Index: modlib/modeller/automodel/generate.py
===================================================================
--- modlib/modeller/automodel/generate.py	(revision 8282)
+++ modlib/modeller/automodel/generate.py	(revision 8283)
@@ -3,6 +3,17 @@
 
 from modeller.alignment import alignment
 
+def _set_seq_id(mdl, aln):
+    """Set the model's seq_id field using the most similar template.
+       This is done automatically by transfer_xyz, but generate methods
+       that don't use transfer_xyz to create the model from the templates
+       will need to do this manually."""
+    target = aln[-1]
+    seq_id = 0.
+    for known in aln[:-1]:
+        seq_id = max(seq_id, known.get_sequence_identity(target))
+    mdl.seq_id = seq_id
+
 def generate_xyz(mdl, aln):
     """Build coordinates from scratch (ignore templates)"""
 
@@ -10,6 +21,7 @@
     mdl.create_topology(aln)
     mdl.build(initialize_xyz=True, build_method='3D_INTERPOLATION')
     mdl.make_valid_pdb_coordinates()
+    _set_seq_id(mdl, aln)
 
 
 def transfer_xyz(mdl, aln):
@@ -47,3 +59,7 @@
     # sequence is correct and any missing atoms are filled in:
     mdl.transfer_xyz(a, cluster_cut=-1.0)
     mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
+
+    # Note that transfer_xyz will set mdl.seq_id to 100%, which is not what
+    # we want. So calculate it correctly here.
+    _set_seq_id(mdl, aln)