When visualizing molecular dynamics, static snapshots don’t always capture the full story. Animations help, but they introduce a common problem: as atoms move along a trajectory, it’s easy to lose sight of the specific region or molecule you’re interested in. Your camera stays fixed, and suddenly, the atoms you care about drift off-screen. Frustrating, right?
The Look at atoms animation in SAMSON offers a simple yet effective solution. It keeps your camera focus locked on selected atoms, even as they move, without changing the camera’s position or orientation. Let’s walk through what this does, how to use it, and when you might want it.
Why Focus Matters in Molecular Animations
When you’re observing a complex molecular system — say, a ligand entering a binding pocket or a phase transition — keeping attention on one part of the system is essential. But when atoms move significantly, your fixed camera can quickly lose sight of the action. Reorienting manually for each frame? Tedious.
The Look at atoms animation tells the camera: stay where you are, but always look at this group of atoms. It’s like giving the camera eyes that follow a dancer across the stage, rather than pinning the dancer to the center of the shot every time you change perspective.
How It Works
This animation keeps the camera position fixed but automatically updates the target position (where the camera is looking) to track the geometric center of selected atoms between two frames.
- Only the target point of the camera moves.
- The atoms to follow are defined by your current selection.
- The camera continues to “look” at those atoms during the animation.
This allows you to animate molecular motion (like dynamics or conformational changes) while keeping your region of interest always in view. No jumps, no drift — just a clear, stable focus.
Step-by-Step: Using Look at Atoms
- Select the atoms you want the camera to follow.
- Position your view exactly how you want it to begin.
- Choose the start frame in the Animator’s Track view.
- Double-click Look at atoms from the Animation panel.
- Set your end frame — adjusting camera positions as needed.
If the grid affects your orientation, you can inspect the animation and toggle Keep camera upwards. And yes, start and end frames can be edited freely.
When Is This Most Useful?
This can be especially helpful if you’re tracking tethered ligands, visualizing reaction centers, or focusing on protein domains during unfolding or domain movements — any situation where atom groups move but your position relative to the system shouldn’t change.
Here’s an example animation where the camera keeps its position but smoothly tracks the selected atoms:
To learn more, visit the full documentation at Look at atoms — SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it today at SAMSON Connect.