diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7ee8ff5fc95fd2460868362145902c60149a8f02..f5e10d58c80624c56635169228f69cf557309919 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1499,6 +1499,13 @@ class ChainMapper:
             else:
                 raise RuntimeError("This shouldnt happen")
 
+        if len(polypep_seqs) == 0 and len(polynuc_seqs) == 0:
+            raise RuntimeError(f"No chain fulfilled minimum length requirement "
+                               f"to be considered in chain mapping "
+                               f"({self.min_pep_length} for peptide chains, "
+                               f"{self.min_nuc_length} for nucleotide chains) "
+                               f"- mapping failed")
+
         # select for chains for which we actually extracted the sequence
         chain_names = [s.GetAttachedView().chains[0].name for s in polypep_seqs]
         chain_names += [s.GetAttachedView().chains[0].name for s in polynuc_seqs]
diff --git a/modules/mol/alg/tests/test_chain_mapping.py b/modules/mol/alg/tests/test_chain_mapping.py
index 36a633b09479e89aa81297cfb45326b4262fea69..8c8846aba8a3de61c6a52991c33041186b00219e 100644
--- a/modules/mol/alg/tests/test_chain_mapping.py
+++ b/modules/mol/alg/tests/test_chain_mapping.py
@@ -353,6 +353,13 @@ class TestChainMapper(unittest.TestCase):
                        aln.GetSequence(1).GetString())
 
 
+  def test_misc(self):
+
+    # check for triggered error when no chain fulfills length threshold
+    ref = _LoadFile("3l1p.1.pdb").Select("cname=A and rnum<8")
+    self.assertRaises(Exception, ChainMapper, ref)
+
+
 if __name__ == "__main__":
   from ost import testutils
   if testutils.SetDefaultCompoundLib():