code: public void updateDistanceMatrix() {
  
  		// Reset the distance Matrix variable
  		distanceMatrix = new ArrayList<Matrix>();
  
  		for (int s = 0; s < size(); s++) {
  			Atom[] ca = atomArrays.get(s);
  			Matrix distMat = AlignUtils.getDistanceMatrix(ca, ca);
  			distanceMatrix.add(distMat);
  		}
  	}
docs: Force recalculation of the distance matrices.