Tracking specific atoms during a molecular simulation is essential when studying dynamic systems, such as interactions in flexible biomolecules or complex molecular assemblies. But how can you keep the camera focused on the part of the system that matters—without manually adjusting the view frame by frame?
SAMSON’s Follow atoms animation provides a solution by automating this task: once set up, the camera follows a group of atoms smoothly over time, locking its focus and position in sync with the atoms’ motion. This can greatly improve your presentation, analysis, and communication of simulation results—letting the audience (and yourself) stay focused on what matters most.
What does Follow atoms do?
The effect ensures that both the camera target and camera position move over time so that the camera consistently tracks the selected atoms. Importantly, the system maintains a fixed distance between the camera and the center of the selected atoms. This is especially helpful for visualization tasks like exploring local conformational changes or tracking molecular docking over time.
When and why to use it
Consider a protein undergoing a conformational shift. You’re particularly interested in how a domain pivots or interacts with a ligand. With traditional camera settings, you’d need to realign your view repeatedly—or risk missing the details. Follow atoms takes care of this automatically, making your animations more coherent and reducing manual adjustments.
Getting started: the basic steps
- Select the atoms you want the camera to follow. You might want to choose a residue, a domain, or an entire macromolecule, depending on your focus.
- Orient the camera to your preferred starting view.
- In the Animator’s Track view, choose your start frame.
- In the Animation panel of the Animator, double-click Follow atoms.
- The camera will now lock its position relative to the selected atoms, preserving both direction and distance.
- Select your desired end frame. You can always adjust both start and end later.
Tips for precise visualization
- If needed, refine the camera behavior by inspecting the animation. For example, toggling Keep camera upwards makes the animation behave differently depending on whether the grid is active.
- You can modify the assigned camera in case you’re working with multiple viewpoints. Just inspect the animation and uncheck the default Apply to active camera box.
- Manual camera adjustments are still possible. While the target remains fixed at the selected atoms’ geometric center, you can tweak the camera position with animation controllers.
Use case in motion
Here’s an example where the camera follows the motion of selected atoms over a trajectory:
Notice how stable and consistent the visualization is even as the atoms—and the whole molecular context—change positions. Your viewers never lose sight of the atoms of interest.
To learn more, visit the detailed documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.