One common challenge in molecular modeling is clearly and effectively communicating molecular motion, such as during simulations, conformational transitions, or reaction pathways. Capturing not just static snapshots but smooth transitions between molecular states is crucial for interpretation and presentation.
If you’ve ever needed to animate a molecular trajectory between key moments in time — perhaps to show a ligand binding event, a conformational flip, or a transport process — the Play path animation in SAMSON may help you do this with precision and fluidity.
What is a Path in SAMSON?
In SAMSON, a path is a node that stores a molecular trajectory or a conformational series. This could originate from a molecular dynamics simulation, a manually created set of keyframes, or any tool that generates a sequence of structures. Once the path exists, you can animate it using the Play path animation effect.
Animating with Play Path
The Play path animation tool allows you to animate a molecular path between two frames in your Animator timeline. This gives you control over when and how a trajectory unfolds, synchronizing visualization with narration during presentations or analysis.
To get started:
- Select the path you want to animate.
- Open the Animation panel of the Animator.
- Double-click Play path to add it to your timeline.
- Adjust the keyframes to reflect the animation duration.
Smoothing Motion: When and Why
If the number of keyframes in your animation doesn’t match the number of structural frames in the path, SAMSON interpolates the motion to avoid abrupt jumps — this is called smoothing. This is particularly useful for creating clean visuals, but if you prefer a frame-by-frame playback (e.g., when analyzing discrete simulation snapshots), you can disable smoothing in the Inspector.
Transition Curves for More Control
To go a step further, consider adjusting the easing curve in the animation settings. This curve modifies how your parameters interpolate across time — for example, slowing down at the start or end of a motion to better highlight complex events. This adds a layer of expressiveness and clarity to your animations, especially when you’re showing detailed mechanisms.
Pro Tip: Synchronizing Multiple Paths
You’re not limited to animating a single path. If you select multiple paths and apply the Play path animation, they will be synchronized automatically. This can be useful for comparing different conformations, viewing ensemble transitions, or tracking multiple molecules moving cooperatively.
Whether you’re deep into structure-based drug design, studying biochemical processes, or simply preparing teaching materials, mastering the Play path animation gives you a powerful visualization tool for dynamic molecular behavior.
To learn more, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/play-path/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.