diff --git a/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py b/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py
index 6b777d717e..cf6db7df76 100644
--- a/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py
+++ b/MDANSE/Src/MDANSE/Chemistry/ChemicalEntity.py
@@ -182,7 +182,10 @@ def center_of_mass(self, configuration: _Configuration) -> NDArray[np.float64]:
         :rtype: numpy.ndarray
         """
         coords = configuration["coordinates"]
-        masses = [ATOMS_DATABASE[at.symbol]["atomic_weight"] for at in self.atom_list]
+        masses = [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+            for at in self.atom_list
+        ]
 
         return center_of_mass(coords, masses)
 
@@ -198,7 +201,10 @@ def mass(self) -> float:
     @property
     def masses(self) -> list[float]:
         """A list of masses of all non-ghost atoms within this chemical entity."""
-        return [ATOMS_DATABASE[at.symbol]["atomic_weight"] for at in self.atom_list]
+        return [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+            for at in self.atom_list
+        ]
 
     def find_transformation_as_quaternion(
         self, conf1: _Configuration, conf2: Union[_Configuration, None] = None
@@ -320,7 +326,7 @@ def center_and_moment_of_inertia(
         mr = Vector(0.0, 0.0, 0.0)
         t = Tensor(3 * [3 * [0.0]])
         for atom in self.atom_list:
-            ma = ATOMS_DATABASE[atom.symbol]["atomic_weight"]
+            ma = ATOMS_DATABASE.get_atom_property(atom.symbol, "atomic_weight")
             r = Vector(configuration["coordinates"][atom.index, :])
             m += ma
             mr += ma * r
@@ -473,7 +479,7 @@ def __init__(
 
         self._parent = None
 
-        self.element = ATOMS_DATABASE[self._symbol]["element"]
+        self.element = ATOMS_DATABASE.get_atom_property(self._symbol, "element")
 
         for k, v in kwargs.items():
             try:
@@ -2460,7 +2466,7 @@ def add_chemical_entity(self, chemical_entity: _ChemicalEntity) -> None:
 
             # add the atoms to the rdkit molecule, ghost atoms are
             # never added to the rdkit molecule object
-            atm_num = ATOMS_DATABASE[at.symbol]["atomic_number"]
+            atm_num = ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_number")
             rdkit_atm = Chem.Atom(atm_num)
 
             # makes sure that rdkit doesn't add extra hydrogens
diff --git a/MDANSE/Src/MDANSE/Chemistry/Databases.py b/MDANSE/Src/MDANSE/Chemistry/Databases.py
index 372a82f118..f04d83cb26 100644
--- a/MDANSE/Src/MDANSE/Chemistry/Databases.py
+++ b/MDANSE/Src/MDANSE/Chemistry/Databases.py
@@ -589,6 +589,24 @@ def save(self) -> None:
         with open(AtomsDatabase._USER_DATABASE, "w") as fout:
             json.dump(d, fout)
 
+    def get_atom_property(self, symbol: str, property: str) -> Union[int, float, str]:
+        """Faster access to the atom property as it avoids the deepcopy
+        in __getitem__.
+
+        Parameters
+        ----------
+        symbol : str
+            Symbol of the atom.
+        property : str
+            Property of the atoms to get.
+
+        Returns
+        -------
+        Union[int, float, str]
+            The atom property.
+        """
+        return self._data[symbol][property]
+
 
 class MoleculesDatabaseError(Error):
     """This class handles the exceptions related to MoleculesDatabase"""
diff --git a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
index 272f02ea2b..c879cae865 100644
--- a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
+++ b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
@@ -65,10 +65,10 @@ def guess_element(atm_label: str, mass: Union[float, int, None] = None) -> str:
         if guess in ATOMS_DATABASE:
             if mass is None:
                 return guess
-            num = ATOMS_DATABASE[guess]["proton"]
+            num = ATOMS_DATABASE.get_atom_property(guess, "proton")
             atms = ATOMS_DATABASE.match_numeric_property("proton", num)
             for atm in atms:
-                atm_mass = ATOMS_DATABASE[atm]["atomic_weight"]
+                atm_mass = ATOMS_DATABASE.get_atom_property(atm, "atomic_weight")
                 diff = abs(mass - atm_mass)
                 if diff < best_diff:
                     best_match = atm
diff --git a/MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py b/MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py
index c3058c54d7..3e3e28d341 100644
--- a/MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py
+++ b/MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py
@@ -30,7 +30,7 @@ def select_element(
     Union[set[int], bool]
         The atom indices of the matched atoms.
     """
-    pattern = f"[#{ATOMS_DATABASE[symbol]['atomic_number']}]"
+    pattern = f"[#{ATOMS_DATABASE.get_atom_property(symbol, 'atomic_number')}]"
     if check_exists:
         return system.has_substructure_match(pattern)
     else:
@@ -56,7 +56,7 @@ def select_hs_on_element(
     Union[set[int], bool]
         The atom indices of the matched atoms.
     """
-    num = ATOMS_DATABASE[symbol]["atomic_number"]
+    num = ATOMS_DATABASE.get_atom_property(symbol, "atomic_number")
     if check_exists:
         return system.has_substructure_match(f"[#{num}]~[H]")
     else:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py
index 081ccd77b3..99a4509dc2 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py
@@ -85,7 +85,10 @@ def configure(self, value):
         self["elements"] = [[at.symbol] for at in selectedAtoms]
         self["names"] = [at.symbol for at in selectedAtoms]
         self["unique_names"] = sorted(set(self["names"]))
-        self["masses"] = [[ATOMS_DATABASE[n]["atomic_weight"]] for n in self["names"]]
+        self["masses"] = [
+            [ATOMS_DATABASE.get_atom_property(n, "atomic_weight")]
+            for n in self["names"]
+        ]
         self.error_status = "OK"
 
     def get_natoms(self):
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py
index 14177755a4..11525dcaee 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py
@@ -120,7 +120,8 @@ def transmutate(self, selection, element):
 
         atomSelConfigurator["unique_names"] = sorted(set(atomSelConfigurator["names"]))
         atomSelConfigurator["masses"] = [
-            [ATOMS_DATABASE[n]["atomic_weight"]] for n in atomSelConfigurator["names"]
+            [ATOMS_DATABASE.get_atom_property(n, "atomic_weight")]
+            for n in atomSelConfigurator["names"]
         ]
         self.error_status = "OK"
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py
index 7d8f0475b2..f17801a32e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py
@@ -73,7 +73,7 @@ def get_weights(self):
         for i in range(ascfg["selection_length"]):
             name = ascfg["names"][i]
             for el in ascfg["elements"][i]:
-                p = ATOMS_DATABASE[el][self["property"]]
+                p = ATOMS_DATABASE.get_atom_property(el, self["property"])
                 if name in weights:
                     weights[name] += p
                 else:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py b/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
index d03b37d534..22df95e6b7 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
@@ -114,7 +114,12 @@ def run_step(self, index):
         atomic_density = self._n_atoms / cell_volume
 
         mass_density = (
-            sum([ATOMS_DATABASE[s]["atomic_weight"] for s in self._symbols])
+            sum(
+                [
+                    ATOMS_DATABASE.get_atom_property(s, "atomic_weight")
+                    for s in self._symbols
+                ]
+            )
             / NAVOGADRO
             / cell_volume
         )
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py b/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py
index d70b28b3d5..4cdfc7bee0 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/Eccentricity.py
@@ -160,7 +160,7 @@ def initialize(self):
         self._selectionTotalMass = np.sum(self._selectionMasses)
 
         self._comMasses = [
-            ATOMS_DATABASE[self._atoms[idx].symbol]["atomic_weight"]
+            ATOMS_DATABASE.get_atom_property(self._atoms[idx].symbol, "atomic_weight")
             for idx in self._comIndexes
         ]
 
@@ -196,7 +196,9 @@ def run_step(self, index):
             atomsCoordinates = series[idxs, :]
             difference = atomsCoordinates - com
 
-            w = ATOMS_DATABASE[name][self.configuration["weights"]["property"]]
+            w = ATOMS_DATABASE.get_atom_property(
+                name, self.configuration["weights"]["property"]
+            )
 
             xx += np.add.reduce(
                 w
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py b/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
index fd9ccd317c..c0a53e5451 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
@@ -125,18 +125,18 @@ def initialize(self):
         # Compute some parameters used for a proper McStas run
         self._mcStasPhysicalParameters = {"density": 0.0}
         self._mcStasPhysicalParameters["weight"] = sum(
-            [ATOMS_DATABASE[s]["atomic_weight"] for s in symbols]
+            [ATOMS_DATABASE.get_atom_property(s, "atomic_weight") for s in symbols]
         )
         self._mcStasPhysicalParameters["sigma_abs"] = (
-            sum([ATOMS_DATABASE[s]["xs_absorption"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_absorption") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         self._mcStasPhysicalParameters["sigma_coh"] = (
-            sum([ATOMS_DATABASE[s]["xs_coherent"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_coherent") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         self._mcStasPhysicalParameters["sigma_inc"] = (
-            sum([ATOMS_DATABASE[s]["xs_incoherent"] for s in symbols])
+            sum([ATOMS_DATABASE.get_atom_property(s, "xs_incoherent") for s in symbols])
             * MCSTAS_UNITS_LUT["nm2"]
         )
         for frameIndex in self.configuration["frames"]["value"]:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/NeutronDynamicTotalStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/NeutronDynamicTotalStructureFactor.py
index a9a54b498e..b2e3423c6f 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/NeutronDynamicTotalStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/NeutronDynamicTotalStructureFactor.py
@@ -447,8 +447,8 @@ def finalize(self):
 
         # Compute coherent functions and structure factor
         for pair in self._elementsPairs:
-            bi = ATOMS_DATABASE[pair[0]]["b_coherent"]
-            bj = ATOMS_DATABASE[pair[1]]["b_coherent"]
+            bi = ATOMS_DATABASE.get_atom_property(pair[0], "b_coherent")
+            bj = ATOMS_DATABASE.get_atom_property(pair[1], "b_coherent")
             ni = nAtomsPerElement[pair[0]]
             nj = nAtomsPerElement[pair[1]]
             ci = ni / nTotalAtoms
@@ -483,7 +483,7 @@ def finalize(self):
 
         # Compute incoherent functions and structure factor
         for element, ni in nAtomsPerElement.items():
-            bi = ATOMS_DATABASE[element]["b_incoherent2"]
+            bi = ATOMS_DATABASE.get_atom_property(element, "b_incoherent2")
             ni = nAtomsPerElement[element]
             ci = ni / nTotalAtoms
 
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py b/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py
index 26b7d767f1..46cf110393 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/SolventAccessibleSurface.py
@@ -102,7 +102,10 @@ def initialize(self):
         # A mapping between the atom indexes and covalent_radius radius for the whole universe.
         self.vdwRadii = dict(
             [
-                (at.index, ATOMS_DATABASE[at.symbol]["covalent_radius"])
+                (
+                    at.index,
+                    ATOMS_DATABASE.get_atom_property(at.symbol, "covalent_radius"),
+                )
                 for at in self.configuration["trajectory"][
                     "instance"
                 ].chemical_system.atom_list
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Temperature.py b/MDANSE/Src/MDANSE/Framework/Jobs/Temperature.py
index dff00ba0e5..e0970a9283 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/Temperature.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/Temperature.py
@@ -115,7 +115,7 @@ def run_step(self, index):
 
         symbol = atom.symbol
 
-        mass = ATOMS_DATABASE[symbol]["atomic_weight"]
+        mass = ATOMS_DATABASE.get_atom_property(symbol, "atomic_weight")
 
         trajectory = self.configuration["trajectory"]["instance"]
 
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
index 47251d5787..3a6db723ff 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
@@ -24,18 +24,18 @@
 
 def atomic_scattering_factor(element, qvalues):
     a = np.empty((4,), dtype=np.float64)
-    a[0] = ATOMS_DATABASE[element]["xray_asf_a1"]
-    a[1] = ATOMS_DATABASE[element]["xray_asf_a2"]
-    a[2] = ATOMS_DATABASE[element]["xray_asf_a3"]
-    a[3] = ATOMS_DATABASE[element]["xray_asf_a4"]
+    a[0] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a1")
+    a[1] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a2")
+    a[2] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a3")
+    a[3] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_a4")
 
     b = np.empty((4,), dtype=np.float64)
-    b[0] = ATOMS_DATABASE[element]["xray_asf_b1"]
-    b[1] = ATOMS_DATABASE[element]["xray_asf_b2"]
-    b[2] = ATOMS_DATABASE[element]["xray_asf_b3"]
-    b[3] = ATOMS_DATABASE[element]["xray_asf_b4"]
+    b[0] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b1")
+    b[1] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b2")
+    b[2] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b3")
+    b[3] = ATOMS_DATABASE.get_atom_property(element, "xray_asf_b4")
 
-    c = ATOMS_DATABASE[element]["xray_asf_c"]
+    c = ATOMS_DATABASE.get_atom_property(element, "xray_asf_c")
 
     return c + np.sum(
         a[:, np.newaxis]
diff --git a/MDANSE/Src/MDANSE/Mathematics/Graph.py b/MDANSE/Src/MDANSE/Mathematics/Graph.py
index 0424515b5a..71cd582700 100644
--- a/MDANSE/Src/MDANSE/Mathematics/Graph.py
+++ b/MDANSE/Src/MDANSE/Mathematics/Graph.py
@@ -56,11 +56,12 @@ def build_connected_components(self):
 
         # Make a copy of the set, so we can modify it.
         nodes = [self._nodes[k] for k in sorted(self._nodes.keys())]
+        nodes.reverse()
 
         # Iterate while we still have nodes to process.
         while nodes:
             # Get a random node and remove it from the global set.
-            n = nodes.pop(0)
+            n = nodes.pop()
 
             # This set will contain the next group of nodes connected to each other.
             group = set([n])
diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py b/MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py
index fc6903d551..692d7ab2b6 100644
--- a/MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py
+++ b/MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py
@@ -49,7 +49,7 @@ def check_composition(self, chemical: ChemicalSystem):
         atom_elements = [atom.symbol for atom in chemical.atoms]
         unique_elements = np.unique(atom_elements)
         radii = {
-            element: ATOMS_DATABASE[element]["covalent_radius"]
+            element: ATOMS_DATABASE.get_atom_property(element, "covalent_radius")
             for element in unique_elements
         }
         self._elements = atom_elements
diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py b/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py
index c10c2fb81d..edb966acf2 100644
--- a/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py
+++ b/MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py
@@ -351,7 +351,12 @@ def read_com_trajectory(
             last = len(self)
 
         indexes = [at.index for at in atoms]
-        masses = np.array([ATOMS_DATABASE[at.symbol]["atomic_weight"] for at in atoms])
+        masses = np.array(
+            [
+                ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+                for at in atoms
+            ]
+        )
 
         frames = np.array([self.coordinates(fnum) for fnum in range(first, last, step)])
         coords = frames[:, indexes, :].astype(np.float64)
diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py b/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
index 4438f7c66d..e660f2f351 100644
--- a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
+++ b/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
@@ -77,8 +77,6 @@ def __init__(self, h5_filename):
         # Define a default name for all chemical entities which have no name
         resolve_undefined_molecules_name(self._chemical_system)
 
-        # Retrieve the connectivity
-        build_connectivity(self._chemical_system)
         ic("Trajectory.__init__ ended")
 
     def close(self):
@@ -231,7 +229,12 @@ def read_com_trajectory(
             last = len(self)
 
         indexes = [at.index for at in atoms]
-        masses = np.array([ATOMS_DATABASE[at.symbol]["atomic_weight"] for at in atoms])
+        masses = np.array(
+            [
+                ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight")
+                for at in atoms
+            ]
+        )
         grp = self._h5_file["/configuration"]
 
         coords = grp["coordinates"][first:last:step, :, :].astype(np.float64)
@@ -615,7 +618,9 @@ def __init__(
 
         atoms = chemical_entity.atom_list
 
-        masses = [ATOMS_DATABASE[at.symbol]["atomic_weight"] for at in atoms]
+        masses = [
+            ATOMS_DATABASE.get_atom_property(at.symbol, "atomic_weight") for at in atoms
+        ]
 
         mass = sum(masses)
 
diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py b/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py
index e3b9bf9c0f..4e80587586 100644
--- a/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py
+++ b/MDANSE/Src/MDANSE/MolecularDynamics/TrajectoryUtils.py
@@ -240,7 +240,9 @@ def build_connectivity(
         coords = conf.to_real_coordinates()[indexes, :]
         cov_radii = np.zeros((n_atoms,), dtype=np.float64)
         for i, at in enumerate(atoms):
-            cov_radii[i] = ATOMS_DATABASE[at.symbol.capitalize()]["covalent_radius"]
+            cov_radii[i] = ATOMS_DATABASE.get_atom_property(
+                at.symbol.capitalize(), "covalent_radius"
+            )
 
         bonds = fast_calculation.cpt_cluster_connectivity_nopbc(
             coords, cov_radii, tolerance
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py b/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py
index 6bff910b50..e7a8107038 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py
@@ -15,10 +15,10 @@
 import logging
 
 import numpy as np
-from icecream import ic
+from scipy.spatial import cKDTree as KDTree
 
-from qtpy import QtCore, QtWidgets
-from qtpy.QtCore import Signal, Slot, Qt
+from qtpy import QtWidgets
+from qtpy.QtCore import Signal, Slot
 from qtpy.QtWidgets import QSizePolicy
 
 import vtk
@@ -28,20 +28,14 @@
 from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
 from MDANSE.Chemistry import ATOMS_DATABASE as CHEMICAL_ELEMENTS
 
-# from MDANSE_GUI.MolecularViewer.database import CHEMICAL_ELEMENTS
 from MDANSE_GUI.MolecularViewer.readers import hdf5wrapper
 from MDANSE_GUI.MolecularViewer.Dummy import PyConnectivity
 from MDANSE_GUI.MolecularViewer.Contents import TrajectoryAtomData
-
-# from MDANSE_GUI.MolecularViewer.ColourManager import ColourManager
 from MDANSE_GUI.MolecularViewer.AtomProperties import (
     AtomProperties,
     ndarray_to_vtkarray,
 )
 
-# from waterstay.extensions.histogram_3d import histogram_3d
-# from waterstay.gui.atomic_trace_settings_dialog import AtomicTraceSettingsDialog
-
 
 def array_to_3d_imagedata(data, spacing):
     nx = data.shape[0]
@@ -129,6 +123,7 @@ def __init__(self, parent):
         self._atoms = []
 
         self._polydata = None
+        self._uc_polydata = None
 
         self._surface = None
 
@@ -140,15 +135,13 @@ def __init__(self, parent):
 
         self._colour_manager = AtomProperties()
 
-        self.build_events()
+        # self.build_events()
 
     def setDataModel(self, datamodel: TrajectoryAtomData):
         self._datamodel = datamodel
 
-    def _new_trajectory_object(self, data: HDFTrajectoryInputData):
-        reader = hdf5wrapper.HDF5Wrapper(
-            "Dummy Name", data.trajectory, data.chemical_system
-        )
+    def _new_trajectory_object(self, fname: str, data: HDFTrajectoryInputData):
+        reader = hdf5wrapper.HDF5Wrapper(fname, data.trajectory, data.chemical_system)
         self.set_reader(reader)
 
     @Slot(str)
@@ -257,10 +250,13 @@ def build_scene(self):
         actor_list = []
 
         line_mapper = vtk.vtkPolyDataMapper()
+        uc_line_mapper = vtk.vtkPolyDataMapper()
         if vtk.vtkVersion.GetVTKMajorVersion() < 6:
             line_mapper.SetInput(self._polydata)
+            uc_line_mapper.SetInput(self._uc_polydata)
         else:
             line_mapper.SetInputData(self._polydata)
+            uc_line_mapper.SetInputData(self._uc_polydata)
 
         line_mapper.SetLookupTable(self._colour_manager._lut)
         line_mapper.ScalarVisibilityOn()
@@ -268,7 +264,12 @@ def build_scene(self):
         line_actor = vtk.vtkLODActor()
         line_actor.GetProperty().SetLineWidth(3 * self._scale_factor)
         line_actor.SetMapper(line_mapper)
+        uc_line_mapper.ScalarVisibilityOn()
+        uc_line_actor = vtk.vtkLODActor()
+        uc_line_actor.GetProperty().SetLineWidth(3 * self._scale_factor)
+        uc_line_actor.SetMapper(uc_line_mapper)
         actor_list.append(line_actor)
+        actor_list.append(uc_line_actor)
 
         temp_radius = float(1.0 * self._scale_factor)
         sphere = vtk.vtkSphereSource()
@@ -334,9 +335,9 @@ def clear_panel(self) -> None:
         self._n_frames = 0
         self.new_max_frames.emit(0)
         self._atoms = []
-        self._fixed_bonds = []
         self._atom_colours = []
         self._polydata = vtk.vtkPolyData()
+        self._uc_polydata = vtk.vtkPolyData()
         self._current_frame = 0
 
         self.update_renderer()
@@ -560,7 +561,7 @@ def set_connectivity_builder(self, coords, covalent_radii):
             self._connectivity_builder.add_point(index, xyz, radius)
 
     @Slot(int)
-    def set_coordinates(self, frame: int):
+    def set_coordinates(self, frame: int, tolerance=0.04):
         """Sets a new configuration.
 
         @param frame: the configuration number
@@ -572,7 +573,14 @@ def set_coordinates(self, frame: int):
 
         self._current_frame = frame % self._reader.n_frames
 
+        # update the atoms
         coords = self._reader.read_frame(self._current_frame)
+        cov_radii = np.array(
+            [
+                CHEMICAL_ELEMENTS.get_atom_property(at, "covalent_radius")
+                for at in self._reader.atom_types
+            ]
+        )
 
         atoms = vtk.vtkPoints()
         atoms.SetNumberOfPoints(self._n_atoms)
@@ -582,21 +590,58 @@ def set_coordinates(self, frame: int):
 
         self._polydata.SetPoints(atoms)
 
-        covalent_radii = [
-            CHEMICAL_ELEMENTS[at]["covalent_radius"] for at in self._reader.atom_types
-        ]
-        self.set_connectivity_builder(coords, covalent_radii)
-        chemical_bonds = self._fixed_bonds
-
+        # determine and set bonds without PBC applied
+        tree = KDTree(coords)
         bonds = vtk.vtkCellArray()
-        for at, bonded_at in chemical_bonds:
-            line = vtk.vtkLine()
-            line.GetPointIds().SetId(0, at)
-            line.GetPointIds().SetId(1, bonded_at)
-            bonds.InsertNextCell(line)
+        contacts = tree.query_ball_tree(tree, 2 * np.max(cov_radii) + tolerance)
+        for i, idxs in enumerate(contacts):
+            if len(idxs) == 0:
+                continue
+            diff = coords[i] - coords[idxs]
+            dist = np.sum(diff * diff, axis=1)
+            sum_radii = (cov_radii[i] + cov_radii[idxs] + tolerance) ** 2
+            js = np.array(idxs)[(0 < dist) & (dist < sum_radii)]
+            for j in js[i < js]:
+                line = vtk.vtkLine()
+                line.GetPointIds().SetId(0, i)
+                line.GetPointIds().SetId(1, j)
+                bonds.InsertNextCell(line)
 
         self._polydata.SetLines(bonds)
 
+        # update the unit cell
+        uc = self._reader.read_pbc(self._current_frame)
+        a = uc.a_vector
+        b = uc.b_vector
+        c = uc.c_vector
+        uc_points = vtk.vtkPoints()
+        uc_points.SetNumberOfPoints(8)
+        for i, v in enumerate([[0, 0, 0], a, b, c, a + b, a + c, b + c, a + b + c]):
+            x, y, z = v
+            uc_points.SetPoint(i, x, y, z)
+        self._uc_polydata.SetPoints(uc_points)
+
+        uc_lines = vtk.vtkCellArray()
+        for i, j in [
+            (0, 1),
+            (0, 2),
+            (0, 3),
+            (1, 4),
+            (1, 5),
+            (4, 7),
+            (2, 4),
+            (2, 6),
+            (5, 7),
+            (3, 5),
+            (3, 6),
+            (6, 7),
+        ]:
+            line = vtk.vtkLine()
+            line.GetPointIds().SetId(0, i)
+            line.GetPointIds().SetId(1, j)
+            uc_lines.InsertNextCell(line)
+        self._uc_polydata.SetLines(uc_lines)
+
         # Update the view.
         self.update_renderer()
 
@@ -621,10 +666,6 @@ def set_reader(self, reader, frame=0):
         self.new_max_frames.emit(self._n_frames - 1)
 
         self._atoms = self._reader.atom_types
-        try:
-            self._fixed_bonds = self._reader._chemical_system._bonds
-        except AttributeError:
-            self._fixed_bonds = []
 
         # Hack for reducing objects resolution when the system is big
         self._resolution = int(np.sqrt(3000000.0 / self._n_atoms))
@@ -637,7 +678,10 @@ def set_reader(self, reader, frame=0):
         # this returs a list of indices, mapping colours to atoms
 
         self._atom_scales = np.array(
-            [CHEMICAL_ELEMENTS[at]["vdw_radius"] for at in self._atoms]
+            [
+                CHEMICAL_ELEMENTS.get_atom_property(at, "vdw_radius")
+                for at in self._atoms
+            ]
         ).astype(np.float32)
 
         scalars = ndarray_to_vtkarray(
@@ -645,6 +689,7 @@ def set_reader(self, reader, frame=0):
         )
 
         self._polydata = vtk.vtkPolyData()
+        self._uc_polydata = vtk.vtkPolyData()
         self._polydata.GetPointData().SetScalars(scalars)
 
         self.set_coordinates(frame)
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py
index a0bca53e2d..77d22b6e07 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/JobTab.py
@@ -69,7 +69,9 @@ def set_current_trajectory(self, new_name: str) -> None:
         )
         # The combobox was changed we need to update the action
         # widgets with the new trajectory
-        self.action.set_trajectory(path=None, trajectory=traj_model._nodes[node_number])
+        self.action.set_trajectory(
+            path=None, trajectory=traj_model._nodes[node_number][0]
+        )
         current_item = self._core.current_item()
         if current_item is not None:
             # we only update the widget if a job is selected from the
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py
index d4231a16af..caea47f689 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/TrajectoryTab.py
@@ -58,7 +58,7 @@ def load_trajectory(self):
             except Exception as e:
                 self._core.error(repr(e))
             else:
-                self._core._model.append_object((fname[0], short_name))
+                self._core._model.append_object(((fname[0], data), short_name))
 
     @classmethod
     def standard_instance(cls):
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py
index ddfdb06340..9142f992e3 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Views/TrajectoryView.py
@@ -23,7 +23,7 @@
 
 
 class TrajectoryView(QListView):
-    item_details = Signal(object)
+    item_details = Signal(tuple)
     item_name = Signal(str)
     error = Signal(str)
 
@@ -53,7 +53,7 @@ def deleteNode(self):
         model = self.model()
         index = self.currentIndex()
         model.removeRow(index.row())
-        self.item_details.emit("")
+        self.item_details.emit(("", None))
 
     @Slot(QModelIndex)
     def item_picked(self, index: QModelIndex):
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
index a0d4b658cf..d58d433414 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/Action.py
@@ -138,7 +138,6 @@ def update_panel(self, job_name: str) -> None:
         job_instance.build_configuration()
         settings = job_instance.settings
         self._job_instance = job_instance
-        print(f"Settings {settings}")
         print(f"Configuration {job_instance.configuration}")
         if "trajectory" in settings.keys():
             if self._input_trajectory is None:
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/TrajectoryInfo.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/TrajectoryInfo.py
index 3652702c45..e104ad9372 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/TrajectoryInfo.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/TrajectoryInfo.py
@@ -16,20 +16,8 @@ def __init__(self, *args, **kwargs):
         self.setOpenExternalLinks(True)
 
     @Slot(object)
-    def update_panel(self, fullpath: object):
-        if len(fullpath) > 0:
-            try:
-                incoming = HDFTrajectoryInputData(fullpath)
-            except:
-                text = f"Could not load trajectory: {fullpath}"
-                filtered = self.filter(text)
-                self.setHtml(filtered)
-                return
-        else:
-            text = ""
-            filtered = self.filter(text)
-            self.setHtml(filtered)
-            return
+    def update_panel(self, data: tuple):
+        fullpath, incoming = data
         try:
             text = incoming.info()  # this is from a trajectory object
         except AttributeError:
diff --git a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/View3D.py b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/View3D.py
index 989342bc10..139c6d00b3 100644
--- a/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/View3D.py
+++ b/MDANSE_GUI/Src/MDANSE_GUI/Tabs/Visualisers/View3D.py
@@ -21,17 +21,16 @@ def __init__(self, *args, **kwargs):
         self._viewer = viewer
         self._controls = controls
 
-    @Slot(object)
-    def update_panel(self, fullpath: object):
-        print(fullpath)
-        if fullpath == "":
-            # a trajectory was deleted and the view emitted an empty
-            # string we need to clear the panel
+    @Slot(tuple)
+    def update_panel(self, data: tuple):
+        fullpath, incoming = data
+        if fullpath == "" or data is None:
+            # a trajectory was deleted we need to clear the panel
             self._viewer.clear_panel()
             return
 
         try:
-            self._viewer._new_trajectory(fullpath)
+            self._viewer._new_trajectory_object(fullpath, incoming)
         except AttributeError:
             self.error.emit(f"3D View could not visualise {fullpath}")
             self._viewer.clear_trajectory()