In molecular simulations, molecules are constantly moving, transforming, binding, and unbinding. As a researcher or educator, you might want to focus on very specific parts of a molecular system: a ligand entering a binding site, a domain rearrangement, or an ion traveling through a channel. But anyone who has tried to keep the camera focused on the action during a trajectory playback knows how frustrating this can be.
This is where the “Follow atoms” animation in SAMSON becomes particularly useful.
What does “Follow atoms” do?
With the Follow atoms animation, the camera in SAMSON automatically follows the geometric center of selected atoms throughout a trajectory. This means that as the selected atoms move, the camera moves with them, maintaining a fixed relative distance. The result? A smooth focus on the features that matter most to you, without the need for constant manual camera adjustments.
This is ideal for:
- Tracking conformational changes of ligands or protein domains
- Zooming in on a molecular site without losing it over a dynamic trajectory
- Creating teaching visuals that keep attention focused on the relevant biochemical event
How to set up “Follow atoms” in three steps
- Select the atoms you want the camera to follow using SAMSON’s standard selection tools.
- Orient your camera the way you’d like the animation to begin.
- Open the Animator panel, select the start frame in the Track view, and double-click on the Follow atoms animation effect.
The camera will then move in such a way that the relative position between the camera and the selected atoms stays constant from start to end frame, making the visualization intuitive and centered.
Customization tips
You’re not locked into static settings. You can adjust or move start and end frames easily. For example:
- Use the Inspector to apply the animation to a different camera (if multiple cameras are defined).
- Use the Keep camera upwards setting to determine whether the camera keeps vertical alignment depending on the grid behavior.
- Change the camera position manually between keyframes for custom storytelling perspectives.
When not to use “Follow atoms”
This animation works best when the target atoms remain distinct and separated from the rest of the system during motion. If tracking atoms that move chaotically or overlap frequently with other structures, combining it with other animation effects like Look at atoms may produce better control.
This effect is not just a visual trick—it makes data interpretation easier while improving communication of scientific ideas. If you’re preparing a presentation or publishing visual data, Follow atoms helps keep the visual context locked and consistent.
See it in motion
To learn more, visit the full documentation for Follow atoms here: https://documentation.samson-connect.net/users/latest/animations/follow-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.