ProteinMotion

Molecular animation
in Python

Animate proteins, DNA, and RNA from a structure or trajectory. Add motion and labels, then export a video. Render cartoons, nucleotide bases, ball-and-stick models, and molecular surfaces.

Get started View source
python -m pip install proteinmotion

Install from PyPI, or use pipx for a global command.

Python 3.11+ · macOS · Windows + NVIDIA · MIT licensed

GPU rendering on Apple silicon Macs and Windows PCs with NVIDIA graphics. ProteinMotion detects your platform and selects rendering and video encoding automatically. Platform setup

1:08 · EEVEE · 60 fpsChapters and code

Molecular representations

Cartoon, ribbon, atoms & surfaces

Animation

Movement, color & transparency

Labels & measurements

Residues, distances & interactions

States & trajectories

NMR ensembles & MD playback

Define each animation
in a Python script.

Create a protein object, add it to a scene, and call play() to animate it. The API follows Manim’s scene syntax. Set the duration of each animation and combine animations in one call to run them together.

Read a complete script

ProteinMotion runs as a standalone package. Use the exported videos in Manim, presentations, or a video editor.

scene.py
python
class MyFilm(ProteinScene):
    def construct(self):
        p = Protein.from_file("protein.cif").cartoon()
        self.add(p)
        self.camera.frame(p)

        helix = p.select(residues=(23, 34))
        self.play(Colorize(helix, "#50e0d0"), run_time=1.5)
        self.play(Write(helix.callout("α helix")))
        self.focus(helix, run_time=1.5)
        self.play(PlayTrajectory(p), run_time=8)

DNA and RNA

Draw bases as slabs, rings, sticks, or ladder rods. Highlight selected nucleotides and show molecular surfaces.

View code and output

Numerical properties

Color residues by B factors, RMSF, or custom values. Use cartoon thickness and a color scale to show the range.

View code and output

Plots that follow the movie

Show distance traces, contact maps, and a sequence strip alongside trajectory playback.

View code and output

Density maps and slices

Load an MRC or CCP4 map, change its contour level, and move a slice through the volume.

View code and output

Depth of field with EEVEE

Set lens focus on selected residues and animate focus changes as the camera moves. The homepage film uses EEVEE for helix close-ups, transparent surroundings, and molecular surfaces. Install Blender separately to render the scene.

View the film and full script

Use with an AI agent

The ProteinMotion Movies skill provides instructions and examples for writing scenes, rendering videos, and checking the results. Use it with an agent that can read local files and run Python commands.

Set up the skill

Example structures and scripts

Protein, DNA double-helix, and transfer RNA examples include their input structures and full scripts.

View examples