If you’ve ever tried to animate a molecular simulation and watched your region of interest drift out of frame, you’re not alone. This is a common challenge in molecular modeling when dealing with complex systems—especially when atoms of interest move significantly during a trajectory.
Whether you’re simulating protein-ligand interactions, DNA strand separation, or atomic diffusion, it’s often useful to keep the camera focused on certain atoms as they move. Otherwise, you risk losing visual contact with key events that matter for understanding mechanisms or preparing publication materials.
Fortunately, the Follow atoms animation feature in SAMSON offers a solution. It allows you to attach the camera to one or more atoms, automatically updating the camera’s position and orientation to track their movement while maintaining a consistent viewing distance.
Why Follow Atoms?
Imagine simulating a ligand navigating through a binding site. Rather than manually reorienting the camera for each frame (a time-intensive process), the Follow atoms animation lets you set it once and capture smooth, coherent motion around your selected atoms.
This is particularly helpful when:
- Your area of interest moves over time (e.g., center of mass shifting in a trajectory).
- You want to generate educational or presentation-ready animations focused on a substructure.
- You’re troubleshooting molecular dynamics and need to keep close watch on a local structural event (like unfolding or dimerization).
How It Works
Start by selecting the atoms you want to follow. These atoms define the geometric center that the camera will continuously target.
Then orient your camera as desired and go to the Animation panel in SAMSON’s Animator. Choose a start frame and double-click on the Follow atoms animation effect. The camera will then interpolate its position so that it maintains a constant distance while tracking the selected atoms in space.
You can move start and end frames to adjust timing. The camera target is always bound to the average position of your selected atoms, while the move vector between the camera and target is preserved automatically across frames.
Fine-Tuning the View
There are additional properties you can tweak if needed. For example:
- Apply to active camera: By default, the animation applies to the currently selected camera, but you can inspect the animation and change this.
- Keep camera upwards: If this option is enabled, SAMSON takes the current grid orientation into account. If you’re using the grid for orientation, this can help maintain an intuitive up-direction across the animation.
Also, while the geometric center remains fixed, you can still adjust camera positions between frames to achieve the framing that works best for your visuals.
Example: Visualizing Motion
Here’s an example of how the Follow atoms animation can help capture movement clearly:
Conclusion
If maintaining visual contact with specific atoms is key to your animation, the Follow atoms animation provides an efficient way to do it. No manual camera repositioning, and no lost details—just smooth tracking of what matters most.
To learn more, visit the full documentation for Follow atoms.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.