code: @Override
  	public String getDefaultOrientation() {
  		StringBuilder s = new StringBuilder();
  		s.append(setCentroid());
  
  		// calculate  orientation
  		Quat4d q = new Quat4d();
  		q.set(polyhedron.getViewMatrix(0));
  		q.normalize();
  		Quat4d r = new Quat4d();
  		r.set(rotationAxisAligner.getRotationMatrix());
  		r.normalize();
  		q.mul(r);
  		q.normalize();
  
  		// set orientation
  		s.append("moveto 0 quaternion{");
  		s.append(jMolFloat(q.x));
  		s.append(",");
  		s.append(jMolFloat(q.y));
  		s.append(",");
  		s.append(jMolFloat(q.z));
  		s.append(",");
  		s.append(jMolFloat(q.w));
  		s.append("};");
  		return s.toString();
  	}
docs: /* (non-Javadoc)
  @see org.biojava.nbio.structure.quaternary.jmolScript.JMolSymmetryScriptInterface#getDefaultOrientation()