Decreased length of T-junction bond from crossover distance of 18.5 to more reasonable 12.5

mrdna/segmentmodel.py

@@ -2994,11 +2994,6 @@ class SegmentModel(ArbdModel):
                 intrahelical junctions between ds and ssDNA """
                 return
 
-            """ Add bond potential """
-            k = 1.0 * count_crossovers((b1,b2))
-            pot = self.get_bond_potential(k,18.5)
-            self.add_bond(b1,b2, pot)
-
             """ Add parallel helices potential, possibly """
             ## Add potential to provide a particular orinetation
             nt1,nt2 = [l.get_nt_pos() for l in (A,B)]
@@ -3016,6 +3011,11 @@ class SegmentModel(ArbdModel):
             if local_twist:
                 if is_T_junction:
                     """ Special case: one helix extends away from another in T-shaped junction """
+                    """ Add bond potential """
+                    k = 1.0 * count_crossovers((b1,b2))
+                    pot = self.get_bond_potential(k,12.5)
+                    self.add_bond(b1,b2, pot)
+
                     if is_end1:
                         b1_forward = A.on_fwd_strand if nt1 == 0 else not A.on_fwd_strand
                         add_local_tee_orientation_potential(b1,b2, b1_forward, B.on_fwd_strand)
@@ -3029,10 +3029,20 @@ class SegmentModel(ArbdModel):
                         add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
 
                 else:
+                    """ Add bond potential """
+                    k = 1.0 * count_crossovers((b1,b2))
+                    pot = self.get_bond_potential(k,18.5)
+                    self.add_bond(b1,b2, pot)
+
                     """ Normal case: add orientation potential """
                     add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
                     add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
-            
+            else:
+                """ Add bond potential """
+                k = 1.0 * count_crossovers((b1,b2))
+                pot = self.get_bond_potential(k,18.5)
+                self.add_bond(b1,b2, pot)
+
 
         """ Add connection potentials """
         processed_crossovers = set()