diff --git a/modules/mol/alg/pymod/ligand_scoring_base.py b/modules/mol/alg/pymod/ligand_scoring_base.py
index 4cd4bb588bbe44dd0eb8473cd80c200a49f13fa8..7a38e4d3baf41fd2a14e9ab8f28b8c04661c6bbd 100644
--- a/modules/mol/alg/pymod/ligand_scoring_base.py
+++ b/modules/mol/alg/pymod/ligand_scoring_base.py
@@ -777,6 +777,8 @@ class LigandScorer:
             new_chain = new_entity.FindChain(residue.chain.name)
             if not new_chain.IsValid():
                 new_chain = new_editor.InsertChain(residue.chain.name)
+                new_editor.SetChainType(new_chain,
+                                        mol.ChainType.CHAINTYPE_NON_POLY)
             else:
                 # Does a residue with the same name already exist?
                 already_exists = new_chain.FindResidue(residue.number).IsValid()