diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 1d36613400011c6565aa7bb10545067d0adbed7f..2307ee2b1651156097de51055b70591673f1dd10 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1339,6 +1339,10 @@ class ChainMapper:
         polypep_seqs = seq.CreateSequenceList()
         polynuc_seqs = seq.CreateSequenceList()
 
+        if len(view.residues) == 0:
+            # no residues survived => return
+            return (view, polypep_seqs, polynuc_seqs)
+
         for ch in view.chains:
             n_res = len(ch.residues)
             n_pep = sum([r.IsPeptideLinking() for r in ch.residues])