code: public static void main(String[] args){
  
  		PDBFileReader pdbr = new PDBFileReader();
  		pdbr.setPath("/tmp/");
  
  
  		//String pdb1 = "1crl";
  		//String pdb2 = "1ede";
  
  		String pdb1 = "1buz";
  		String pdb2 = "1ali";
  
  		//String pdb1 = "5pti";
  		//String pdb2 = "5pti";
  
  		// NO NEED TO DO CHANGE ANYTHING BELOW HERE...
  
  		StructurePairAligner sc = new StructurePairAligner();
  		StrucAligParameters params = new StrucAligParameters();
  		params.setMaxIter(1);
  		sc.setParams(params);
  
  		// step1 : read molecules
  		try {
  			Structure s1 = pdbr.getStructureById(pdb1);
  			Structure s2 = pdbr.getStructureById(pdb2);
  
  			System.out.println("aligning " + pdb1 + " vs. " + pdb2);
  			System.out.println(s1);
  			System.out.println();
  			System.out.println(s2);
  			// step 2 : do the calculations
  			sc.align(s1,s2);
  
  
  			ScaleableMatrixPanel smp = new ScaleableMatrixPanel();
  			JFrame frame = new JFrame();
  			frame.addWindowListener(new WindowAdapter(){
  				@Override
  				public void windowClosing(WindowEvent e){
  					JFrame f = (JFrame) e.getSource();
  					f.setVisible(false);
  					f.dispose();
  				}
  
  
  
  			});
  
  			smp.setMatrix(sc.getDistMat());
  			smp.setFragmentPairs(sc.getFragmentPairs());
  			smp.setAlternativeAligs(sc.getAlignments());
  
  			for (int i = 0; i < sc.getAlignments().length; i++) {
  				AlternativeAlignment aa =sc.getAlignments()[i];
  				System.out.println(aa);
  
  			}
  
  			frame.getContentPane().add(smp);
  
  			frame.pack();
  			frame.setVisible(true);
  
  		} catch (Exception e) {
  			e.printStackTrace();
  		}
  
  	}
docs: Number of minor ticks per unit scaled