sphere_grid_bounds (
        grid_data,
        center,
        radius,
        )

zero_volume_inside_atom ( atom )

zero_array_boundary ( array,  step=None )

zero_data_in_sphere (
        grid_data,
        center,
        radius,
        )

zero_volume_outside_box (
        data,
        ijk_min,
        ijk_max,
        )

set_box_value (
        data,
        value,
        ijk_min,
        ijk_max,
        outside=None,
        )

zero_volume_inside_selected_atom ()

volume_sphere ( atom,  dr )

zero_data_outside_sphere (
        grid_data,
        center,
        radius,
        )

zero_volume_outside_atom ( atom )

set_value_outside_box (
        data,
        value,
        ijk_min,
        ijk_max,
        )

writable_volume ()

zero_volume_inside_selection_box ()

zero_volume_boundary ( step=None )

The step parameter allows zeroing more than one plane at some of the 6 faces of the volume so that subsampling using every planes will still have zeros on the boundary.

zero_volume_inside_box (
        data,
        ijk_min,
        ijk_max,
        )

ChimeraExtension.py

gui.py