When preparing molecular presentations, one challenge commonly faced by modelers is how to add dynamic motion to a static selection of atoms without overly distorting the system or distracting from molecular features. A static model can feel lifeless, but too much motion can be misleading or confusing in a scientific context.
The Rock animation in SAMSON offers a simple yet effective way to gently bring molecular systems to life. By causing atoms or molecular groups to oscillate around their centroid, the Rock animation allows you to convey 3D structure and spatial orientation with more clarity—without altering the integrity of the underlying system.
Why Use the Rock Animation?
Viewers often struggle to perceive depth and structural relationships in complex biomolecular models. Especially with flat representations, it can be difficult to appreciate spatial orientation between domains, helices, or ligands in binding pockets.
The Rock animation tackles this by introducing a small, oscillating motion around the geometric center of selected atoms. This motion is aligned with the Z-axis and provides a back-and-forth rocking effect, making it easier to understand 3D relationships in a molecule or complex.
Applied well, this can enhance educational content, molecular storytelling, or visual abstracts without overwhelming your audience with complex camera motions.
How It Works
- Select the group of particles you want to animate. This might be a binding pocket, protein domain, or small molecule.
- Open the Animator (from the Presenting panel) and navigate to the Animation panel.
- Double-click the Rock animation effect. This automatically adds a rock motion to the selected group between two keyframes.
- Adjust the keyframes along the timeline to control the motion duration.
Tweak the Feel of the Motion
You can customize the way motion evolves over time by editing the Easing curve. This changes how the orientation interpolates between your keyframes. Whether you want a sharp bounce or a smoother swing, the easing curve gives you that control.
Applications and Examples
The Rock animation is subtle yet powerful. Here are some practical cases where it can help:
- Highlight active sites: Rock only the catalytic center while keeping the rest of the protein fixed.
- Focus attention: In larger complexes, rock the domain of interest while keeping other parts static.
- Educational content: Show conformational flexibility or domain movements.
You can see an example of this animation in practice on this SAMSON document, which illustrates a gentle rocking of a biomolecule to enhance perception of its 3D structure.
Final Notes
This technique is a useful tool for structural biologists, chemoinformaticians, and scientific communicators. By introducing just enough motion, you help your audience grasp structure and function more intuitively, all while preserving scientific fidelity.
To learn more details about how to apply and configure the Rock animation, visit the SAMSON documentation page: https://documentation.samson-connect.net/users/latest/animations/rock/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net