One of the recurring challenges in molecular modeling is finding intuitive ways to visualize how molecules change over time. Whether you’re analyzing conformational transitions, exploring reaction mechanisms, or preparing a compelling presentation of a simulation, being able to animate a molecular trajectory efficiently, clearly, and without spending hours on manual keyframing is a real need.
Fortunately, SAMSON offers a flexible animation effect called Play path that helps modelers play back molecular paths — like trajectories or interpolated movements between states — in just a few clicks. Understanding how to use this feature effectively can make a big difference when working with dynamic molecular systems.
What Is a Path in SAMSON?
In SAMSON, a path node stores a molecular trajectory — a sequence of structural states. These states could range from the snapshots of a molecular dynamics simulation to interpolated conformations between binding poses. When you want to turn this sequence into a smooth animation, the Play path function is your go-to tool.
Getting Started with Play Path
To add a Play path animation:
- Select a path node in the viewport. This is the trajectory or sequence you want to animate.
- Open the Animation panel in the Animator window.
- Double-click on the Play path animation effect. A new animation is added linking two keyframes.
That’s it — SAMSON will now play your molecule’s motion between the selected states. Depending on your keyframes’ timing, the motion will be scaled accordingly between the two endpoints.
Smoothing the Animation
One concern that arises often is: What if the number of animation frames doesn’t match the number of path frames?
In this case, SAMSON helps by smoothing the trajectory. This creates an interpolated version that ensures visual continuity. However, if you prefer a frame-by-frame rendering from the original path (for example, to match MD simulation frames precisely), you can disable smoothing in the Inspector.
Customization via Properties
The Easing curve is another useful tool offered through the Inspector. This lets you control the interpolation speed: linear, ease-in, ease-out, and more. For example, if you want your animation to slowly enter motion and decelerate at the end (a natural visual cue), modifying the easing curve can get you there.
Unlike static snapshots, animated paths help convey structures in motion — whether protein loops, small ligand rotations, or entire complexes transforming. This not only aids in your understanding but becomes a powerful communication tool when sharing results.
When and Why to Use It
The Play path feature is particularly helpful when you:
- Want to cycle between conformations during a simulation preview
- Need to present the molecular motion between poses in a publication or conference talk
- Have multiple dynamic paths you want to animate in sync — Play path allows synchronizing multiple paths with ease
Conclusion
The Play path animation in SAMSON gives molecular modelers an intuitive way to bring their dynamic structures to life with minimal setup and extensive flexibility. Whether you’re troubleshooting a process, preparing an illustration, or simply exploring possible conformational states, Play path can enhance your work without overwhelming your workflow.
To learn more and see other animation options, visit the official documentation page for Play path.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.