I saw several excellent remarks about Ramachandran plots come by, but the main points still seem missing, I think.
Phi and psi are not fixed parameters with limited freedom like angles, bond lengths or planarities. By keeping a certain bond lengths restrained at, for example, 1.543+/-0.021 Angstrom, you know what you are doing, and you know that exceptions are very, very rare (assuming that the weight on this restraint is set appropriately). Phi and psi, though, can have very many values. And especially near beta-bulges or near the ends of helices (or in active sites) one can easily do great damage to the realism of the coordinates if phi-psi restraints would be used in accordance with the local secondary structure. The variability of a bond length or bond angle is determined by simple physical, mainly local parameters such as through-bond and through-space forces acting on the direct neighbour atoms, and this happens in a way that we understand and that we can model in a coherent fashion. Phi and psi angles, similarly, are greatly influenced by interaction of the four atoms that determine each torsion angle with atoms in their direct local environment. Robbie explained this nicely in his message. These forces, though, are already restrained by the bond length, bond angle, and clash avoidance restraints. If you now put in additional restraints for phi and psi, you start counting certain interactions double in the restraints. Unless you spend a lot of time on re-calibrating all restraints, you are likely to generate areas where the sum of all restraints is too high and areas where not enough restraints are left. Again, I am not a crystallographer, but I am sure that that must make R-free go up. If using phi-psi restraints would make structures geometrically better while at the same time make R and R-free go down, than we should surely stimulate phi-psi restraints, but till this is proven, we shouldn't use them. If one day the community concludes that phi-psi constraints are a good thing, then please don't worry about the validation aspects. I am sure we will come-up with novel validation methods. Gert Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
