Methods and compositions for determining the three dimensional structure of a particle are provided. In the subject methods, a plurality of images of the identically heavy atom labeled particles of interest is obtained. Each of the images in the plurality is obtained by rigidly attaching at least four heavy atom clusters to the particle of interest and imaging the particle in an electron microscope. The three-dimensional structure of the particle is then derived from the plurality of images of the labeled particle. This derivation step preferably includes an alignment step in which the orientation of the images is determined using the heavy atom cluster projections. In preferred embodiments, the heavy atom clusters serve to reveal particle homogeneity, particle location, particle orientation, image artifacts, and image parameters required for computational image restoration. The subject methods are particularly suited for use in determining the three dimensional structure of biological particles, e.g. proteins.