When visualizing molecular dynamics, it can be frustrating to lose sight of the area you’re most interested in. As the system evolves over time, atoms move, interactions change, and key regions may drift out of view—even if you had carefully positioned the camera beforehand. This can make it harder to observe and communicate precisely what’s happening in your simulation.
The ‘Look at atoms’ animation in SAMSON offers a solution. It allows the camera to continuously track a group of atoms without changing your point of view. This means you can maintain a consistent viewing position while always looking at the right place.
Why this feature matters
Whether you’re creating videos to present your results, or simply exploring your simulation interactively, it’s very helpful to be able to keep a region of interest (e.g. an active site, reaction center, binding pocket, etc.) centered on screen. The ‘Look at atoms’ animation makes this easy to set up and control, especially when used in combination with trajectory animations.
How it works
When activated, the animation keeps the camera target locked to the geometric center of the atoms you selected—so as these atoms move over time, the camera’s focus follows them. Importantly, the camera’s position stays fixed. It behaves as if you had a tripod set up at a fixed point in the lab, and you’re simply rotating it to keep your eye on a moving molecule.
This is different from the ‘Follow atoms’ animation, which changes the camera’s position in space to follow the atoms. Use ‘Look at atoms’ when you want to observe movements from a fixed spot, such as tracking how a molecule twists, bends, or interacts with its surroundings.
Setting it up
- First, select the group of atoms you want the camera to follow.
- Position the camera where you’d like it to stay.
- Open the Animator, pick the start frame, and double-click on ‘Look at atoms’ in the Animation panel.
- Set the end frame to define the duration of the animation.
You can later adjust the start and end frames to focus on different parts of your simulation, extend the duration, or loop it over a trajectory. The animation will keep the camera pointing at the moving centroid of the selection regardless of how the atoms move over time.
Fine-tuning your setup
If needed, you can inspect the animation to control further options like whether it applies only to the active camera, or whether the camera should stay upright relative to the grid. These settings help in making your animation more consistent and aesthetically pleasing, especially when rotating views aren’t desirable.
You can also manually adjust the camera position within the Animator track view for more control, while the target remains anchored to your selection. This gives you precision in presenting dynamic events from exactly the angle you want.
Visual example
This animated example shows how the camera keeps its position but rotates to follow atoms as they move.
Conclusion
By anchoring the camera’s gaze to the atoms that matter most, ‘Look at atoms’ helps you maintain visual clarity and narrative continuity. It’s a powerful tool when you want to highlight molecular transformations, reactions, or other dynamic phenomena from a stable perspective.
To learn more, visit the original documentation page: https://documentation.samson-connect.net/users/latest/animations/look-at-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.