Fig. 1

Full ortho/foamy virus capsid superposition. The superposed structures are shown in part (a) as a stereo pair, coloured as green = ortho virus (HIV, PDB code: 3nte-A) and magenta = foamy virus capsid. (The amino terminus is marked by a small sphere). Part (b) shows the cumulative RMSD plot for this superposition which plots the RMSD value (Y-axis) for increasingly larger sets of residues as ranked by their SAP similarity score (X-axis). The sharp rise in this trace marks the transition into subsets that include positions from the displaced domain