When simulating complex molecular systems in motion—protein-ligand interactions, polymer dynamics, or viral capsid assembly—keeping track of relevant parts of the system visually can be surprisingly difficult. As molecules twist, translate, or diffuse across the simulation space, camera viewpoints tend to remain static unless the user manually adjusts them. This results in a disorienting viewing experience or the important atoms simply leaving the visible field.
If you’re a molecular modeler facing this challenge, SAMSON offers a useful and often overlooked animation tool: the Follow atoms effect. This feature makes it easy to keep specific atoms centered in your view throughout an animation, even when those atoms are moving dynamically.
Why follow atoms?
Imagine you’re simulating a signal transduction pathway, and you want to visually track a molecule as it makes its way through a membrane channel. Or perhaps you’re studying a ligand sliding into a binding pocket during molecular dynamics simulations. Instead of tediously keyframing camera positions or readjusting views manually, Follow atoms ensures that your camera dynamically adjusts itself, keeping the region of interest in focus throughout your animation.
How does it work?
Once you’ve selected the atoms you want to follow, and oriented the camera as desired, simply double-click the Follow atoms animation effect in the Animation panel. The camera’s behavior is clever: it keeps a fixed vector between the camera position and its target (centered on the selected atoms), so as the atoms move, both the camera and its focal point move too, preserving your original observation geometry.
Getting started
- Select the atoms you want the camera to follow.
- Set the camera view as you’d like it to appear at the start of the animation.
- Choose a start frame in the Track view.
- Add the Follow atoms animation effect from the Animation panel.
- Set an end frame. The motion path will be generated automatically.
Tips for precise control
- You can move the start and end keyframes freely to adjust timing.
- If needed, inspect the animation to apply it to a custom camera instead of the active one.
- Want to preserve the camera’s vertical orientation? Try toggling the Keep camera upwards property depending on your grid settings.
- The target will remain centered on the selected atoms, even if the camera position is modified manually.
A visual example
The animation below shows how the camera continuously follows a moving group of atoms, keeping the scene focused throughout the trajectory. This is particularly helpful in long simulations when tracking target particles without interruption.
Conclusion
If you’re aiming to generate more insightful molecular animations or just want to avoid losing sight of important details mid-simulation, Follow atoms can save you a lot of time while improving clarity.
Learn more about the Follow atoms animation in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.