EMAN conventions can be found here: https://github.com/azazellochg/3DEM-conventions/blob/master/eman2.md
My list of frequently used commands / options in EMAN2.
Calculate average and standard deviation images for a stack of images (stack.hdf). I usually use it on a random set of 50-100 (non-)gain-corrected movies to check if gain reference was done properly.
The script will change box coordinates: apply coarse factor to downscale/upscale coordinates, change box size if requested, remove boxes too close to the mictrograph edge. New box files are in new_boxes folder.
This script simply removes boxes that are too close to the micrograph edge.
A simple script to do camera normalization correction (see Afanasyev et al., Scientific Reports 5, 2015), given a known avg and std images for the uncorrected movie stack
Simple script for coordinate conversion from XMIPP3 to EMAN (.pos to .box)