I wrote:
Isn't it the case that vdw interactions are turned off between atoms in a residue, and perhaps with the residues before and after?
No it is not the case, at least in refmac5 and SHELLXL. Thanks to those who clarified this. Jim Naismith's earlier post, which I had not seen, suggests a better explanation (perhaps obvious to others) for why positional refinement does not drive residues toward the nearest Rama optimum: the vdw repulsions determining the Ramachandran plot involve hydrogens, and none of my models have explicit hydrogens. Ed
Otherwise positional refinement would in fact tend to drive the residues into the rama-allowed region? Might it be a good idea to use torsion restraints, or intra-residue vdw repulsion, in the last stage of refinement after calculating an unbiased ramachandran plot; especially in low-resolution problems where we need all the restraints we can get? Ed
