diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index eb85cef7925ccc283ba17aee993bb2bdd0ecb496..4e311ddc0ad5b0bc01d165d6778865f27dcf09cf 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -770,7 +770,7 @@ void EntityImpl::SetTransform(const geom::Mat4 transfmat)
     identity_transf_ = false;    
   }
   this->UpdateTransformedPos();
-  this->MarkXCSDirty();
+  this->MarkOrganizerDirty();
 }
 
 void EntityImpl::AttachObserver(const EntityObserverPtr& o)
@@ -1049,6 +1049,7 @@ void EntityImpl::UpdateOrganizer()
        e=atom_map_.end(); i!=e; ++i) {
     atom_organizer_.Add(i->second, i->second->GetPos());
   }
+  dirty_flags_&=~DirtyOrganizer;
 }
 
 void EntityImpl::IncXCSEditorCount() 
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index d30d6d183fa41959ae596f8752a5686952846985..1113e23f121d52740aa4450ddea2971acac696d2 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -92,6 +92,16 @@ BOOST_AUTO_TEST_CASE(throw_invalid_ent_view)
   BOOST_CHECK_NO_THROW(CheckHandleValidity(ent.CreateEmptyView()));
 }
 
+BOOST_AUTO_TEST_CASE(bzdng250)
+{
+  EntityHandle eh=make_test_entity();
+  eh.EditXCS().ApplyTransform(geom::Mat4(-1, 0, 0, 0,
+                                          0, 1, 0, 0,
+                                          0, 0,-1, 0,
+                                          0, 0, 0, 1));
+  BOOST_CHECK_NO_THROW(eh.FindResidue("A", 1).FindTorsion("PHI").GetAngle());
+}
+
 BOOST_AUTO_TEST_CASE(entity_creator) 
 {
   EntityHandle eh = CreateEntity();