Most amino acids have some atoms in common. 
For example, all have the same backbone atoms
(atoms 1-4 = N CA C and O), and ones like 
phenylalanine and tyrosine share many sidechain 
atoms. 

Would it be possible for Mutate to compare the 
starting atoms & final atoms in a mutation and 
preserve any bands that are attached to conserved 
atoms? For example, say a band goes to atom 11
(a CZ carbon) of phenylalanine. If this phe is 
mutated to a tyrosine, let the band to atom 11
be preserved. Also, if a band goes to atom 5
(a CB carbon) of alanine, and this ala is mutated
to any other sidechain with a CB carbon at
atom 5 (all sidechains except glycine), let
the band to atom 5 be preserved.