In molecular modeling, visual clarity is essential. Particularly when working with dynamic systems like molecular dynamics simulations, it can be a challenge to keep track of the exact region of interest — especially if that region is moving. Have you ever tried to animate a specific domain or ligand along a trajectory, only to lose sight of it halfway through the animation?
The Follow atoms animation in SAMSON provides a simple and effective solution to this common issue. It allows you to define a group of atoms and have the camera automatically follow their geometric center throughout an animation — maintaining a constant spatial relationship.
Why this matters
Whether you’re presenting your results, documenting protein-ligand binding events, or simply analyzing how a molecule evolves over time, it’s often important to follow a mobile part of the structure. Manually adjusting the camera frame-by-frame—or even using standard center-of-mass alignments—can be time-consuming and imprecise.
How it works
The Follow atoms animation in SAMSON lets the camera track a selected group of atoms by moving both the camera target and position so that the viewing angle stays informative and constant throughout the animation. Here’s how:
- Select the atoms you wish to follow (e.g., a ligand or domain)
- Position your camera the way you’d like at the starting frame.
- In the Animator, double-click the Follow atoms animation from the animation panel to apply it.
- Set the end frame — the camera will interpolate between frames in a smooth way.
This creates a short sequence where the camera moves in sync with your selection, letting you observe local conformational changes or interactions throughout a dynamic simulation, without losing track of your atoms of interest.
What’s happening under the hood?
Behind the scenes, SAMSON uses the current camera vector and links it to the geometric center of your selected atoms. At the start and end keyframes, SAMSON computes the camera parameters, maintaining the distance and vector direction. As a result, the atoms of interest remain visually anchored at the same screen location over the course of the animation.
Customization
You can further fine-tune behavior:
- Use the Apply to active camera setting if you have multiple cameras.
- Inspect the animation to toggle options like Keep camera upwards, which controls how the camera orientation behaves depending on grid settings.
Quick visual example
Here’s what it looks like when following a molecular group over time:
Interested in trying it?
This animation option is part of the broader animation system in SAMSON, designed for intuitive storytelling in molecular design. Whether you are creating molecular movies or analyzing protein dynamics, this can greatly simplify your workflow and presentation clarity.
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/follow-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net