code: @Override
  	public String colorBySequenceCluster() {
  		QuatSymmetrySubunits subunits = rotationAxisAligner.getSubunits();
  		int n = subunits.getSubunitCount();
  		List<Integer> modelNumbers = subunits.getModelNumbers();
  		List<String> chainIds = subunits.getChainIds();
  		List<Integer> seqClusterIds = subunits.getClusterIds();
  		int clusters = Collections.max(seqClusterIds) + 1;
  		Color[] col = ColorBrewer.BrBG.getColorPalette(clusters);
  		Color4f[] colors = ColorConverter.convertColor4f(col);
  		Map<Color4f, List<String>> colorMap = new HashMap<Color4f, List<String>>();
  
  		for (int i = 0; i < n; i++) {
  			Color4f c = colors[seqClusterIds.get(i)];
  			List<String> ids = colorMap.get(c);
  			if (ids == null) {
  				ids = new ArrayList<String>();
  				colorMap.put(c,  ids);
  			}
  			String id = getChainSpecification(modelNumbers, chainIds, i);
  			ids.add(id);
  
  		}
  
  		return defaultColoring + getJmolColorScript(colorMap) + getJmolLigandScript();
  	}
docs: /* (non-Javadoc)
  @see org.biojava.nbio.structure.quaternary.jmolScript.JMolSymmetryScriptInterface#colorBySequenceCluster()