Visualizing molecular motion is one of the most compelling ways to understand complex structural dynamics. Whether you’re working on protein flexibility, ligand binding, or simply preparing an educational presentation, showing how a structure might move can strengthen your message.
But there’s a common challenge: how can you convey subtle structural changes without overwhelming your audience with full molecular dynamics simulations? This is where a lightweight, focused animation like the Rock animation in SAMSON shines.
What is the Rock animation?
The Rock animation creates a rocking effect for a selected group of atoms or particles around their centroid. The rocking motion is performed around a vector aligned with the Z-axis, passing through this central point. It’s a simple yet effective way to add movement to static molecular scenes and can serve as a visual cue to highlight certain regions of interest (e.g., an active site, a flexible loop, or interface contact points).
Why use Rock?
Compared to full-scale simulation data, which may require extensive computational resources, the Rock animation is quick to apply and offers just enough movement to draw attention. Here are some typical use cases where it’s particularly helpful:
- Emphasizing structural flexibility during a lecture or presentation.
- Illustrating possible motion in docking or binding studies.
- Animating parts of large assemblies while keeping others static for contrast.
- Creating visually engaging molecular scenes for educational materials.
How to apply it in SAMSON
- Select the group of atoms or particles you want to animate. You can use SAMSON’s selection tools to highlight a subunit, a residue, or any custom atom group.
- In the Animation panel of the Animator, find the Rock animation and double-click it.
- The rock motion appears between two keyframes by default. You can move the keyframes on the timeline to adjust timing and duration.
- If needed, change how the motion evolves over time by modifying the Easing curve. This controls the speed progression of the animation and can give a more natural feel.
Tip: Test it with a real example
Want to see this in action? Check out this public presentation using the Rock animation on SAMSON Connect: 2BRD – Rock animation. This small example illustrates how effective a simple movement can be when you want to tell a story with your molecular model.
To learn more about how the Rock animation works and its properties, visit the original documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.