On Sunday, 15 July 2012, Dale Tronrud wrote:
> There are good reasons for maintaining "order" in this human-induced
> numbering scheme. A common operation is to superimpose two molecules
> and calculate the rmsd of the positional differences. This calculation
> is not useful when the Val CG1 and CG2 are swapped in one molecule relative
> to the other. Suddenly you have, maybe a handful, of atoms that differ
> in position by about 3.5 A when most of us would consider this to be
> nonsense. We want the rmsd between equivalent atoms regardless of the
> "human-induced numbering scheme". There are two ways this can come about.
> 1) The overlay program could swap the labels on one to match the other or
> 2) The labels can be defined to be consistent from the start.
3) The closest-to-superimposed atoms could be paired regardless of
their labels
4) Chemically equivalent atoms could be given the same name, which
is then not unique but allows it to match any other atoms with
the same name
I'd normally choose (3) in practice, because it's the only method that
works reliably without universal agreement going forward and universal
remediation looking backward.
cheers,
Ethan
