Helical skeletons and topologies. (A) The density map (grey) was simulated to 10 Å resolution using protein 1B5L from the Protein Data Bank (PDB). The helical skeletons (red S1 to S5) were detected using Helix Tracer . (B) The helix segments are highlighted (black) on the proteins sequence. Two alternative topologies are shown as diagrams in (C) correct and (D) wrong topology, in which the N to C direction for the loop (arrow) and for the skeleton (cross and dot) is labelled. The true assignment is labelled on the skeleton with H1 being the first helix segment on the protein sequence.