Animation is a valuable communication tool in molecular design and modeling. It helps bring clarity to complex systems, making dynamic behaviors and relationships easier to understand and share with others—especially in presentations or teaching. But for molecular modelers who want to visually emphasize that a molecule or molecular complex is dynamic without relying on full simulations, the question remains: what’s the simplest method to do that?
One effective solution available in SAMSON is the Rock animation. It allows you to create a subtle rocking motion for any selected group of atoms or particles, making your models appear more vivid and organic, with minimal setup time. This blog post explains what the Rock animation is, how it works, and how you can use it effectively.
Why Use the Rock Animation?
Often, static representations of molecules aren’t enough to clearly convey function, interaction, or spatial organization—especially during presentations. The Rock animation helps resolve this by:
- Attracting attention to a particular molecular region without exaggeration
- Suggesting flexibility or dynamic behavior in assemblies or protein complexes
- Adding life and visual interest to molecular scenes, useful for education or outreach
- Providing context in comparative scenarios with other molecules or movements
How It Works
The Rock animation rotates a group of selected particles around a vector that passes through the geometric center of the group and aligns with the global Z-axis. This makes the animation feel like a soft back-and-forth motion—similar to the way a boat might rock gently in water.
Getting started is simple:
- Select the group of particles you want to animate. This could be a ligand, a domain of a protein, or even an entire macromolecule.
- Double-click the Rock animation from the Animation panel in the Animator.
- The motion occurs between two keyframes. Adjust the timing and duration of these keyframes to control the pacing of the rock effect.
You can refine how the animation behaves over time by adjusting the easing curve. For example, a linear easing produces a uniform motion, while sinusoidal or quadratic curves make the motion feel more natural or organic.
Visual Example
Here’s a visual example of the Rock animation applied to a molecular model:
Use Cases
- Highlighting binding pockets or domains on enzymes in educational videos
- Creating a rhythmic motion to indicate areas of molecular mobility or flexibility
- Improving visual storytelling in pitch decks or research presentations
- Adding subtle motion to molecular posters or scientific animations for outreach
Try It With an Example
If you’d like to see a ready-made example, check out the following to explore how the Rock animation has been applied in a real molecular setup:
To explore more, visit the documentation page: Rock Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at www.samson-connect.net