diff --git a/doc/conf.py b/doc/conf.py
index cbfb38f77..1b3c05fab 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -195,7 +195,7 @@
     "within_subsection_order": FileNameSortKey,
     # Do not run example scripts with a trailing '_noexec'
     "filename_pattern": "^((?!_noexec).)*$",
-    "ignore_pattern": r"(.*ignore\.py)|(.*pymol\.py)",
+    "ignore_pattern": r"(.*ignore\.py)",
     "download_all_examples": False,
     # Never report run time
     "min_reported_time": sys.maxsize,
diff --git a/doc/examples/scripts/structure/alphabet/structure_search.png b/doc/examples/scripts/structure/alphabet/structure_search.png
deleted file mode 100644
index d24320157..000000000
Binary files a/doc/examples/scripts/structure/alphabet/structure_search.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/alphabet/structure_search.py b/doc/examples/scripts/structure/alphabet/structure_search.py
index 696c54627..edf83dc15 100644
--- a/doc/examples/scripts/structure/alphabet/structure_search.py
+++ b/doc/examples/scripts/structure/alphabet/structure_search.py
@@ -24,6 +24,7 @@
 import numpy as np
 import biotite
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.sequence as seq
 import biotite.sequence.align as align
 import biotite.sequence.graphics as graphics
@@ -374,8 +375,20 @@ def filter_undefined_spans(sequence, min_length):
 _, transform = struc.superimpose(query_anchors, target_anchors)
 # Apply this transformation to full structure
 target_chain = transform.apply(target_chain)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "structure_search_pymol.py"
+
+# Visualization with PyMOL
+pymol_interface.cmd.set("cartoon_rect_length", 1.0)
+pymol_interface.cmd.set("depth_cue", 0)
+pymol_interface.cmd.set("cartoon_cylindrical_helices", 1)
+pymol_interface.cmd.set("cartoon_helix_radius", 1.5)
+pymol_query = pymol_interface.PyMOLObject.from_structure(query_chain)
+pymol_target = pymol_interface.PyMOLObject.from_structure(target_chain)
+pymol_query.show_as("cartoon")
+pymol_target.show_as("cartoon")
+pymol_query.color("biotite_lightgreen")
+pymol_target.color("biotite_lightorange")
+pymol_query.orient()
+pymol_interface.show((1500, 1000))
 # sphinx_gallery_thumbnail_number = 3
 
 ########################################################################################
diff --git a/doc/examples/scripts/structure/alphabet/structure_search_pymol.py b/doc/examples/scripts/structure/alphabet/structure_search_pymol.py
deleted file mode 100644
index 0e8434d58..000000000
--- a/doc/examples/scripts/structure/alphabet/structure_search_pymol.py
+++ /dev/null
@@ -1,26 +0,0 @@
-import ammolite
-from matplotlib.colors import to_rgb
-import biotite
-
-PNG_SIZE = (1000, 750)
-
-ammolite.cmd.set("cartoon_rect_length", 1.0)
-ammolite.cmd.set("depth_cue", 0)
-ammolite.cmd.set("cartoon_cylindrical_helices", 1)
-ammolite.cmd.set("cartoon_helix_radius", 1.5)
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-pymol_query = ammolite.PyMOLObject.from_structure(query_chain)
-pymol_target = ammolite.PyMOLObject.from_structure(target_chain)
-pymol_query.show_as("cartoon")
-pymol_target.show_as("cartoon")
-pymol_query.color("biotite_lightgreen")
-pymol_target.color("biotite_lightorange")
-pymol_query.orient()
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/contacts/contact_sites.png b/doc/examples/scripts/structure/contacts/contact_sites.png
deleted file mode 100644
index be2a5b554..000000000
Binary files a/doc/examples/scripts/structure/contacts/contact_sites.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/contacts/contact_sites.py b/doc/examples/scripts/structure/contacts/contact_sites.py
index d4723426b..f4509c346 100644
--- a/doc/examples/scripts/structure/contacts/contact_sites.py
+++ b/doc/examples/scripts/structure/contacts/contact_sites.py
@@ -15,6 +15,7 @@
 
 import numpy as np
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.io.pdbx as pdbx
 
@@ -25,7 +26,8 @@
 
 # Fetch and load structure
 pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("2or1", "bcif"))
-structure = pdbx.get_structure(pdbx_file, model=1)
+structure = pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
+structure = structure[~struc.filter_solvent(structure)]
 
 
 # Separate structure into the DNA and the two identical protein chains
@@ -70,5 +72,41 @@
     res_name = protein_l.res_name[protein_l.res_id == res_id][0]
     print(res_name.capitalize() + str(res_id))
 
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "contact_sites_pymol.py"
+
+# Visualization with PyMOL
+pymol_obj = pymol_interface.PyMOLObject.from_structure(structure)
+pymol_obj.color("gray", np.isin(structure.chain_id, ["A", "B"]))
+pymol_obj.color("biotite_brightorange", structure.chain_id == "L")
+pymol_obj.color("biotite_lightgreen", structure.chain_id == "R")
+# Set view
+pymol_interface.cmd.set_view(
+    (
+        -0.044524662,
+        0.767611504,
+        0.639355302,
+        0.998693943,
+        0.018437184,
+        0.047413416,
+        0.024606399,
+        0.640637815,
+        -0.767439663,
+        0.000000000,
+        0.000000000,
+        -115.614288330,
+        56.031833649,
+        23.317802429,
+        3.761308193,
+        73.517341614,
+        157.711288452,
+        -20.000000000,
+    )
+)
+# Highlight contacts
+residue_mask = np.isin(structure.res_id, common_ids)
+pymol_obj.show("sticks", np.isin(structure.chain_id, ["L", "R"]) & residue_mask)
+for chain, color in zip(("L", "R"), ("biotite_dimorange", "biotite_darkgreen")):
+    pymol_obj.color(
+        color,
+        (structure.chain_id == chain) & (structure.atom_name != "CA") & residue_mask,
+    )
+pymol_interface.show((1500, 800))
diff --git a/doc/examples/scripts/structure/contacts/contact_sites_pymol.py b/doc/examples/scripts/structure/contacts/contact_sites_pymol.py
deleted file mode 100644
index a4eb3622e..000000000
--- a/doc/examples/scripts/structure/contacts/contact_sites_pymol.py
+++ /dev/null
@@ -1,64 +0,0 @@
-import ammolite
-import numpy as np
-from matplotlib.colors import to_rgb
-import biotite
-import biotite.structure as struc
-
-PNG_SIZE = (1000, 550)
-
-# General configuration
-ammolite.cmd.set("cartoon_side_chain_helper", 1)
-ammolite.cmd.set("cartoon_discrete_colors", 1)
-ammolite.cmd.set("depth_cue", 0)
-ammolite.cmd.set("cartoon_oval_length", 0.8)
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-# Add bonds to structure and convert to PyMOL
-structure = structure[~struc.filter_solvent(structure)]
-structure.bonds = struc.connect_via_residue_names(structure)
-pymol_obj = ammolite.PyMOLObject.from_structure(structure)
-
-# Set overall colors
-pymol_obj.color("gray", np.isin(structure.chain_id, ["A", "B"]))
-pymol_obj.color("biotite_brightorange", structure.chain_id == "L")
-pymol_obj.color("biotite_lightgreen", structure.chain_id == "R")
-
-# Set view
-ammolite.cmd.set_view(
-    (
-        -0.044524662,
-        0.767611504,
-        0.639355302,
-        0.998693943,
-        0.018437184,
-        0.047413416,
-        0.024606399,
-        0.640637815,
-        -0.767439663,
-        0.000000000,
-        0.000000000,
-        -115.614288330,
-        56.031833649,
-        23.317802429,
-        3.761308193,
-        73.517341614,
-        157.711288452,
-        -20.000000000,
-    )
-)
-
-# Highlight contacts
-residue_mask = np.isin(structure.res_id, common_ids)
-pymol_obj.show("sticks", np.isin(structure.chain_id, ["L", "R"]) & residue_mask)
-for chain, color in zip(("L", "R"), ("biotite_dimorange", "biotite_darkgreen")):
-    pymol_obj.color(
-        color,
-        (structure.chain_id == chain) & (structure.atom_name != "CA") & residue_mask,
-    )
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/contacts/leaflet.png b/doc/examples/scripts/structure/contacts/leaflet.png
deleted file mode 100644
index 5ab551ac8..000000000
Binary files a/doc/examples/scripts/structure/contacts/leaflet.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/contacts/leaflet.py b/doc/examples/scripts/structure/contacts/leaflet.py
index 1a8655ecd..828b06af2 100644
--- a/doc/examples/scripts/structure/contacts/leaflet.py
+++ b/doc/examples/scripts/structure/contacts/leaflet.py
@@ -25,6 +25,7 @@
 from tempfile import NamedTemporaryFile
 import networkx as nx
 import numpy as np
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.io as strucio
 
@@ -111,7 +112,32 @@ def find_leaflets(structure, head_atom_mask, cutoff_distance=15.0, periodic=Fals
 # Save marked lipids to structure file
 temp = NamedTemporaryFile(suffix=".pdb")
 strucio.save_structure(temp.name, structure)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "leaflet_pymol.py"
-
 temp.close()
+
+
+# Visualization with PyMOL
+pymol_interface.cmd.set("sphere_scale", 1.5)
+# Remove hydrogen and water
+structure = structure[(structure.element != "H") & (structure.res_name != "TIP")]
+structure.bonds = struc.connect_via_distances(structure)
+pymol_obj = pymol_interface.PyMOLObject.from_structure(structure)
+# Configure lipid tails
+pymol_obj.color("biotite_lightgreen", structure.chain_id == "A")
+pymol_obj.color("biotite_brightorange", structure.chain_id == "B")
+pymol_obj.show("sticks", np.isin(structure.chain_id, ("A", "B")))
+# Configure lipid heads
+pymol_obj.color(
+    "biotite_darkgreen", (structure.chain_id == "A") & (structure.atom_name == "P")
+)
+pymol_obj.color(
+    "biotite_dimorange", (structure.chain_id == "B") & (structure.atom_name == "P")
+)
+pymol_obj.show(
+    "spheres", np.isin(structure.chain_id, ("A", "B")) & (structure.atom_name == "P")
+)
+# Adjust camera
+pymol_obj.orient()
+pymol_interface.cmd.turn("x", 90)
+pymol_obj.zoom(buffer=-10)
+# Display
+pymol_interface.show((1500, 1000))
diff --git a/doc/examples/scripts/structure/contacts/leaflet_pymol.py b/doc/examples/scripts/structure/contacts/leaflet_pymol.py
deleted file mode 100644
index 59b2e98a0..000000000
--- a/doc/examples/scripts/structure/contacts/leaflet_pymol.py
+++ /dev/null
@@ -1,46 +0,0 @@
-import ammolite
-import numpy as np
-from matplotlib.colors import to_rgb
-import biotite
-import biotite.structure as struc
-
-PNG_SIZE = (1000, 700)
-
-
-# General configuration
-ammolite.cmd.set("sphere_scale", 1.5)
-ammolite.cmd.set("depth_cue", 0)
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-# Remove hydrogen and water and convert to PyMOL
-structure = structure[(structure.element != "H") & (structure.res_name != "TIP")]
-structure.bonds = struc.connect_via_distances(structure)
-pymol_obj = ammolite.PyMOLObject.from_structure(structure)
-
-# Configure lipid tails
-pymol_obj.color("biotite_lightgreen", structure.chain_id == "A")
-pymol_obj.color("biotite_brightorange", structure.chain_id == "B")
-pymol_obj.show("sticks", np.isin(structure.chain_id, ("A", "B")))
-
-# Configure lipid heads
-pymol_obj.color(
-    "biotite_darkgreen", (structure.chain_id == "A") & (structure.atom_name == "P")
-)
-pymol_obj.color(
-    "biotite_dimorange", (structure.chain_id == "B") & (structure.atom_name == "P")
-)
-pymol_obj.show(
-    "spheres", np.isin(structure.chain_id, ("A", "B")) & (structure.atom_name == "P")
-)
-
-# Adjust camera
-pymol_obj.orient()
-ammolite.cmd.turn("x", 90)
-pymol_obj.zoom(buffer=-10)
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/misc/biological_assembly.png b/doc/examples/scripts/structure/misc/biological_assembly.png
deleted file mode 100644
index 1290b2e49..000000000
Binary files a/doc/examples/scripts/structure/misc/biological_assembly.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/misc/biological_assembly.py b/doc/examples/scripts/structure/misc/biological_assembly.py
index 83586dcca..7ca9959d7 100644
--- a/doc/examples/scripts/structure/misc/biological_assembly.py
+++ b/doc/examples/scripts/structure/misc/biological_assembly.py
@@ -28,8 +28,7 @@
 `this page <https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies>`_.
 
 In this example, we will create the complete biological assembly of the
-capsid from the *Sulfolobus turreted icosahedral virus*
-- a hetero 1080-mer!
+capsid from the lambda phage.
 
 At first we will check, which assemblies are available to us.
 """
@@ -37,13 +36,15 @@
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
-from tempfile import NamedTemporaryFile
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
-import biotite.structure.io as strucio
 import biotite.structure.io.pdbx as pdbx
 
-pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("3J31", "bcif"))
+PDB_ID = "7VII"
+
+
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
 
 assemblies = pdbx.list_assemblies(pdbx_file)
 print("ID    name")
@@ -61,19 +62,38 @@
 # It returns the chosen assembly as :class:`AtomArray`.
 # Note that the assembly ID is a string, not an integer.
 
-biological_unit = pdbx.get_assembly(pdbx_file, assembly_id="1", model=1)
-print("Number of protein chains:", struc.get_chain_count(biological_unit))
+assembly = pdbx.get_assembly(
+    pdbx_file,
+    assembly_id="1",
+    model=1,
+    # To identify later which atoms belong to which protein type
+    extra_fields=["label_entity_id"],
+)
+
+print("Number of protein chains:", struc.get_chain_count(assembly))
 
 ########################################################################
-# Now we could do some analysis on the biological unit.
-# But for this example we will simply save the entire assembly as *PDB*
-# file for later visualization.
+# The assembly consists of two different protein types, so called entities.
+# Each entity may be represented by multiple chain IDs.
 
-# For brevity, save only CA atoms to file for visualization
-biological_unit = biological_unit[biological_unit.atom_name == "CA"]
-temp = NamedTemporaryFile(suffix=".cif")
-strucio.save_structure(temp.name, biological_unit)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "biological_assembly_pymol.py"
+entity_info = pdbx_file.block["entity"]
+print("ID    description")
+print()
+for entity_id, description in zip(
+    entity_info["id"].as_array(), entity_info["pdbx_description"].as_array()
+):
+    print(f"{entity_id:2}    {description}")
+
+########################################################################
+# Now we could do some analysis on the biological unit.
+# But for this example we will visualize the entire assembly.
 
-temp.close()
+# Show capsid structure as CA spheres to increase rendering speed
+assembly = assembly[assembly.atom_name == "CA"]
+pymol_object = pymol_interface.PyMOLObject.from_structure(assembly)
+pymol_object.color("biotite_dimgreen", assembly.label_entity_id == "1")
+pymol_object.color("biotite_lightorange", assembly.label_entity_id == "2")
+pymol_object.set("sphere_scale", 2.0)
+pymol_object.show_as("spheres")
+pymol_object.zoom(buffer=25)
+pymol_interface.show((1500, 1500))
diff --git a/doc/examples/scripts/structure/misc/biological_assembly_pymol.py b/doc/examples/scripts/structure/misc/biological_assembly_pymol.py
deleted file mode 100644
index 3175b4eb9..000000000
--- a/doc/examples/scripts/structure/misc/biological_assembly_pymol.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import ammolite
-import matplotlib.pyplot as plt
-import numpy as np
-
-PNG_SIZE = (1000, 1000)
-
-
-# Convert to PyMOL
-# Skip adding bonds, since all atoms but CA are filtered out
-pymol_obj = ammolite.PyMOLObject.from_structure(biological_unit)
-
-# Set spheres and color
-pymol_obj.zoom(buffer=50)
-ammolite.cmd.set("sphere_scale", 1.5)
-pymol_obj.show_as("spheres")
-chain_ids = np.unique(biological_unit.chain_id)
-for chain_id, color in zip(chain_ids, plt.get_cmap("tab20").colors):
-    pymol_obj.color(color, biological_unit.chain_id == chain_id)
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/misc/homolog_superimposition.png b/doc/examples/scripts/structure/misc/homolog_superimposition.png
deleted file mode 100644
index 54677db1f..000000000
Binary files a/doc/examples/scripts/structure/misc/homolog_superimposition.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/misc/homolog_superimposition.py b/doc/examples/scripts/structure/misc/homolog_superimposition.py
index 4db689581..b97a4b892 100644
--- a/doc/examples/scripts/structure/misc/homolog_superimposition.py
+++ b/doc/examples/scripts/structure/misc/homolog_superimposition.py
@@ -2,9 +2,7 @@
 Superimposition of homologous protein structures
 ================================================
 
-This script superimposes the structure of a streptavidin monomer
-into an avidin monomer.
-The visualization was conducted with PyMOL.
+This script superimposes the structure of a streptavidin monomer into an avidin monomer.
 
 - *Green*:  Avidin
 - *Orange*: Strepatvidin
@@ -14,6 +12,7 @@
 # License: BSD 3 clause
 
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.io.pdbx as pdbx
 
@@ -32,5 +31,13 @@ def _extract_monomer(complex):
 )
 
 streptavidin, _, _, _ = struc.superimpose_homologs(avidin, streptavidin)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "homolog_superimposition_pymol.py"
+
+# Visualization with PyMOL
+pymol_avidin = pymol_interface.PyMOLObject.from_structure(avidin)
+pymol_streptavidin = pymol_interface.PyMOLObject.from_structure(streptavidin)
+pymol_avidin.color("biotite_lightgreen")
+pymol_streptavidin.color("biotite_lightorange")
+pymol_avidin.show_as("cartoon")
+pymol_streptavidin.show_as("cartoon")
+pymol_avidin.orient()
+pymol_interface.show((1500, 1000))
diff --git a/doc/examples/scripts/structure/misc/homolog_superimposition_pymol.py b/doc/examples/scripts/structure/misc/homolog_superimposition_pymol.py
deleted file mode 100644
index 1760d527e..000000000
--- a/doc/examples/scripts/structure/misc/homolog_superimposition_pymol.py
+++ /dev/null
@@ -1,30 +0,0 @@
-import ammolite
-from matplotlib.colors import to_rgb
-import biotite
-
-PNG_SIZE = (1000, 750)
-
-# General configuration
-ammolite.cmd.set("cartoon_oval_length", 0.8)
-ammolite.cmd.set("depth_cue", 0)
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-# Convert to PyMOL
-pymol_avidin = ammolite.PyMOLObject.from_structure(avidin)
-pymol_streptavidin = ammolite.PyMOLObject.from_structure(streptavidin)
-
-# Set overall colors
-pymol_avidin.color("biotite_lightgreen")
-pymol_streptavidin.color("biotite_lightorange")
-
-# Set view
-pymol_avidin.show_as("cartoon")
-pymol_streptavidin.show_as("cartoon")
-pymol_avidin.orient()
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/modeling/docking.png b/doc/examples/scripts/structure/modeling/docking.png
deleted file mode 100644
index f468cf380..000000000
Binary files a/doc/examples/scripts/structure/modeling/docking.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/modeling/docking.py b/doc/examples/scripts/structure/modeling/docking.py
index eb9a3fcfa..efb1031f5 100644
--- a/doc/examples/scripts/structure/modeling/docking.py
+++ b/doc/examples/scripts/structure/modeling/docking.py
@@ -33,6 +33,7 @@
 from scipy.stats import spearmanr
 import biotite.application.autodock as autodock
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
 import biotite.structure.info as info
 import biotite.structure.io.pdbx as pdbx
@@ -145,6 +146,36 @@
 ref_ligand = ref_ligand[ref_ligand.element != "H"]
 docked_ligand = docked_ligand[docked_ligand.element != "H"]
 
-# Visualization with PyMOL...
+
+# Visualization with PyMOL
 # sphinx_gallery_thumbnail_number = 2
-# sphinx_gallery_ammolite_script = "docking_pymol.py"
+pymol_receptor = pymol_interface.PyMOLObject.from_structure(receptor)
+pymol_ref_ligand = pymol_interface.PyMOLObject.from_structure(ref_ligand)
+pymol_docked_ligand = pymol_interface.PyMOLObject.from_structure(docked_ligand)
+# Visualize receptor as surface
+pymol_receptor.show_as("surface")
+pymol_receptor.color("white")
+pymol_interface.cmd.set("surface_quality", 2)
+# Visualize as stick model
+pymol_interface.cmd.set("stick_radius", 0.15)
+pymol_interface.cmd.set("sphere_scale", 0.25)
+pymol_interface.cmd.set("sphere_quality", 4)
+# The reference is a blue 'shadow'
+pymol_ref_ligand.show("spheres")
+pymol_ref_ligand.color("blue")
+pymol_ref_ligand.set("stick_color", "blue")
+pymol_ref_ligand.set("sphere_transparency", 0.6)
+pymol_ref_ligand.set_bond("stick_transparency", 0.6)
+# Visualize docked model
+pymol_docked_ligand.show("spheres")
+pymol_docked_ligand.color("gray", docked_ligand.element == "C")
+pymol_docked_ligand.set("stick_color", "grey80")
+# Adjust camera
+pymol_docked_ligand.orient()
+pymol_interface.cmd.rotate("y", 180)
+pymol_interface.cmd.rotate("x", -15)
+pymol_docked_ligand.zoom(buffer=-1)
+pymol_interface.cmd.set("depth_cue", 0)
+pymol_interface.cmd.clip("slab", 100)
+# Display
+pymol_interface.show((1500, 600))
diff --git a/doc/examples/scripts/structure/modeling/docking_pymol.py b/doc/examples/scripts/structure/modeling/docking_pymol.py
deleted file mode 100644
index 8f9adc263..000000000
--- a/doc/examples/scripts/structure/modeling/docking_pymol.py
+++ /dev/null
@@ -1,50 +0,0 @@
-import ammolite
-from matplotlib.colors import to_rgb
-import biotite
-
-PNG_SIZE = (1000, 400)
-
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-# Convert to PyMOL
-pymol_receptor = ammolite.PyMOLObject.from_structure(receptor)
-pymol_ref_ligand = ammolite.PyMOLObject.from_structure(ref_ligand)
-pymol_docked_ligand = ammolite.PyMOLObject.from_structure(docked_ligand)
-
-# Visualize receptor as surface
-pymol_receptor.show_as("surface")
-pymol_receptor.color("white")
-ammolite.cmd.set("surface_quality", 2)
-
-# Visualize as stick model
-ammolite.cmd.set("stick_radius", 0.15)
-ammolite.cmd.set("sphere_scale", 0.25)
-ammolite.cmd.set("sphere_quality", 4)
-
-# The reference is a blue 'shadow'
-REF_COLOR = "skyblue"
-REF_ALPHA = 0.4
-pymol_ref_ligand.show("spheres")
-pymol_ref_ligand.color(REF_COLOR)
-pymol_ref_ligand.set("stick_color", REF_COLOR)
-pymol_ref_ligand.set("sphere_transparency", 1 - REF_ALPHA)
-pymol_ref_ligand.set_bond("stick_transparency", 1 - REF_ALPHA)
-
-pymol_docked_ligand.show("spheres")
-pymol_docked_ligand.color("black", docked_ligand.element == "C")
-pymol_docked_ligand.set("stick_color", "grey80")
-
-# Adjust camera
-pymol_docked_ligand.orient()
-ammolite.cmd.rotate("y", 180)
-ammolite.cmd.rotate("x", -15)
-pymol_docked_ligand.zoom(buffer=-1)
-ammolite.cmd.set("depth_cue", 0)
-ammolite.cmd.clip("slab", 100)
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)
diff --git a/doc/examples/scripts/structure/modeling/normal_modes.gif b/doc/examples/scripts/structure/modeling/normal_modes.gif
deleted file mode 100644
index fda4f7cde..000000000
Binary files a/doc/examples/scripts/structure/modeling/normal_modes.gif and /dev/null differ
diff --git a/doc/examples/scripts/structure/modeling/normal_modes.py b/doc/examples/scripts/structure/modeling/normal_modes.py
index ac760c459..745d86d85 100644
--- a/doc/examples/scripts/structure/modeling/normal_modes.py
+++ b/doc/examples/scripts/structure/modeling/normal_modes.py
@@ -33,12 +33,11 @@
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
-from tempfile import NamedTemporaryFile
 import numpy as np
 from numpy import newaxis
 import biotite.database.rcsb as rcsb
+import biotite.interface.pymol as pymol_interface
 import biotite.structure as struc
-import biotite.structure.io as strucio
 import biotite.structure.io.pdbx as pdbx
 
 # A CSV file containing the eigenvectors for the CA atoms
@@ -58,7 +57,7 @@
 
 # Load structure
 pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))
-structure = pdbx.get_structure(pdbx_file, model=1)
+structure = pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
 
 
 # Filter first peptide chain
@@ -106,9 +105,33 @@
 
 # An atom array stack containing all frames
 oscillating_structure = struc.from_template(protein_chain, oscillation)
-# Save as PDB for rendering a video with PyMOL
-temp = NamedTemporaryFile(suffix=".pdb")
-strucio.save_structure(temp.name, oscillating_structure)
-# sphinx_gallery_static_image = "normal_modes.gif"
 
-temp.close()
+# Visualization with PyMOL
+pymol_object = pymol_interface.PyMOLObject.from_structure(oscillating_structure)
+pymol_object.color("biotite_lightgreen", oscillating_structure.chain_id == "A")
+# Set custom view
+pymol_interface.cmd.set_view(
+    (
+        0.605540633,
+        0.363677770,
+        -0.707855821,
+        -0.416691631,
+        0.902691007,
+        0.107316799,
+        0.678002179,
+        0.229972601,
+        0.698157668,
+        0.000000000,
+        0.000000000,
+        -115.912551880,
+        32.098876953,
+        31.005725861,
+        78.377349854,
+        89.280677795,
+        142.544403076,
+        -20.000000000,
+    )
+)
+# Prepare output video frames
+pymol_interface.cmd.mset()
+pymol_interface.play((600, 600))
diff --git a/doc/examples/scripts/structure/modeling/normal_modes_pymol.py b/doc/examples/scripts/structure/modeling/normal_modes_pymol.py
deleted file mode 100644
index 1c0ad0e2c..000000000
--- a/doc/examples/scripts/structure/modeling/normal_modes_pymol.py
+++ /dev/null
@@ -1,53 +0,0 @@
-from os.path import isdir, join
-from pymol import cmd
-
-INPUT_STRUCTURE = "normal_modes.pdb"
-OUTPUT_DIR = "normal_modes"
-
-
-# Load structure and remove water
-cmd.load(INPUT_STRUCTURE)
-
-# Add secondary structure
-cmd.dss()
-
-# Define colors
-cmd.set_color("biotite_lightgreen", [111 / 255, 222 / 255, 76 / 255])
-
-# Set overall colors
-cmd.color("biotite_lightgreen", "chain A")
-
-# Set view
-cmd.set_view(
-    (
-        0.605540633,
-        0.363677770,
-        -0.707855821,
-        -0.416691631,
-        0.902691007,
-        0.107316799,
-        0.678002179,
-        0.229972601,
-        0.698157668,
-        0.000000000,
-        0.000000000,
-        -115.912551880,
-        32.098876953,
-        31.005725861,
-        78.377349854,
-        89.280677795,
-        142.544403076,
-        -20.000000000,
-    )
-)
-
-# Prepare output video frames
-cmd.mset()
-cmd.set("ray_shadows", 0)
-if not isdir(OUTPUT_DIR):
-    os.mkdir(OUTPUT_DIR)
-cmd.mpng(join(OUTPUT_DIR, "img_"), mode=2, width=600, height=600)
-
-
-# Render animated GIF
-# convert -delay 3 -loop 0 -dispose 2 normal_modes/*.png normal_modes.gif
diff --git a/doc/examples/scripts/structure/protein/peptide_assembly.png b/doc/examples/scripts/structure/protein/peptide_assembly.png
deleted file mode 100644
index f4f1b1872..000000000
Binary files a/doc/examples/scripts/structure/protein/peptide_assembly.png and /dev/null differ
diff --git a/doc/examples/scripts/structure/protein/peptide_assembly.py b/doc/examples/scripts/structure/protein/peptide_assembly.py
index de9f24704..9b3c371a8 100644
--- a/doc/examples/scripts/structure/protein/peptide_assembly.py
+++ b/doc/examples/scripts/structure/protein/peptide_assembly.py
@@ -22,13 +22,12 @@
 # License: BSD 3 clause
 
 import itertools
-from tempfile import NamedTemporaryFile
 import numpy as np
 from numpy.linalg import norm
+import biotite.interface.pymol as pymol_interface
 import biotite.sequence as seq
 import biotite.structure as struc
 import biotite.structure.info as info
-import biotite.structure.io as strucio
 
 C_N_LENGTH = 1.34
 N_CA_LENGTH = 1.46
@@ -40,7 +39,7 @@
 
 # Reference peptide bond atom coordinates taken from 1l2y:
 # CA, C, N, O, H
-PEPTIDE_COORD = np.array(
+peptide_coord = np.array(
     [
         [-8.608, 3.135, -1.618],
         [-7.117, 2.964, -1.897],
@@ -70,8 +69,8 @@ def create_raw_backbone_coord(number_of_res):
         else:
             # Rotate about z-axis -> backbone lies in z-plane
             rot_axis = [0, 0, angle_direction]
-            # Calculate the coordinates of a new atoms by rotating the
-            # previous bond by the given angle
+            # Calculate the coordinates of a new atoms by rotating the previous
+            # bond by the given angle
             new_coord = struc.rotate_about_axis(
                 coord[i - 2],
                 axis=rot_axis,
@@ -116,46 +115,42 @@ def append_residue(chain, residue):
     return chain
 
 
-def assemble_peptide(sequence):
-    res_names = [seq.ProteinSequence.convert_letter_1to3(r) for r in sequence]
-    backbone_coord = create_raw_backbone_coord(len(sequence))
-
-    chain = struc.AtomArray(0)
-    for i, res_name in enumerate(res_names):
-        residue = info.residue(res_name)
-
-        # Superimpose residue to corresponding backbone coordinates
+sequence = seq.ProteinSequence("WRKFWKYLK")
+res_names = [seq.ProteinSequence.convert_letter_1to3(r) for r in sequence]
+backbone_coord = create_raw_backbone_coord(len(sequence))
+
+
+chain = struc.AtomArray(0)
+for i, res_name in enumerate(res_names):
+    residue = info.residue(res_name)
+
+    # Superimpose residue to corresponding backbone coordinates
+    _, transformation = struc.superimpose(
+        backbone_coord[3 * i : 3 * i + 3],
+        residue.coord[np.isin(residue.atom_name, ["N", "CA", "C"])],
+    )
+    residue = transformation.apply(residue)
+
+    chain = append_residue(chain, residue)
+
+    if i != 0:
+        # Fix positions of peptide hydrogen and oxygen atom
+        ca_i, c_i, o_i = [
+            np.where(chain.atom_name == atom_name)[0][-2]
+            for atom_name in ["CA", "C", "O"]
+        ]
+        n_i, h_i = [
+            np.where(chain.atom_name == atom_name)[0][-1] for atom_name in ["N", "H"]
+        ]
         _, transformation = struc.superimpose(
-            backbone_coord[3 * i : 3 * i + 3],
-            residue.coord[np.isin(residue.atom_name, ["N", "CA", "C"])],
+            chain.coord[[ca_i, c_i, n_i]], peptide_coord[:3]
         )
-        residue = transformation.apply(residue)
-
-        chain = append_residue(chain, residue)
-
-        if i != 0:
-            # Fix positions of peptide hydrogen and oxygen atom
-            ca_i, c_i, o_i = [
-                np.where(chain.atom_name == atom_name)[0][-2]
-                for atom_name in ["CA", "C", "O"]
-            ]
-            n_i, h_i = [
-                np.where(chain.atom_name == atom_name)[0][-1]
-                for atom_name in ["N", "H"]
-            ]
-            _, transformation = struc.superimpose(
-                chain.coord[[ca_i, c_i, n_i]], PEPTIDE_COORD[:3]
-            )
-            chain.coord[[o_i, h_i]] = transformation.apply(PEPTIDE_COORD[3:])
-    return chain
-
+        chain.coord[[o_i, h_i]] = transformation.apply(peptide_coord[3:])
 
-# Sequence of an antimicrobial peptide
-sequence = seq.ProteinSequence("WRKFWKYLK")
-chain = assemble_peptide(sequence)
-out_file = NamedTemporaryFile(suffix=".bcif", delete=False)
-strucio.save_structure(out_file.name, chain)
-# Visualization with PyMOL...
-# sphinx_gallery_ammolite_script = "peptide_assembly_pymol.py"
 
-out_file.close()
+# Visualization with PyMOL
+pymol_object = pymol_interface.PyMOLObject.from_structure(chain)
+pymol_object.show_as("sticks")
+pymol_object.orient()
+pymol_object.zoom(buffer=-7.5)
+pymol_interface.show((1500, 600))
diff --git a/doc/examples/scripts/structure/protein/peptide_assembly_pymol.py b/doc/examples/scripts/structure/protein/peptide_assembly_pymol.py
deleted file mode 100644
index 7afdc6a06..000000000
--- a/doc/examples/scripts/structure/protein/peptide_assembly_pymol.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import ammolite
-from matplotlib.colors import to_rgb
-import biotite
-import biotite.structure as struc
-
-PNG_SIZE = (1000, 400)
-
-
-# Define colors
-for color_name, color_value in biotite.colors.items():
-    ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
-
-# Convert to PyMOL
-chain.bonds = struc.connect_via_distances(chain)
-pymol_obj = ammolite.PyMOLObject.from_structure(chain)
-
-# Visualize as stick model
-pymol_obj.show_as("sticks")
-pymol_obj.color("biotite_lightgreen", (chain.res_id % 2 == 0) & (chain.element == "C"))
-pymol_obj.color("biotite_dimgreen", (chain.res_id % 2 != 0) & (chain.element == "C"))
-ammolite.cmd.set("depth_cue", 0)
-
-# Adjust camera
-pymol_obj.orient()
-pymol_obj.zoom(buffer=-7.5)
-
-# Save image
-ammolite.cmd.ray(*PNG_SIZE)
-ammolite.cmd.png(__image_destination__)