Communicating the behavior and interactions of molecular systems is rarely straightforward. Whether you are preparing material for a presentation, teaching structural biology, or generating content for a paper, showing how molecules move and interact over time is a common challenge.
SAMSON, an integrative molecular design platform, makes it possible to animate molecules effectively using its built-in Animator. In this article, we’ll explore how the Animator simplifies the process of creating high-quality molecular presentations—and how it can help you save time while improving how you communicate your science.
Why animations matter in molecular modeling
Animations allow modelers to reveal the dynamics behind 3D structures: docking events, assembly processes, or even trajectories from molecular dynamics simulations. Instead of static images, you can display transitions and behaviors that clarify complex ideas to both expert and general audiences.
Unfortunately, many tools that allow this level of control are either hard to use, require scripting, or involve working with multiple pieces of software. SAMSON’s Animator offers an integrated solution inside a single molecular design environment.
What SAMSON’s Animator offers
The Animator in SAMSON lets you build, control, preview, and export molecular animations. It allows you to choose from a wide range of animation types—everything from molecular docking to custom camera moves. These animations are organized through an intuitive interface composed of three essential parts:
- Track View: a timeline where you manage keyframes and view the structure of your animation.
- Animation Panel: a categorized list of all available animations—motion, camera, entrance/exit effects, highlights, and others.
- Animator Controls: play, pause, scrub through frames, adjust timing, and more.
Key types of animations
Motion Animations are designed for molecular operations such as docking, assembly, or trajectory playback. These can be used in combination with Hold atoms animations to ensure stable positions between frames.
Camera Animations such as orbit, zoom, and custom paths allow you to guide the viewer’s perspective. SAMSON even provides visual camera controllers within the viewport, so you always know where things will be framed.
For additional control, you can overlay Visual Effects to highlight specific features of your system (fade in/out, appear/disappear, pulsing effects, etc.) or insert pauses and slide-like transitions using Other animations. If you’re preparing a video or presentation, this level of control can make the difference between just instructional and truly clear communication.
Preview, edit, and export
SAMSON’s Animator lets you preview animations interactively before exporting. You can scrub the timeline, tweak keyframes, and adjust easing curves in the Inspector. When you’re ready, the Export Movie functionality supports mp4, gif, and webm formats.
Who is this for?
If you’ve ever struggled to explain a dynamic molecular event with static structural images, tried to script a scene in PyMOL, or spent hours in animation software stitching trajectories with overlays, then SAMSON might offer a more streamlined approach.
Whether you’re a researcher building a talk, a professor preparing lecture slides, or a student creating a visual abstract, SAMSON’s Animator gives you a focused set of tools for telling molecular stories—visually and clearly.
Learn more about animations and presentations in SAMSON in the detailed documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.