This program is normally run via the EMAN2 Project Manager.

e2refinetorelion3d is run after an EMAN2 refinement has been completed. When it is run, it will take the input particle set and convert it to many normalized .mrcs files, each of which represents a single micrograph with all particles from that micrograph in it, stacked along the z-axis. It creates the "all_images.star" file which contains all of the information about the particles on a per-particle basis (CS, Defocus, Microscope Voltage, etc). It will take the input EMAN2 3D map and convert it to a Relion-style formatted map called 3DRefMap.mrc. One final thing this program does is created a directory, run01, that contains an submission script for submitting an MPI Relion job (on our clusters specifically. It will likely need to be modified to specfically address the computing environment you have). Because of the nature of Relion and of Cryo-EM itself, it is unwise to attempt to do these reconstructions on a local machine. Distributed computing works very well in these situations though the submission script could be used to extract the Relion command that could be run on a local machine.

Helpful Links:

Tutorial is under construction

RELION Webpage

Program Options: I/O:

Expert Options: (used only if this information is not present in the previous EMAN2 reconstruction