I think that your problem is not of "same chain ID", but "same residue ID". What you see in that pdb file is either an "insertion code" or an "alternative residue" (I'm not sure of that now). Both are described in the PDB doc and are taken care by Jmol using special atom expression syntaxes. I don't recall them, but they are documented. Check "RasMol biomolecular residue specifications" in http://chemapps.stolaf.edu/jmol/docs/#atomexpressions either ^insertionCode or %altLoc
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