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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