When simulating molecular systems, it’s easy to lose sight of the atoms you care most about. Molecules twist and turn, and regions of interest may drift out of view just when interactions start to get interesting. That’s where the Look at atoms animation in SAMSON becomes a practical tool to improve how you observe molecular events.
Instead of chasing down atoms manually or constantly reorienting your camera, the Look at atoms effect keeps the camera focused on atoms you’ve selected, no matter how they move. This is especially useful during trajectory analysis, conformational changes, or molecular interactions, where maintaining visual contact with specific regions is key for understanding structural dynamics.
What Does ‘Look at atoms’ Do?
This animation causes the camera’s target point to follow the selected atoms by tracking their geometric center. Meanwhile, the camera position (i.e., where you look from) stays fixed. As a result, your point of view doesn’t move, but what you’re looking at does — following the motion of the atoms you selected.
Adding the Animation
- Select your atoms: Begin by selecting the atoms you want the camera to follow within your structure. Think of it as telling the camera: “Keep your eyes on these.”
- Set the view: Adjust your camera position and orientation how you want the scene to look initially.
- Insert the animation: In the Animator panel, go to the desired start frame and double-click
Look at atoms. This inserts an animation keyframe. - Define the duration: Move to an end frame and define how long you want the focus to be maintained.
The animation will interpolate the camera’s target position so that it tracks the center of the selected atoms through time. The position of the camera itself remains untouched, ensuring a consistent viewpoint throughout the animation.
Use Cases and Benefits
- Trajectory analysis: Watch how active sites behave during dynamics without repositioning your view repeatedly.
- Molecular docking: Assess how ligands move near binding pockets while keeping a stable orientation.
- Communication: Produce clearer visualizations in videos or presentations that draw attention to specific residues or domains.
Customization Options
You can fine-tune this behavior using the animation’s properties. For instance, by inspecting the animation, you can:
- Apply to active camera: Choose which camera the animation uses.
- Keep camera upwards: Decide whether orientation aligns with the grid, which is helpful for predictable up/down axes.
Moreover, even though the target is automatically moved with the atoms, you can still tweak the camera’s position using animation controllers for advanced visual effects.
Visual Consistency without Manual Adjustments
Many molecular modelers want to avoid disorienting scene shifts in their animations. With Look at atoms, you get automatic visual tracking without changing your vantage point — offering clarity and stability to your molecular movies.
To learn more about this feature, see the official documentation at 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.