Example gallery

9.9 s

Blend one protein through cartoon, ribbon, ball-and-stick, and solvent-excluded surface views.

11 s

Orbit and zoom the camera, ease it onto the helix, and return to the whole protein.

10 s

Fade proteins in and out, rotate them about any axis, and shift or scale them in the scene.

7.5 s

Give concurrent actions their own durations and delays inside one play() call.

11 s

Render all 21 chains of GroEL–GroES, ghost all but one subunit, and look down the barrel.

8.4 s

Blend a tetramer between secondary-structure, rainbow, chain, and hydropathy palettes.

8.5 s

Tint selected residues one after another, then restore the original palette.

8.5 s

Ghost everything except the β sheet, grow its side chains, then fade the whole protein.

11 s

Van der Waals, solvent-accessible, and solvent-excluded surfaces side by side, then colored by hydropathy.

6.0 s

The studio, soft, dramatic, and flat Studio lighting presets on the same surface.

6.0 s

Rough, medium, and glossy materials, and the film recipe with grain, bloom, and halation.

9.3 s

Mark a helix with a translucent sphere, a wire box, and an atom halo.

10 s

Point to the helix with a callout, then label the Leu8–Ile44–Val70 hydrophobic patch.

9.2 s

Write glyph outlines, stack captions, move text, and change a string in place.

9.7 s

A ruler that follows an NMR ensemble, with a trace of the same distance across the models.

11 s

Calcium ions drawn on the cartoon, and the side chains within 3 Å of them.

11 s

Fade the fold, grow the side chains within 4 Å of a bound ribose, and label key residues.

9.3 s

Grow every side chain from its Cα, N to C terminus, then remove them in reverse.

8.0 s

The i → i+4 backbone hydrogen bonds of an α helix, detected from the coordinates.

8.5 s

Screened Coulomb estimates between charged side chains: attractive pairs in blue, repulsive in red.

9.0 s

Cut a window through the surface onto a buried ribose; the window follows the camera.

9.9 s

A tunnel with a ring every 5 Å shows how far a ligand lies below the surface.

11 s

Thread the actual cartoon geometry into view with eased motion, then reverse it.

9.5 s

Glowing wires trace the four chains of hemoglobin, then the cartoon fades in.

8.5 s

Color the cartoon by Cα B factor and widen it where the crystal structure is most mobile.

8.2 s

Color a predicted model by pLDDT beside its predicted aligned error heatmap.

10 s

Paint the surface by hydropathy, then by conservation across a Pfam family alignment.

10 s

A live contact map, distance trace, and sequence track that follow an NMR ensemble.

9.8 s

An electron-density contour at two σ levels and a density slice moving through a helix.

12 s

Play through deposited NMR models as a cartoon, then with every atom.

9.5 s

Adenylate kinase closes around its inhibitor in a morph between two crystal structures.

9.5 s

Hemoglobin goes from T to R as one αβ dimer turns against the other.

10 s

Morph calmodulin into troponin C through 114 residues matched by their contact maps.

9.0 s

Twist the coordinates with any Python function, then morph back to the saved structure.

9.2 s

Turn φ and then ψ of one residue, with arcs on the bonds and its point on a Ramachandran plot.

12 s

Wind a peptide from a β strand into an α helix while the cartoon follows DSSP.

11 s

Spin χ1 and χ2 of three hydrophobic side chains through full turns.

8.0 s

Blend a double helix between base slabs, filled rings, sticks, and ladder rods.

10 s

Highlight the anticodon loop of tRNA-Phe, change the base style, and show its surface.

9.0 s

Classic helix bands, beta arrows, and round loops enter with smooth easing. The animation moves the actual cartoon geometry; it illustrates an entrance, not protein folding.

9.0 s

Ball-and-stick geometry threads into place with glossy materials and subtle grain, bloom, and halation. Residues move as rigid groups; connecting bonds can stretch.

9.5 s

Switch from cartoon to a solvent-excluded surface, open a tunnel onto bound ribose RIP A272 with depth rings every 5 Å, and return to cartoon. Uses a 0.6 Å surface grid and dramatic lighting.

7.5 s

Select a helix by residue range, reuse a molecular style, and give text, styling, and camera motion separate durations. Studio film effects finish the image.

1:04

Tunnels into GroEL–GroES, with a ring every 5 Å, compare the ADP pocket 21 Å beneath the outer surface with residues on the ring's inner wall 44 Å down. A ghosted side view, a fly-down, and a carved surface follow.

23 s

Four wires fly in from four sides and thread the α and β subunits of human deoxyhemoglobin from their C termini, one after another. The cartoon and the four hemes then fade in, and the wires pull back out.

18 s

Deoxyhemoglobin (2DN2) morphs to oxyhemoglobin (2DN1, expanded to its tetramer), superposed on α1β1. α2β2 turns 14° in the image plane while O₂ appears at each heme. A heatmap shows Cα–Cα distances changing between the αβ dimers but not within them. The path illustrates the difference between the two structures.

17 s

Open adenylate kinase (4AKE) closes around the inhibitor Ap5A (1AKE), superposed on the CORE. The LID turns 52° and the NMP-binding domain 45°; a ruler between them shortens from 43.7 Å to 19.1 Å, and Ap5A, present only in 1AKE, fades in.

1:02

φ and ψ of one alanine turn with live protractors and a Ramachandran plot. Baldwin’s peptide then winds into an α helix as its i → i+4 hydrogen bonds form, φ/ψ angles measured in protein G fold the β-hairpin of residues 41–56, and ubiquitin’s residues fill the favored regions. Torsions rotate atoms about bonds; the motion is an illustration, not a folding pathway.

41 s

Calmodulin’s four Ca²⁺ ions appear with the cartoon, and the side chains within 3 Å of each ion grow from Cα. A GroEL subunit then shows its bound ADP and Mg²⁺, with residues beyond 8 Å faded to reveal the pocket.

31 s

Two Cd²⁺ ions in EF-hands III and IV, with their coordinating side chains, and a sulfate held by Arg47. The switch to ball-and-stick and back shows the atom colors blending between representations.

26 s

The Leu8, Ile44, and Val70 hydrophobic patch of ubiquitin grows from the cartoon, then every side chain appears in N-to-C order. Side chains follow the interpolated NMR conformers.

30 s

Mg²⁺ and Mn²⁺ ions on transfer RNA, with the phosphate groups and nucleotides around them. Spermine then lies across a Z-DNA duplex, and the nucleotides it contacts replace their base slabs with atoms.

12 s

C1′ contact maps select five matching nucleotides between two DNA strands. Matched residues move in order with a 0.25-second delay; unmatched residues fade out and in.

23 s

A DNA double helix with slabs, filled rings, sticks, and ladder rods. Residue colors and strand transparency carry through to atoms and a molecular surface.

15 s

Select the anticodon loop of yeast tRNA, fade its surroundings, then color a molecular surface by deposited B factors. Modified nucleotides retain their names and parent-base colors.

1:08

A continuous camera tour with helix close-ups, focus pulls, transparent surroundings, backbone atoms, and a surface colored by B factor. Rendered with Blender EEVEE at 1080p/60 fps.

1:41

Calmodulin changes representation, color, and conformation, then morphs into troponin C. The video also shows labels, camera focus, distances, hydrogen bonds, and electrostatic estimates.

23 s

An idealized backbone with explicit hydrogens. The video shows all 12 expected i-to-i+4 hydrogen bonds, then zooms into one bond to compare H···O and N···O distances.

25 s

Residue colors change in sequence across a ubiquitin structure. The video switches between cartoon, ball-and-stick, and surface views, then updates the surface during NMR playback.

20 s

Compare 3D and 2D distance lines. Highlight hydrogen bonds using inferred backbone hydrogens, then display screened Coulomb estimates using example formal charges.

19 s

Add amino acid names and region labels to ubiquitin. Lines connect the labels to the selected residues as the structure moves.

10 s

Write draws each letter’s outline and fills it in. Unwrite erases the text. The example includes Greek letters and delays between letters.

24 s

The camera focuses on the helix and tail of ubiquitin. Spheres, boxes, and atom highlights mark the selected regions during NMR playback.

24 s

All 116 deposited ubiquitin models, aligned using core Cα atoms. The animation interpolates between consecutive models.

24 s

The same ensemble with 602 heavy atoms per model and element-colored bonds and spheres.

12 s

A contact-map match selects 114 Cα pairs. Matched residues move in sequence from N to C; unmatched residues fade out or in.

12 s

Each matched residue moves with its Cα atom. Source atoms fade out as target atoms fade in.

9.0 s

The complete GroEL/GroES coordinate set: 21 chains, 8,015 Cα residues, and 58,870 selected heavy atoms.