alt-loc should be fine; the entire group is being replaced, so there is no
problem with names. Can't help with the 400 -- even if you could do that,
you would not want to using Jmol, I think. Better tools for that. But for
small numbers, we could add mutations as alt-loc. Actually, that's a lot
easier that creating a whole new group. Way before 400 you will run into
the problem that the allowed number of bonds that link residues will be
exceeded (20? something like that).
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