When visualizing dynamic molecular systems, it’s easy to lose track of critical components as they move during a simulation. This is especially frustrating when preparing explanatory videos or presentations: the atoms you’re trying to highlight drift off-screen, requiring constant manual adjustments to the camera orientation. Fortunately, if you’re using the SAMSON platform, there’s a simple way to solve this.
The Look at atoms animation effect in SAMSON offers a practical solution. Instead of fixing the camera to move with the atoms (which can be disorienting), this animation lets the camera continuously reorient to keep selected atoms in view. Imagine placing a tripod nearby and adjusting its orientation as the atoms move: the position stays put, but you’re always looking at the action.
What does it do, exactly?
The Look at atoms animation keeps your camera targeting a geometric center of a selected group of atoms, while the camera position stays fixed throughout the animation frames. This is particularly helpful when observing localized molecular motions—like monitoring an active site during a molecular dynamics trajectory—without introducing the distraction of camera motion.
How to set it up
Here’s a step-by-step guide for using the Look at atoms effect:
- Select your atoms: Use the standard selection tools to specify the group of atoms the camera should look at.
- Set the initial view: Orient the camera the way you like—it will keep this position while continuously aiming at the selected atoms.
- Select the start frame: In the Animator’s Track View, choose the frame where the animation begins.
- Add the Look at atoms effect: Double-click the
Look at atomsanimation option from the Animation Panel. This creates two keyframes—start and end—with the camera targeting the moving atom group. - Adjust the end frame: Extend or shorten the duration of the animation based on the molecular event or trajectory timeframe you’re interested in.
You can fine-tune the animation using the inspector. For example, if the environment includes a grid, enabling the Keep camera upwards option ensures consistent camera orientation relative to the up direction.
Use cases: where it becomes essential
This animation is especially valuable when:
- Following a chemical reaction: Stay focused on the reaction center while the molecule evolves over time.
- Visualizing flexible protein domains: Keep an eye on the active site or hinge region without the entire protein bouncing out of view.
- Preparing video content: Create smooth visual narratives without excessive camera jitter or manual corrections.
One of the biggest advantages of this approach is that viewers retain a sense of spatial continuity—as the background stays anchored, molecular movement becomes the highlight.
If you need to adjust the camera’s position after applying the animation effect, you still can—just remember that the target point will always stick to the atoms’ geometric center. This balance between fixed positioning and dynamic orientation brings clarity to otherwise chaotic animations.
To learn more, visit the full documentation here: https://documentation.samson-connect.net/users/latest/animations/look-at-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.