Visualizing molecular dynamics or conformational transitions often involves analyzing and comparing several trajectory paths. Whether you are inspecting a ligand binding pathway, protein folding steps, or exploring alternative conformations, understanding how molecules move over time is key. But how can you effectively synchronize and display multiple paths in a single animation?
In SAMSON, the Play path animation effect lets you animate movement along one or more paths. This becomes especially useful during trajectory comparisons or when showcasing conformational variability. Here’s a closer look at why and how you would use this functionality.
Why Play Multiple Paths at Once?
When molecular modelers generate different sampling trajectories (from simulations, interactive exploration, or docking runs), comparing them visually helps identify common structural regions and transitions. Playing these simultaneously allows:
- Direct visual comparison of structurally distinct paths
- Communication of differences in conformational timing or extent
- Exploration of molecular flexibility in presentations or publications
How to Do It in SAMSON
1. First, select the paths you want to play. These are typically nodes that store coordinate sequences (trajectories).
2. Then, add the Play path animation via the Animation panel in the Animator. You simply double-click on the effect to add it to your animation timeline.
3. When multiple paths are added, they are automatically synchronized. This means animations will start and end together, regardless of the number of frames in each path.
4. If the number of frames in your keyframe range differs from the number of frames in the path, SAMSON interpolates (smooths) the motion. You can turn off path smoothing if desired, from the Inspector.
Tuning Your Animation
Use keyframes to control when paths get played in your animation timeline. Feel free to move these frames to accelerate or slow down the motion.
To further refine the look and feel of the path playback, you can customize how motion parameters are interpolated between frames by adjusting the easing curve.
Summary
Synchronizing and animating multiple paths together can be a simple yet powerful way to better understand molecular motion. SAMSON’s Play path animation effect provides a flexible and visual approach to trajectory exploration. Whether you’re preparing a publication figure or just analyzing movement across alternate states, this feature helps make molecular behavior more accessible.
To learn more, visit the original 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.