The “vop boxes” command is intended to do this but ends of giving box dimensions that differ by 1 grid point (like 149 by 149 by 150).  A few other people have asked about this recently.  So I’ve fixed vop boxes in tonight’s Chimera daily build so you can say

vop boxes #0 #1 isize 150

where #0 is the density map and #1 are the markers and “isize 150” means extract a map for each marker that is 150 by 150 by 150 grid points.  This “isize” option is new.  The previous option “size” still exists but is specified in Angstroms.  If you use that option it will also give cubes, but depending on where the marker is centered between grid points, the cube sizes could differ by 1 grid point for different markers.  So I added the isize option so you could get exactly the same number of grid points for each marker.  This isn’t exactly true — you don’t always get cubes — if the marker is too close to the edge of the density map so the box would go outside the map, then the extracted region is not a cube.  Would be nice if it could fill it with zeros and make it a cube but it doesn’t do this now.

Tom