1. Load the electron density map (as em-map) and the reference structure (as struc).
2. Increase the sampling rate of the map:

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

3. Trim the map to 7 Å around the structure:

   map_trim em-map, struc, 7

4. 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:

   

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