One of the recurring pains in molecular modeling is the clear and synchronized visualization of structural transitions—whether you’re browsing a molecular dynamics trajectory, comparing different conformers, or showing simulation results in a presentation. When you need to animate changes seamlessly across structures or simulations, small misalignments or non-intuitive transitions can quickly turn an insightful animation into a confusing experience.
The Play path animation in SAMSON offers a solution tailored specifically for synchronizing and visualizing trajectories. Whether you have a single path recording a molecular event or multiple paths capturing different simulation outputs, Play path helps you convert data into digestible animations for analysis and sharing.
What Is the Play Path Animation?
In SAMSON, a “path” is a visual representation of a trajectory—essentially, a sequence of structural changes stored as a path node. The Play path animation lets you replay one or several paths between keyframes. This is particularly useful when you want to demonstrate a physical process like ligand unbinding, protein folding, or simply illustrate differences in conformations.
Here’s where it gets better: multiple paths can be synced together. This means you can compare motions across systems or correlate movement between different parts of a complex, making it easier to analyze functional motions.
Getting Started: Setting Up the Animation
To create a Play path animation:
- Select the path or paths you want to animate. If you have multiple paths, be sure they represent compatible information (e.g., same number of frames, related systems).
- Double-click on Play path in the Animation panel of the Animator.
- Adjust the animation’s keyframes to fit your desired time window. You can always move keyframes later to fine-tune the timing.
Note: The Play path animation interpolates structure positions when the number of animation frames differs from the number of path frames. This default smoothing ensures smooth transitions, but you may disable it in the Inspector panel for a more literal frame-by-frame playback.
Advanced Tips: Easing Curves for Smooth Interpolation
To control how your animation evolves over time, SAMSON allows you to adjust the Easing curve. Whether you want the motion to start slow and accelerate or move at constant speed, the easing curve offers fine-grained timing control over each parameter in your animation.
Best Use Cases
- Trajectory Playback: Quickly visualize molecular dynamics (MD) paths directly from imported structure series.
- Comparing Conformations: Sync paths generated from different protonation states or tautomers.
- Demonstrating Mechanisms: Use animations for pedagogical demos, such as showing enzyme catalysis steps or ligand entry/exit paths.
Why This Matters
Instead of static snapshots or separate movies, Play path gives modelers a flexible way to combine paths and create a unified storytelling experience through animation. By using smooth transitions and synchronized playback, you promote better understanding of structural motion across time or conditions. It’s more than visual appeal; it’s interpretability.
To learn more, visit the documentation page: 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 at https://www.samson-connect.net.