diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 214760d..8aa8549 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.5
+current_version = 0.2.6
 commit = True
 tag = False
 
diff --git a/pyscal_rdf/structure.py b/pyscal_rdf/structure.py
index 38bdf98..d94f721 100644
--- a/pyscal_rdf/structure.py
+++ b/pyscal_rdf/structure.py
@@ -248,6 +248,7 @@ def delete(self, ids=None, indices=None, condition=None, selection=False):
         masks = self.atoms._generate_bool_list(ids=ids, indices=indices, condition=condition, selection=selection)
         delete_list = [masks[self.atoms["head"][x]] for x in range(self.atoms.ntotal)]
         delete_ids = [x for x in range(self.atoms.ntotal) if delete_list[x]]
+        actual_natoms = self.natoms
         self.atoms._delete_atoms(delete_ids)
 
         if self.graph is not None:
@@ -257,7 +258,7 @@ def delete(self, ids=None, indices=None, condition=None, selection=False):
             self.add_vacancy(c, number=val)
             #now we need to re-add atoms, so at to remove
             self.graph.graph.remove((self.sample, CMSO.hasNumberOfAtoms, None))
-            self.graph.graph.add((self.sample, CMSO.hasNumberOfAtoms, Literal(self.natoms-val, datatype=XSD.integer)))
+            self.graph.graph.add((self.sample, CMSO.hasNumberOfAtoms, Literal(actual_natoms-val, datatype=XSD.integer)))
             #revamp composition
             #remove existing chem composution
             chemical_species = self.graph.graph.value(self.sample, CMSO.hasSpecies)
@@ -288,23 +289,14 @@ def delete(self, ids=None, indices=None, condition=None, selection=False):
             position_identifier = self.graph.graph.value(URIRef(f'{self.sample}_Position'), CMSO.hasIdentifier).toPython()
             species_identifier = self.graph.graph.value(URIRef(f'{self.sample}_Species'), CMSO.hasIdentifier).toPython()
 
-            #open the file for reading
-            with open(filepath, 'r') as fin:
-                data = json.load(fin)
-                positions = data[position_identifier]['value']
-                species = data[species_identifier]['value']
-
             #clean up items
-            positions = [pos for count, pos in enumerate(positions) if count not in delete_ids]
-            species = [pos for count, pos in enumerate(species) if count not in delete_ids]
-
             datadict = {
                 position_identifier:{
-                    "value": positions,
+                    "value": self.schema.atom_attribute.position(),
                     "label": "position", 
                 },
                 species_identifier:{
-                    "value": species,
+                    "value": self.schema.atom_attribute.species(),
                     "label": "species", 
                 },
             }
diff --git a/setup.py b/setup.py
index edf4ab1..a2c8380 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='pyscal_rdf',
-    version='0.2.5',
+    version='0.2.6',
     author='Abril Azocar Guzman, Sarath Menon',
     author_email='sarath.menon@pyscal.org',
     description='Ontology based structural manipulation and quering',