PROTEAND generates interactive graphical representations that highlight uncertainty in atomic coordinates. It represents structural uncertainty in three ways: (1) The traditional way: The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids: At each atom position, the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes: Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual alpha helices.