diff --git a/mmtbx/hydrogens/reduce_hydrogen.py b/mmtbx/hydrogens/reduce_hydrogen.py
index 533a4ec64d..8ebec6b38e 100644
--- a/mmtbx/hydrogens/reduce_hydrogen.py
+++ b/mmtbx/hydrogens/reduce_hydrogen.py
@@ -123,6 +123,7 @@ def run(self):
     p.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
     p.pdb_interpretation.use_neutron_distances = self.use_neutron_distances
     p.pdb_interpretation.proceed_with_excessive_length_bonds=True
+    p.pdb_interpretation.allow_polymer_cross_special_position=True
     #p.pdb_interpretation.automatic_linking.link_metals = True
 
     t0 = time.time()