Do better job selecting stack in pdb reader

mrdna/readers/segmentmodel_from_pdb.py

@@ -195,9 +195,13 @@ def find_stacks( u, centers, transforms, selection_text='all' ):
 
     ## Convert distances to stacks
     stacks_above = -np.ones(len(sel), dtype=np.int)
+    _z = np.array((0,0,1))
     for i in np.unique(idx1):
         js = idx2[ idx1 == i ]
-        j = np.argmin(dists[i])
+        angles = [np.arccos( transforms[j].T.dot( transforms[i].dot(_z) ).dot( _z ) ) for j in js]
+        angles = np.array( angles )
+        tmp = np.argmin(dists[i][js] + 1.0*angles)
+        j = js[tmp]
         stacks_above[i] = j
 
     return stacks_above