Invisibility of particular helices or sheets would be useful in bigger proteins. Maybe also invisibility of loop regions and so on i.e. choice between seeing only loops or only sheet or only helices etc. Obviously 3D view would be nice so one can visualize the folding better. What about water/solvent molecules and choice of cofactors in folding? Ability to measure distances between certain residues and expression as percentage of ideal, in general, choice for more quantative evaluation of differences.