Molecular modelers often spend significant time analyzing the pathways between two conformations of a molecule: from binding and folding events to transitions between states discovered via simulations. While forward trajectories are the norm, playing them in reverse can offer unique insights—especially when interpreting results, presenting molecular processes, or simply exploring alternative conformational changes without rerunning simulations.
This is where SAMSON’s Play reverse path animation comes into play. It makes it easy to revisit a molecular path backward, directly inside the Animator interface, without needing to generate additional data or perform new calculations.
Why reverse animations?
Playing a trajectory in reverse may seem counterintuitive at first, but it solves several important visualization and analysis pains:
- Inspecting dissociation events: If only an association path is recorded, visualizing it in reverse helps understand what happens during dissociation—this can be crucial in drug design or protein-protein interaction studies.
- Creating cyclic or reversible animations: When two conformations are connected, looping animations (forward and then reverse) provide smooth and complete visualizations—very useful during presentations or for educational purposes.
- Exploring energetics intuitively: By watching reverse paths, researchers might perceive energetic barriers and transitions more clearly, particularly if enhanced sampling methods have been used.
How to use the ‘Play reverse path’ animation in SAMSON
The process is straightforward:
- Select a Path node in your model. This node stores the trajectory to be animated.
- Open the Animation panel in the Animator.
- Double-click on the Play reverse path effect to add it to your timeline.
- Adjust the keyframes in the timeline to control duration and playback segment.
The playback will show the molecule moving from its final state to its initial conformation, following the defined trajectory but in reverse.
Synchronization of multiple reverse paths
If you’re working with several related paths (e.g., multiple simulations of the same event or different parts of a large complex), you can select multiple path nodes and apply the animation to all of them. SAMSON synchronizes these during playback—useful for comparing responses of domains or subunits.
Options and customization
If the number of animation frames differs from the number of frames in the path, SAMSON will smooth the path by default. You can disable this feature in the Inspector for a more faithful step-by-step representation. Additionally, under the animation properties, you can fine-tune how movement is interpolated using the Easing curve, which lets you define acceleration and deceleration between keyframes (linear, ease-in-out, etc.).
When to use this feature
Reverse playback is particularly handy when:
- Visualizing exit pathways of ligands from binding sites when only entry paths are recorded.
- Creating presentation-ready animations that show system cycles (e.g., enzyme open ↔ closed states).
- Generating hypotheses about alternative mechanisms or exploring how structures might revert naturally.
To learn more, visit the original documentation page: Play reverse path – Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.