code: public static String getJmolString(MultipleAlignment multAln,
  			List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
  			boolean colorByBlocks) {
  
  		// Color by blocks if specified
  		if (colorByBlocks)
  			return getMultiBlockJmolString(multAln, transformedAtoms,
  					colorPalette, colorByBlocks);
  		Color[] colors = colorPalette.getColorPalette(multAln.size());
  
  		StringBuffer j = new StringBuffer();
  		j.append(DEFAULT_SCRIPT);
  
  		// Color the equivalent residues of every structure
  		StringBuffer sel = new StringBuffer();
  		sel.append("select *; color lightgrey; backbone 0.1; ");
  		List<List<String>> allPDB = new ArrayList<List<String>>();
  
  		// Get the aligned residues of every structure
  		for (int i = 0; i < multAln.size(); i++) {
  
  			List<String> pdb = MultipleAlignmentJmolDisplay.getPDBresnum(i,
  					multAln, transformedAtoms.get(i));
  
  			allPDB.add(pdb);
  			sel.append("select ");
  			int pos = 0;
  			for (String res : pdb) {
  				if (pos > 0)
  					sel.append(",");
  				pos++;
  
  				sel.append(res);
  				sel.append("/" + (i + 1));
  			}
  			if (pos == 0)
  				sel.append("none");
  			sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
  					+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
  		}
  
  		j.append(sel);
  		j.append("model 0;  ");
  		j.append(LIGAND_DISPLAY_SCRIPT);
  
  		return j.toString();
  	}
docs: Generate a Jmol command String that colors the aligned residues of every
  structure.