Whether you’re analyzing the dynamics of a ligand interacting with its binding pocket or observing the conformational changes of a flexible protein domain, maintaining a clear visual focus on the region of interest throughout a molecular animation can be difficult. Molecules move. Trajectories shift. And your camera? Unless manually adjusted, it stays static, leading to off-centered visuals that obscure precisely what you want to observe.
Fortunately, SAMSON offers an elegant solution with the Follow atoms animation — a feature that allows the camera to follow the movement of selected atoms, typically tracking the geometric center of those atoms across frames. This makes it much easier to keep key interactions or events within view during your entire animation.
Why Follow Atoms?
Imagine you are simulating a molecular docking process. You want the camera to stick with the ligand as it diffuses through the solvent and approaches its target binding site — possibly tumbling and rotating along the way. Instead of constantly adjusting your view manually or post-processing your video, the Follow atoms animation keeps the ligand centered, simplifying both the analysis and communication of the event.
How It Works
The Follow atoms animation works by locking both the camera target and camera position to the selected atoms. The camera moves such that its relative position (distance and direction) to the selected atoms remains constant. This gives a stable and fluid viewpoint on your atoms of interest as they move through space during your trajectory.
This is particularly useful when studying localized motions—like loop dynamics in proteins or rearrangement of active site residues—because it ensures a consistent, zoomed-in perspective without manual tracking.
How to Set It Up in SAMSON
- Select the atoms you want the camera to follow by using SAMSON’s selection tools.
- Position the view as you want it to be at the start of the animation using camera controls (move, zoom, rotate, etc).
- In the Animator’s Track view, choose the desired start frame.
- Double-click Follow atoms in the Animation panel.
- Set the end frame according to the duration of your motion or trajectory.
- Optionally, inspect the animation to fine-tune settings like which camera to apply the animation to, or whether the camera should remain upright relative to the grid.
Things to Keep in Mind
- The camera will follow the geometric center of the selected atoms. For best results, choose atoms that give a meaningful center — typically atoms in the rigid core of a ligand or a sidechain of interest.
- If you adjust the view manually during playback, you may override part of the animation settings. Use the Animator controls to maintain consistency.
- This animation works best when combined with trajectory playback (e.g. from a molecular dynamics simulation) — you’ll see how fluid the camera tracks your region of interest.
Visual Analysis Made Clearer
Seeing your ligand remain centered throughout its molecular journey, or keeping a mobile loop in frame as it transitions from open to closed states, can make both scientific interpretation and presentation much more effective. The Follow atoms feature in SAMSON is a simple but powerful tool to enhance clarity and insight in your animated molecular studies.
To learn more, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.