Commit 99709ad5 authored by cmaffeo2's avatar cmaffeo2
Browse files

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

parent ab28bc85
......@@ -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()
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment