diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 650e5a53ac7a1669fada692f35485aa03f9c781a..24633aeafe48faa60a4e49a25f9e4411dca0f552 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -696,7 +696,7 @@ class Segment(ConnectableElement, Group):
                 if l.is_3prime_side_of_connection: continue
 
             ## Stop if we found the 3prime end
-            if l.on_fwd_strand == is_fwd and l.type_ == "3prime":
+            if l.on_fwd_strand == is_fwd and l.type_ == "3prime" and l.connection is None:
                 # print("  found end at",l)
                 return pos, None, None, None, None
 
@@ -2429,18 +2429,23 @@ class SegmentModel(ArbdModel):
                     break
                 except:
                     print("Unexpected error:", sys.exc_info()[0])
+                    # import pdb
+                    # pdb.set_trace()
+                    # seg.get_strand_segment(pos, is_fwd, move_at_least)
+                    # strand.add_dna(seg, pos, end_pos, is_fwd)
                     raise
 
                 if next_seg is None:
                     break
                 else:
                     seg,pos,is_fwd = (next_seg, next_pos, next_dir)
+            strand.history = list(history)
             return history
 
         strand_counter = 0
         history = []
         for seg in self.segments:
-            locs = seg.get_5prime_locations()
+            locs = filter(lambda l: l.connection is None, seg.get_5prime_locations())
             if locs is None: continue
             # for pos, is_fwd in locs:
             for l in locs: