Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

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Bob, when we load 2 structures and do

compare {2.1} {1.1} subset alpha rotate translate;

is there a residue to residue mapping as a result?


Eric, I've been trying distance coloring by matching consecutive residues in 
both chains (i.e. first residue in one chain  vs. 1st in the other, and so on; it 
does not matter sequence or resNo) It works somehow but fails when one of 
the chains has a gap or a portion that does not match the other, then the 
match becomes shifted and CA to CA distance is always too high. It may 
work in pairs of proteins that are more similar; not well with the examples you 
mentioned.