Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6 to 10 A resolution. At such resolutions, the secondary structure elements such as helices and beta-strands appear to be skeletons and can be computationally detected. However, it is not known which segment of the protein sequence corresponds to which of the skeletons. The topology in this paper refers to the linear order and the directionality of the secondary structures. For a protein with N helices and M strands, there are (N!2N)(M!2M) different topologies, each of which maps N helix segments and M strand segments on the protein sequence to N helix and M strand skeletons. Since the backbone position is not available in the skeleton, each topology of the skeletons corresponds to additional freedom to position the atoms in the skeletons.