When working with molecular simulations, it can be surprisingly tricky to visually follow the part of the molecule you’re actually interested in. Atoms move in space, but cameras often stay fixed—forcing you to constantly adjust the view manually or lose track of the region you’re exploring. This becomes particularly frustrating when analyzing trajectories involving flexible biomolecules, ligands navigating pockets, or dynamic assemblies. Fortunately, there’s a simple solution in SAMSON: the Follow atoms animation.
This animation feature lets you select atoms and automatically keeps the camera focused on their motion throughout an animation. Whether you’re studying protein conformational changes or following a ligand docking process, it saves you from manual camera adjustments while preserving a consistent viewpoint.
How it works
When you enable the Follow atoms animation, the camera adjusts its target and position to remain at a constant distance from the geometric center of the selected atoms. The camera effectively becomes tethered to them, moving through space as they do.
This is different from the “Look at atoms” mode, where the camera stays still but simply rotates to keep the atoms centered. In contrast, Follow atoms involves motion and orientation, giving a more immersive and focused visualization of atom dynamics.
Getting started
- Select the atoms you want to follow using SAMSON’s standard selection tools.
- Orient your view so it starts in the angle you prefer—this defines the initial camera position.
- In the Animator’s Track view, choose your start frame.
- Double-click the Follow atoms effect from the Animation panel.
- Set your desired end frame.
This sets up the camera to follow the center of the selected atoms between the two frames. The direction and distance between the atoms and the camera stay preserved, giving you a smooth, continuous motion that’s synced to molecular behavior.
Adjustments and refinements
If you want more control, you can inspect the animation and:
- Apply it to a different camera (if you’re working with multiple views).
- Decide whether to keep the camera aligned with the grid, which affects vertical orientation.
You can also adjust the camera position directly with animation controllers, while the target remains locked on the atom group.
Why this feature matters
Following atoms is much more than a cosmetic feature—it helps you:
- Track specific ligands or side chains moving through molecular environments.
- Analyze localized dynamics during conformational changes.
- Clarify how domains move in multi-part assemblies.
- Produce cleaner animations for communication or publication.
Instead of struggling to reposition your camera every time the molecule drifts, the Follow atoms animation lets you focus on interpretation, not navigation.
To dive into the technical details and explore additional features, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/follow-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.