Index: modlib/modeller/automodel/loopmodel.py
===================================================================
--- modlib/modeller/automodel/loopmodel.py	(revision 8489)
+++ modlib/modeller/automodel/loopmodel.py	(working copy)
@@ -15,7 +15,6 @@
     inimodel = None
     loop_potential = None
     _defined_indices = None
-    _defined_selection = None
 
     def __init__(self, env, sequence, alnfile=None, knowns=[], inimodel=None,
                  deviation=None, library_schedule=None, csrfile=None,
@@ -92,9 +91,9 @@
                              atom_files=filename)
         return aln
 
-    def _check_for_added_atoms(self, loop_selection):
+    def _check_for_added_atoms(self, loop_selection, defined_selection):
         # Atoms in the loop region always count as defined
-        s = self._defined_selection | loop_selection
+        s = defined_selection | loop_selection
         # Note that we store atom indices rather than a selection object,
         # since selection objects cannot be sent across the network correctly
         # to slaves when building models in parallel.
@@ -138,15 +137,17 @@
         self.transfer_xyz(aln)
         self.seq_id = seq_id
 
-        if self._defined_selection is None \
-           and not self.loop.write_selection_only:
-            self._defined_selection = selection(self).only_defined()
+        if not self.loop.write_selection_only:
+            defined_selection = selection(self).only_defined()
+        else:
+            defined_selection = None
 
         # Fill in any missing atoms using internal coordinates
         self.build(build_method='INTERNAL_COORDINATES', initialize_xyz=False)
 
         self.res_num_from(model(self.env, file=filename), aln)
         self.special_patches(aln)
+        return defined_selection
 
     def build_seq(self, filename, num):
         """Build all loop models for a given starting model"""
@@ -160,10 +161,10 @@
         self.group_restraints = self.loop_potential
 
         aln = self.read_loop_alignment(filename)
-        self.create_loop_topology(aln, filename)
+        defined_selection = self.create_loop_topology(aln, filename)
         atmsel = self._check_select_loop_atoms()
         if not self.loop.write_selection_only:
-            self._check_for_added_atoms(atmsel)
+            self._check_for_added_atoms(atmsel, defined_selection)
         self.loop_restraints(atmsel, aln)
 
         # Select corresponding restraints only: