Animations can be a remarkably effective way to communicate complex molecular mechanisms, structural changes, or simulation data — especially in presentations or publications. But for many molecular modelers, creating animations still sounds like a time-consuming or technically difficult task. If that’s you, this post is for you 👇
SAMSON, the integrative molecular design platform, includes a powerful built-in tool called the Animator. It allows you to create engaging and instructive molecular animations easily, directly from your working environment. Whether you want to dock molecules, move atoms, or explain structural transitions through cinematic camera paths, the Animator makes it possible.
Why Animate in Molecular Modeling?
Animations help to illustrate time-evolving processes, clarify molecular interactions, and emphasize structural features that might otherwise be missed in static images. They’re particularly helpful for:
- Explaining assembly/disassembly of complexes
- Visualizing docking mechanisms
- Following trajectories from simulations
- Rotating around key molecular features or binding sites
Let’s dive into how SAMSON’s Animator can make all this (and more) straightforward.
Inside the Animator: What You Can Do
The Animator is composed of several intuitive sections:
- Track View: Timelines for each animation. Each animation has its own track, with keyframes that define important moments.
- Controls: Playback tools (play, pause, loop, etc.), frame navigation, and global preferences.
- Animation Panel: A categorized list of available animations, including motion, entrance/exit effects, camera motions, and even background changes.
Creating Your First Molecular Animation
Let’s say you’ve loaded a molecule from the PDB (e.g., 1AF6). You’ve added a Ribbons representation to highlight secondary structure. Now, you’d like to animate a basic transition, like orbiting around the structure while fading in the ribbon model.
- Open the Animator from
Interface > Animator - Create a new presentation via
Visualization > Add > Presentation - In the Animation panel, double-click Orbit camera. The viewport displays a controller to define the path.
- Position your view and adjust the orbit path using the handles.
- Select the Ribbons visual model in the Document view, then double-click Appear in the Animation panel to make it gradually appear.
That’s it! You can now press Space to play your animation or export it to a movie format (MP4, GIF, WebM) using the Save movie button in the Animator.
Tackle Real-World Molecular Modeling Tasks
Want to demonstrate docking? Use the Dock animation on ligands. Interested in showing a structural transition? Combine Move atoms with Hold atoms and camera moves. For presentations or teaching, you can even use Set background to add slides or watermarks, creating a more comprehensive visual narrative.
Animations can be precisely customized: move and extend keyframes, use easing curves for pacing, and adjust properties via the Inspector. All of this gives you control without overwhelming complexity.
Conclusion
If you’ve ever wanted your molecular story to be clearer, faster to grasp, or just more engaging — animations can help, and SAMSON makes them accessible. The Animator turns your scientific models into dynamic visual explanations that colleagues, students, and reviewers will understand more easily.
Want to learn more about animations in SAMSON? Visit the documentation page:
https://documentation.samson-connect.net/users/latest/presenting/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.