diff --git a/src/bundles/clashes/src/clashes.py b/src/bundles/clashes/src/clashes.py
index 824241deb1..dc97b8efdb 100644
--- a/src/bundles/clashes/src/clashes.py
+++ b/src/bundles/clashes/src/clashes.py
@@ -128,7 +128,7 @@ def find_clashes(session, test_atoms,
                     if r:
                         chain_pos[r] = i
     from chimerax.atom_search import AtomSearchTree
-    tree = AtomSearchTree(search_atoms, scene_coords=inter_model)
+    tree = AtomSearchTree(search_atoms, scene_coords=use_scene_coords)
     clashes = {}
     from chimerax.geometry import distance
     intra_mol_map = {}