The beta-complex is a construct derived from the Voronoi diagram of spherical balls of arbitrary radii and has proven a powerful capability for proximity reasoning among spherical balls in three-dimensional space. Important applications related to molecular shapes in structural/computational molecular biology have been correctly, efficiently, and conveniently solved in the unified framework of the beta-complex and the Voronoi diagram. The beta-complex is a generalization of the ordinary alpha-complex. However, there are similarities and dissimilarities between the two complexes and it is necessary to correctly understand these similarities and dissimilarities to choose the right complex to solve application problems at hand. This paper presents the similarities and dissimilarities between these constructs and illustrates the consequence of the dissimilarity in application problems from both theoretical and practical points of view using examples of atomic arrangements.