Fixed crossover angle potentials

CanonicalNucleotideAtoms.py

@@ -18,7 +18,7 @@ def stringToIntTuples(string, tupleLen, offset):
     return ret
 
 class CanonicalNucleotideFactory(Group):
-    DefaultOrientation = rotationAboutAxis([0,0,1], 80)
+    DefaultOrientation = rotationAboutAxis([0,0,1], 180)
     def __init__(self, prefix, seq):
         self.sequence = seq     # TODO: used?
         self.resname = resnames[seq]

segmentmodel.py

@@ -1783,23 +1783,18 @@ class SegmentModel(ArbdModel):
 
             if local_twist:
                 k = (1.0/2) * 1.5 * kT * (1.0 / (1-np.exp(-float(1)/147))) * 0.00030461742; # kcal_mol/degree^2
+                pot = self.get_angle_potential(k,120)
                 if 'orientation_bead' in b1.__dict__:
-                    # t0 = 90 + 60
-                    t0 = 150
-                    if A.on_fwd_strand: t0 = 30 # TODO handle antiparallel segments
                     o = b1.orientation_bead
-                    pot = self.get_angle_potential(k,t0)
                     self.add_angle( o,b1,b2, pot )
                 if 'orientation_bead' in b2.__dict__:
-                    t0 = 150
-                    if B.on_fwd_strand: t0 = 30
                     o = b2.orientation_bead
-                    pot = self.get_angle_potential(k,t0)
                     self.add_angle( b1,b2,o, pot )
 
 
-                t0 = 90
                 if 'orientation_bead' in b1.__dict__:
+                    t0 = 90
+                    if A.on_fwd_strand: t0 = -90
                     o1 = b1.orientation_bead
                     if u2 is not None:
                         k = k_fn( dists[b2][u2] )
@@ -1807,9 +1802,11 @@ class SegmentModel(ArbdModel):
                         self.add_dihedral( o1,b1,b2,u2, pot )
                     elif d2 is not None:
                         k = k_fn( dists[b2][d2] )
-                        pot = self.get_dihedral_potential(k,t0)
+                        pot = self.get_dihedral_potential(k,-t0)
                         self.add_dihedral( o1,b1,b2,d2, pot )
                 if 'orientation_bead' in b2.__dict__:
+                    t0 = 90
+                    if B.on_fwd_strand: t0 = -90
                     o2 = b2.orientation_bead
                     if u1 is not None:
                         k = k_fn( dists[b1][u1] )
@@ -1817,7 +1814,7 @@ class SegmentModel(ArbdModel):
                         self.add_dihedral( o2,b2,b1,u1, pot )
                     elif d1 is not None:
                         k = k_fn( dists[b1][d1] )
-                        pot = self.get_dihedral_potential(k,t0)
+                        pot = self.get_dihedral_potential(k,-t0)
                         self.add_dihedral( o2,b2,b1,d1, pot )