diff --git a/modules/mmcif/pyext/src/data.py b/modules/mmcif/pyext/src/data.py
index e0f325f3ea..6634708b6b 100644
--- a/modules/mmcif/pyext/src/data.py
+++ b/modules/mmcif/pyext/src/data.py
@@ -594,15 +594,16 @@ def __init__(self, system):
 
     def _add_protocol(self, prot):
         self.system.orphan_protocols.append(prot)
+        return prot
 
-    def _add_hierarchy(self, h, modeled_assembly, all_software):
+    def _add_hierarchy(self, h, top_h, modeled_assembly, all_software):
         num_models = 0  # assume we always start with no models
         prot_types = (IMP.core.SampleProvenance, IMP.core.CombineProvenance)
         pp_types = (IMP.core.FilterProvenance, IMP.core.ClusterProvenance)
         in_postproc = False
         prot = _Protocol()
-        for p in reversed(list(IMP.core.get_all_provenance(
-                                          h, types=prot_types + pp_types))):
+        for p in reversed(list(_get_all_state_provenance(
+                h, top_h, types=prot_types + pp_types))):
             if isinstance(p, pp_types):
                 num_models = prot.add_postproc(p, num_models, modeled_assembly)
                 in_postproc = True
@@ -615,7 +616,7 @@ def _add_hierarchy(self, h, modeled_assembly, all_software):
                                            all_software)
                 in_postproc = False
         if len(prot.steps) > 0:
-            self._add_protocol(prot)
+            return self._add_protocol(prot)
 
 
 class _CoordinateHandler(object):
diff --git a/modules/mmcif/pyext/src/util.py b/modules/mmcif/pyext/src/util.py
index 60b03ba0ac..8bf4df4483 100644
--- a/modules/mmcif/pyext/src/util.py
+++ b/modules/mmcif/pyext/src/util.py
@@ -177,7 +177,7 @@ def _add_hierarchy(self, h, state):
             if num_state_reps == 1:
                 self.representation.extend(state.repsegments[component])
         self._software.add_hierarchy(h)
-        self.protocols._add_hierarchy(h, state.modeled_assembly,
+        self.protocols._add_hierarchy(h, None, state.modeled_assembly,
                                       self._software)
         self._external_files.add_hierarchy(h)
 
@@ -421,6 +421,7 @@ def __init__(self):
         self._external_files = IMP.mmcif.data._ExternalFiles(self.system)
         self._model_assemblies = IMP.mmcif.data._ModelAssemblies(self.system)
         self._representations = IMP.mmcif.data._Representations(self.system)
+        self._protocols = IMP.mmcif.data._Protocols(self.system)
 
     def add_model(self, hiers, restraints, name=None, states=None,
                   ensembles=None):
@@ -457,11 +458,17 @@ def _add_hierarchy(self, h, top_h, state, name, ensemble):
             comp = self._add_chain(c)
             asyms.append(comp.asym_unit)
             ch.add_chain(c, comp.asym_unit)
-        self._representations.add(ch._representation)
-        self._model_assemblies.add(asyms)
+        representation = self._representations.add(ch._representation)
+        assembly = self._model_assemblies.add(asyms)
         self._add_hierarchy_ensemble_info(h, top_h, ensemble)
         self._software.add_hierarchy(h, top_h)
+        protocol = self._protocols._add_hierarchy(h, top_h, assembly,
+                                                  self._software)
         self._external_files.add_hierarchy(h, top_h)
+        model = ihm.model.Model(assembly=assembly, protocol=protocol,
+                                representation=representation)
+        ensemble.model_group.append(model)
+        ensemble.num_models += 1
         return ensemble
 
     def _add_hierarchy_ensemble_info(self, h, top_h, ensemble):
diff --git a/modules/mmcif/test/test_data.py b/modules/mmcif/test/test_data.py
index 907acee060..d1641b4fe3 100644
--- a/modules/mmcif/test/test_data.py
+++ b/modules/mmcif/test/test_data.py
@@ -201,7 +201,7 @@ def test_protocols_add_hierarchy(self):
         prov = IMP.core.SampleProvenance.setup_particle(
             IMP.Particle(m), "Monte Carlo", 100, 10, 1)
         IMP.core.add_provenance(m, top, prov)
-        protocols._add_hierarchy(top, None, software)
+        protocols._add_hierarchy(top, None, None, software)
         protocol, = s.orphan_protocols
         step, = protocol.steps
         self.assertEqual(step.num_models_begin, 0)