It’s common in molecular modeling to focus on how a specific part of a system behaves over time—for example, tracking the motion of a ligand inside a binding pocket or following the rearrangement of an active site in a protein. However, viewing these changes clearly can be frustrating when you can’t keep your camera aligned with the part of the molecule that interests you.
Fortunately, if you’re using SAMSON, the integrative molecular design platform, there’s a simple yet effective solution: the Follow atoms animation. With this animation, you can make sure the camera smoothly follows a moving molecular region so that it stays visible even as the entire system evolves during a simulation.
What does “Follow atoms” do?
The Follow atoms animation automatically adjusts the camera position and target point to ensure a fixed distance to your atoms of interest. Unlike a static view, which can quickly lose relevance as atoms shift, this dynamic view keeps your camera “glued” to the selected atoms, making it easier to analyze their behavior relative to their surroundings.
This can be particularly useful when illustrating or studying:
- The path of a diffusing molecule
- Conformational changes during molecular dynamics
- Binding/unbinding events
- Local rearrangements in complex systems
Instead of manually adjusting your viewpoint frame by frame, the Follow atoms animation allows you to automate this tracking and focus on your data instead of the camera controls.
How to add the Follow atoms animation
Here’s how to set it up:
- Select the atoms you’d like the camera to follow. These can be part of any molecular structure in your scene.
- Orient your view to define the initial position of the camera. This is important because it sets the viewing angle and distance.
- Open the Animator’s Track view and choose your start frame.
- In the Animation panel, double-click on the Follow atoms effect.
- Adjust the end frame of the animation as needed. The camera will interpolate its position between start and end while tracking your selected atoms.
Behind the scenes, SAMSON calculates the geometric center of the selected atoms and moves the camera target accordingly. The camera position shifts too—but in such a way that it maintains the original vector between the camera and the atoms. This ensures a natural, steady motion without abrupt jumps in perspective.
Camera behavior options
While the default behavior works for most cases, some situations call for additional customization. You can inspect the animation and adjust properties such as:
- Apply to active camera: Determines which camera the animation is applied to (helpful if working with multiple views).
- Keep camera upwards: Controls whether the camera stays upright depending on whether the grid is enabled. This is useful for maintaining orientation consistency throughout the animation.
Fine-tuning the view
While the geometric center of your selected atoms defines the camera target, you’re still free to tweak the camera’s position using the animation controllers. This gives you flexibility to choose different angles while still benefiting from automatic tracking.
In summary, the Follow atoms feature in SAMSON makes it easier to analyze and communicate molecular behaviors, especially when key atoms are moving across the system. Whether you’re preparing figures for publication or simply exploring a simulation, this tool can help you stay focused—literally.
To learn more about how to use the Follow atoms animation in SAMSON, 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 download SAMSON at https://www.samson-connect.net.