Short info that could be of interest for people new in cryo-E.
From the command line in a linux terminal you can look up the box size of the map you just created in Chimera by using EMAN2:
You can then change the box size (in pixels) the map by using Relion from the command line.
For example if you want to change the box size of your map to 300x300x300 pixels from whatever it was before, you just type:
relion_image_handler --i map_you_want_to_change.mrc --new_box 300 --o new_boxSize_map.mrc
This will write a new map (called new_boxSize_map.mrc) with a box size of 300x300x300 pixels.
You can also use relion_image_handler (among other things) for rescaling a map to a new pixel size (in Å).
Let say you want to change the pixel size of your map from before to 4 Å:
relion_image_handler --i map_you_want_to_change.mrc --rescale_angpix 4 --o new_pixelSize_map.mrc