surface because small holes and crevices are eliminated. The surface of object B is not distinguished from its interior however the object’s volume is extended and the surface is smoothed by setting the virtual atoms radii to (!3/2+1)g. The parameters s, r, Oa, Ob and w determine the shapes of the objects and their grid representations; the grid interval, the rotational grid step and n are scanning parameters. Importantly, the grid interval employed in FitEM2EMIN is not necessarily the same grid interval as in the EM map; this freedom is made feasible by the virtual atoms representation of the EM maps that allows projection of these spheres onto cubic grids of any size. The values of r and s were selected to be 215 and 1, respectively. These values were previously determined for the high-to-high (atomic) resolution docking program MolFit [23]. The self-matching calibration tests described in the Results section show them to be adequate for low-to-low resolution matching. 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