coloring of amino acids

Hey, I have been trying to generate a file (containing an amino acid chain) that could be viewable by DS Visualizer, and additionally have single atoms colored in a way prescribed by the file.

Is that possible at all? Does anyone have a clue how to do it? I tried hacking a PDB file by changing the true data to false one (say, by altering amino acid names) but then DS Visualizer just crashed.

All I need is to get a few colors, say 2, and specify which amino acid should by colored by which color.

Thanks in advance!