Abstract: Coordinate uncertainties in crystal structures of biological macromolecules can vary from 0.01 Angstroem for a well determined atom in a high-resolution structure to 1 Angstroem for a mobile atom in a structure determined at low resolution. Given this wide range, it is essential to take into account the coordinate uncertainties in the comparison of structural models in order to discriminate significant differences from noise. Furthermore, given the rapid growth of available structure data, new methods for the analysis of large numbers of structural models need to be implemented.