One of the most common challenges faced by molecular modelers is visualizing changes in molecular conformations over time. Whether you’re working with molecular dynamics (MD) simulations, conformational sampling, or interactive modifications, seeing how a system evolves in space and time is key to understanding the underlying processes. But turning a complex trajectory into a smooth, comprehensible animation can be more difficult than it sounds. That’s where the Play path animation in SAMSON comes in handy.
The Play path animation allows you to replay molecular motions along a defined trajectory or path by interpolating between two keyframes. This means you can animate a molecular transition, for example, from an open to closed conformation, or play through a full simulation, all within the same environment you use to model and analyze your system.
Why Play Path?
Imagine you’ve generated a molecular trajectory showing ligand binding or a conformational change. Sharing static snapshots doesn’t always do justice to the dynamics—colleagues might not intuitively see what’s unfolding at the molecular level. The Play path animation bridges that gap with a simple yet powerful tool: a synchronized, controllable animation that transforms trajectories into visual narratives.
How It Works
At its core, Play path takes one or more path nodes—objects that store trajectories in SAMSON—and animates them between two timeline keyframes. Steps to get started:
- Select a path you want to animate. This might be from a simulation or one you’ve created manually.
- Open the Animation panel in the Animator.
- Double-click the Play path effect to apply it to the selected path.
- Adjust keyframes on the timeline to define the start and end of the animation period.
If your animation has more frames than the underlying path, SAMSON will automatically smooth the motion to avoid jumps. This can be toggled off in the Inspector in case you want frame-by-frame accuracy for presentations or data interpretation.
Controlling the Flow
Smooth transitions are not only visually appealing—they’re often necessary for clear communication. The Play path animation supports easing curves, which let you control the interpolation speed between frames. Want a slow start and a fast finish? Or maybe a bounce to show molecular recoil? Customize the motion profile for clearer scientific storytelling.
Multiple Paths, One Timeline
If you have several related molecular motions or trajectories, you can animate multiple path nodes together. SAMSON synchronizes them automatically, keeping your animation orderly and aligned—an asset for comparing similar behaviors across different structures or conformations.
Whether you’re preparing a teaching video, showcasing your research results, or just checking how your model behaves under certain conditions, the Play path animation in SAMSON offers a straightforward solution.
To learn more about using the Play path animation, visit the full documentation at https://documentation.samson-connect.net/users/latest/animations/play-path/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.