Visualizing molecular trajectories is a key aspect of understanding conformational changes, reaction mechanisms, docking paths, and other molecular phenomena. However, presenting trajectory data in a clear and synchronized manner can be time-consuming, especially when working with complex molecular systems.
SAMSON, the integrative platform for molecular design, simplifies this task through its Play path animation. Whether you’re comparing multiple conformations across time or showcasing a specific transition, this animation can help you produce synchronized, smooth visualizations from your path data. In this post, we explore how to use the Play path animation and how it can solve a common visualization pain point for molecular modelers.
Why use ‘Play path’?
In SAMSON, paths are data structures used to store trajectories, such as those resulting from simulations or interpolations between conformations. If you’re working on a dynamic system—such as a protein folding simulation or ligand docking—and you want to present or analyze how a structure evolves frame by frame, you can store the sequence of frames in a path node.
Animating these paths manually would typically require scripting or tedious frame-by-frame alignment. Instead, the ‘Play path’ animation automates this process by allowing you to:
- Animate a trajectory (path) between selected keyframes
- Play multiple paths in a synchronized fashion
- Optional smoothing of frames when counts differ
- Customize animation easing curves for better control
Getting started
First, select one or more paths that you want to animate. Then, follow these steps:
- Open the Animator in SAMSON (via the Presenting menu).
- Locate the Animation panel.
- Double-click the Play path animation effect.
- Adjust the keyframes in the timeline to set the duration and synchronization.
Here’s a visual example from the documentation to help you understand the setup:
Fine-tuning your animation
By default, if the number of animation frames differs from the number of frames in your path, SAMSON applies a smoothing algorithm to interpolate motion. If you’d rather use original frames without smoothing, you can disable this feature via the Inspector.
Additionally, you can define how smoothly or abruptly the interpolation happens between frames by editing the Easing curve. This is particularly helpful when preparing animations for educational presentations or scientific communication, where timing and pacing strongly impact understanding.
Conclusion
The Play path animation is a straightforward and powerful way to animate structural transitions and compare trajectories visually. It saves time, avoids the need for scripting, and produces smooth, synchronized animations that can greatly aid in collaborative discussions and presentations.
If you frequently work with path data in your molecular modeling workflow, adding this animation tool to your repertoire can streamline your visualization process.
Learn more about the ‘Play path’ animation in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.