When working with molecular simulations, understanding a system’s behavior often requires going back and forth between different conformations or timepoints. Whether you’re reviewing docking animations, conformational transitions, or reaction paths, having precise control over the direction of playback can make interpretation easier.
One frequently encountered frustration by molecular modelers is the lack of native support in many platforms for replaying a trajectory in reverse. This functionality is especially helpful when you want to validate a mechanism, check pathway reversibility, or simply observe how a ligand leaves a binding site.
In SAMSON, this challenge is addressed with the Play reverse path animation effect. In this blog post, we’ll walk you through how to use it effectively, and why smoothly reversing a path might streamline your analysis workflow.
What is the Play Reverse Path Animation?
The Play reverse path animation in SAMSON allows users to replay a set of coordinates (a Path node) between two keyframes in reverse order.
This can be used to:
- Review a molecular trajectory in the opposite direction
- Cycle between conformations forward and backward
- Explore the symmetry or reversibility of interactions such as ligand binding or protein folding
Unlike simply scrubbing a timeline backward, the reverse path animation ensures your visualization is smooth and synchronized across selections.
Adding the Animation
Here is how to get started:
- Select the Path node you want to reverse. This node typically holds a trajectory.
- Open the Animation panel of the Animator.
- Double-click on the animation effect named Play reverse path.
- The animation will be created between two keyframes. You can adjust their position on the timeline to control the playback duration.
Controlling Animation Behavior
When the number of frames in your path doesn’t match the number of frames in the animation, SAMSON automatically applies smoothing to interpolate the movement.
This is helpful for producing polished animations, but if you need strict frame-by-frame fidelity (e.g., for analysis), you can disable smoothing using the Inspector.
Advanced Playback Control
The Easing curve setting in the Inspector allows for fine-tuning how motion is interpolated between frames over time. For instance, you can ease in or out of a movement, modeling realistic acceleration or deceleration patterns during molecular motion.
Whether you’re creating a presentation or just trying to better understand a transition state, these controls add needed flexibility to how your data is viewed and communicated.
Conclusion
The Play reverse path animation in SAMSON is a practical solution for anyone revisiting molecular dynamics trajectories in reverse. It’s easy to set up, and its synchronization capabilities allow you to compare multiple trajectories while refining your timeline with simple controls.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/play-reverse-path/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.