code: public static List<String> getPDBresnum(int structNum,
  			MultipleAlignment multAln, Atom[] ca){
  
  		List<String> lst = new ArrayList<String>();
  
  		for(Block block : multAln.getBlocks() ) {
  
  			for (int i=0; i<block.length(); i++){
  				Integer pos = block.getAlignRes().get(structNum).get(i);
  				if (pos==null) continue; //gap
  				else if (pos < ca.length) {
  					String pdbInfo = JmolTools.getPdbInfo(ca[pos]);
  					lst.add(pdbInfo);
  				}
  			}
  		}
  		return lst;
  	}
docs: Utility method used in the {@link MultipleAlignmentJmol} Frame,
  when the aligned residues of a structure in the alignment have
  to be selected for formatting them (coloring and style).
  
  @param structNum the structure index (row) of the alignment
  @param multAln the MultipleAlignment that contains the equivalent
  positions
  @param ca the atom array of the structure specified
  (corresponding to the structure index)
  @return List of pdb Strings corresponding to the aligned positions
  of the structure.