code: private static double getRise(Matrix4d transformation, Point3d p1,
  			Point3d p2) {
  		AxisAngle4d axis = getAxisAngle(transformation);
  		Vector3d h = new Vector3d(axis.x, axis.y, axis.z);
  		Vector3d p = new Vector3d();
  		p.sub(p1, p2);
  		return p.dot(h);
  	}
docs: Returns the rise of a helix given the subunit centers of two adjacent
  subunits and the helix transformation
  
  @param transformation
  helix transformation
  @param p1
  center of one subunit
  @param p2
  center of an adjacent subunit
  @return