diff --git a/arbdmodel.py b/arbdmodel.py
index a270c5b78a879500c0f7ee06e87ce70802079976..81ce94e61a1c1087f12320d608c1f2bbff4aa540 100644
--- a/arbdmodel.py
+++ b/arbdmodel.py
@@ -464,7 +464,7 @@ class PdbModel(Transformable, Parent):
 
                 ## TODOTODO test
                 if np.log10(idx) >= 5:
-                    idx = "******"
+                    idx = " *****"
                 else:
                     idx = "{:>6d}".format(idx)
 
diff --git a/segmentmodel.py b/segmentmodel.py
index 3a6a458c8a43da885f6c1a4b17ba64d9bb98fc8e..88f152cc660f1bd95332ed310eacf04d71f2ebb2 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -418,15 +418,15 @@ class Segment(ConnectableElement, Group):
             axis = axis / np.linalg.norm(axis)
             rotAxis = np.cross(axis,np.array((0,0,1)))
             rotAxisL = np.linalg.norm(rotAxis)
+            zAxis = np.array((0,0,1))
 
             if rotAxisL > 0.001:
-                theta = np.arcsin(rotAxisL)
-                orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta*180/np.pi, normalizeAxis=False )
+                theta = np.arcsin(rotAxisL) * 180/np.pi
+                if axis.dot(zAxis) < 0: theta = 180-theta
+                orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta, normalizeAxis=False ).T
             else:
-                if axis.dot(np.array((0,0,1))) > 0:
-                    orientation0 = np.eye(3)
-                else:
-                    orientation0 = rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
+                orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
+                               rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
             orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
             orientation = orientation.dot(orientation0)
         else:
@@ -2318,10 +2318,10 @@ class SegmentModel(ArbdModel):
                     elif dot1 < -0.5 and dot2 < -0.5:
                         ## TODO, reverse
                         ...
-                        print("Warning: {} and {} are on antiparallel helices (not yet implemented)... skipping".format(A,B))
+                        print("Warning: {} and {} are on antiparallel helices (not yet implemented)... skipping".format(A1,B1))
                         continue
                     else:
-                        print("Warning: {} and {} are on helices that do not point in similar direction... skipping".format(A,B))
+                        print("Warning: {} and {} are on helices that do not point in similar direction... skipping".format(A1,B1))
                         continue
 
                     ## Go through each nucleotide between the two