When visualizing molecular dynamics, staying focused—literally—can be a challenge. Molecules twist, bend, and tumble through space, and it’s easy to lose track of specific atoms or active regions as they shift across the screen. But what if your camera could watch the atoms move, without you needing to constantly re-center the view?
In SAMSON, the Look at atoms animation offers a simple but useful way to do exactly that: it allows your camera to stay still while its target point follows the atoms of your choice. This is particularly helpful when you want to analyze a region of interest—like a ligand binding site or a catalytic group—throughout a simulation, without having your perspective constantly drift or rotate.
Why this matters
When presenting or analyzing a molecular trajectory, keeping the camera fixed while the atoms move provides visual stability. It helps collaborators understand motion relative to a constant frame. It can also reduce viewer fatigue when interpreting long or complex animations. And for researchers creating publication-quality visuals, it makes the motion much easier to interpret.
How it works
The Look at atoms animation attaches the camera target—not the position—to follow the geometric center of the atoms you select. As the simulation progresses, the camera keeps looking at them, even as they wander through three-dimensional space. This gives the sense that the atoms are always in the center of the screen, while the rest of the system moves accordingly.
To add this animation in SAMSON:
- Select the atoms you want the camera to follow.
- Adjust the camera view as desired—this view will be kept constant.
- Open the Animator’s Track view and go to the frame where you want the animation to begin.
- Double-click on the Look at atoms animation in the Animation panel.
- Set the end frame for the animation. The camera will keep looking at your selected atoms between these frames.
Want to fine-tune the effect? You can:
- Change who does the looking: By default, animations use the active camera. You can change this in the Inspector panel if needed.
- Adjust the “Keep camera upwards” option: This changes the effect if the viewing grid is enabled, which may help you maintain a consistent orientation across the animation.
- Fine-tune the position: While the target follows the atoms, you can still move the camera position manually to get the best framing.
Here’s how it looks in action:
When to use it
Typical scenarios for using Look at atoms include:
- Tracking a ligand entering or leaving a binding pocket.
- Observing conformational changes in a loop or domain while keeping it centered.
- Creating animations where viewers can focus on a site of interest without being distracted by rotations and panning.
This animation is particularly useful for educational videos, presentations, or exploratory steps when trying to understand dynamic behavior in a specific region.
To learn more, visit the full documentation page here: Look at atoms animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.