If you’ve ever worked with molecular dynamics simulations or generated conformational pathways, you know how important—and sometimes tedious—it can be to visually inspect your trajectories. Understanding transitions step by step can guide decisions in drug design, protein folding analysis, or conformational sampling. Yet, replaying full trajectories or navigating through key molecular conformations can feel cumbersome without the right tools.
In SAMSON, the integrative molecular design platform, there’s an animation effect called Play path that can simplify this process significantly. It lets you animate stored trajectories—called paths in SAMSON terminology—between two frames. Whether you’re following a complex folding mechanism or simply moving between molecular poses, this tool makes it easy to visualize changes clearly and smoothly.
Why use Play path?
Instead of clicking frame by frame through your trajectory, Play path animates the whole sequence for you. Even better, if you select several paths, they will be synchronized: a feature extremely useful when comparing different conformational routes or visualizing changes to multiple molecules simultaneously.
Here’s a common situation: the number of frames in your intended animation doesn’t match the number of frames in your trajectory. The Play path animation handles this gracefully by smoothing the animation automatically. If you need each frame to correspond precisely to a snapshot in your dataset, you can disable this smoothing in the Inspector.
Step-by-step: Adding the animation
To take advantage of Play path, just follow these steps:
- Select the path or trajectory you want to play. This is usually a path node in SAMSON.
- In the Animation panel, double-click Play path. This adds the animation to your sequence.
- Adjust the start and end keyframes as needed. The entire path will be interpolated between these frames.
Controlling the motion
A particularly useful feature is the ability to customize the way your path is animated. In the Inspector, you can modify the Easing curve. This determines how motion speeds up or slows down through the animation. For example, if you want a smooth acceleration or deceleration, you can adjust the curve accordingly.
When to use it
Use Play path anytime you need to:
- Visualize a molecular dynamics trajectory as an animation
- Cycle between known conformations to understand transitions
- Compare multiple conformational routes synchronously
This feature won’t replace detailed frame-by-frame analysis, but it’s a powerful way to quickly spot trends or check your work before a deeper dive.
To learn more, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.