diff --git a/prody/proteins/mmtffile.py b/prody/proteins/mmtffile.py
index 66896c282..0480e7045 100644
--- a/prody/proteins/mmtffile.py
+++ b/prody/proteins/mmtffile.py
@@ -323,6 +323,9 @@ def set_info(atomgroup, mmtf_data,get_bonds=False,altloc_sel='A'):
     if altloc_sel != 'all':
         #mask out any unwanted alternative locations
         mask = (altlocs == '') | (altlocs == altloc_sel)
+
+    if np.all(mask == False):
+        mask = (altlocs == '') | (altlocs == altlocs[0])
         
     atomgroup.setCoords(coords[:,mask])
     atomgroup.setNames(atom_names[mask])