diff --git a/projects/novelfams/translate2modelcif.py b/projects/novelfams/translate2modelcif.py
index 2abf2040481a8d01c515e477fdbb97be469b4cc8..d4392f0857d13e9ab7ed223c7e2a0d49ab0f2ebf 100644
--- a/projects/novelfams/translate2modelcif.py
+++ b/projects/novelfams/translate2modelcif.py
@@ -262,7 +262,12 @@ def _get_sequence(chn, use_auth=False):
 
 
 class _InvalidCoordinateError(RuntimeError):
-    """Exception for weird coordinates ina PDB file, used internally to skip
+    """Exception for weird coordinates in a PDB file, used internally to skip
+    such PDB files."""
+
+
+class _NoEntitiesError(RuntimeError):
+    """Exception for PDB files w/o entities (empty?), used internally to skip
     such PDB files."""
 
 
@@ -270,6 +275,14 @@ def _get_entities(pdb_file, fam_name):
     """Gather data for the mmCIF (target) entities."""
     try:
         ost_ent = io.LoadPDB(pdb_file)
+    except OSError as exc:
+        if str(exc).endswith(" doesn't contain any entities"):
+            _warn_msg(
+                f"PDB file '{pdb_file}' does not have entities (maybe empty)."
+            )
+            raise _NoEntitiesError() from exc
+        _warn_msg(f"Exception for '{pdb_file}'")
+        raise
     except Exception as exc:
         if str(exc).startswith("invalid coordinate on line "):
             _warn_msg(
@@ -599,7 +612,7 @@ def _main():
                 f_name,
                 opts,
             )
-        except _InvalidCoordinateError:
+        except (_InvalidCoordinateError, _NoEntitiesError):
             continue
 
         # report progress after a bit of time