Complex sentence: For each bond between two atoms, a portion of each sphere was cut away to create a pait of matching flat faces, so that the distances between the sphere centers was proportional to the distance between the atom nuclei.
Split into simpler sentences: For each bond between two atoms, a portion of each sphere was cut away to create a pair of matching flat faces. The cuts were dimensioned so that the distances between the sphere centers was proportional to the distance between the atom nuclei.