folder.

1. Copy all of your micrograph files into the Micrographs folder.
2. Picking particles for Relion

• All methods outlined in the particle picking section are compatible with Relion. The output .box file needs to be named the same name as the micrograph with the exception that it has a .box extension.

1. Estimating the CTF
2. Extracting particles
3. 2D classification:

• To remove junk
• For 2D class averages

1. 3D classification
2. 3D refinement
3. Post-processing