Load the electron density map (as em-map) and the reference structure (as struc).

Increase the sampling rate of the map:

as cartoon, struc
as dots, em-map
map_double em-map, -1

Trim the map to 7 Å around the structure:

map_trim em-map, struc, 7

Create dot map (dot-map), mesh map (mesh-map), or surface map (surface-map) from the em-map, contoured at 2.0 sigma, surrounding struc, within a radius of 3 Å.

isodot dot-map, em-map, 2.0, struc, carve=3.0
isomesh mesh-map, em-map, 2.0, struc, carve=3.0
isosurface surface-map, em-map, 2.0, struc, carve=3.0

Result: