A new method for mapping macromolecular topography Abstract: A new method, using circular variance, is introduced for mapping macromolecular topography. Circular variance, generally used to measures angular spread, can be used to characterize of molecular structures based on a simple idea. It will be shown that the circular variance of vectors drawn from some origin to a set of points is well correlated with the degree to which that origin is inside/outside the chosen points. In addition, it has continuous derivatives that are also easy to compute. This concept will be shown to be useful for (i) distinguishing between atoms near the surface of a macromolecule and those in either the deep interior or remote exterior; (ii) identifying invaginations (even shallow ones) and (iii) detecting linker regions that interconnect two domains.