Working with conformational pathways and molecular dynamics trajectories often requires efficient ways to visualize movement between structures or along predefined paths. Molecular modelers frequently face this need, whether to analyze results, showcase simulations, or communicate structural changes over time.
To help with this, SAMSON, the integrative molecular design platform, offers a useful animation feature called Play path. This feature allows users to animate the progression along a trajectory or between conformations by leveraging paths stored in the SAMSON data model.
Why Use the Play Path Animation?
Visualizing how a molecule transforms from one conformation to another—or how a ligand travels through a channel—can be critical for presentations, publications, or simply better understanding a complex simulation. The Play path animation lets you define a progression along a pre-existing path node and play it between two keyframes on a timeline. Whether you’re cycling through a few local minima or playing through a long simulation, this animation method provides a straightforward way to synchronize visualizations across multiple paths.
Getting Started
To apply the Play path animation:
- Select the path you want to animate. You can choose one or several; if you select more than one, their playback will be synchronized.
- Open the Animation panel in the Animator.
- Double-click the Play path animation to add it to the timeline.
- Adjust the starting and ending keyframes to control the playback span on the timeline.
Controlling the Playback
The animation will linearly interpolate movement through the frames of the path. However, if the number of animation frames doesn’t match the number of trajectory frames in the path, SAMSON will automatically apply a smoothing filter. This helps in visualizing transitions more fluidly. But what if you want frame-by-frame mapping without smoothing?
You can toggle path smoothing in the Inspector. Disabling smoothing is particularly useful when each frame contains meaningful data (e.g., frames of a simulation).
Customize Timing with Easing Curves
In SAMSON, you can further customize how the system moves through the animation using easing curves to interpolate between frames. This allows for playing the animation with non-linear timing—for example, to accelerate at the beginning and decelerate at the end, which often mimics more physically realistic behavior.
Synchronizing Multiple Paths
If your work involves comparing different molecular pathways—say, alternative transition paths between two conformations—you can animate several path nodes in parallel. This helps users compare motions side-by-side in the same timeframe, which is useful for structural biologists, medicinal chemists, and anyone exploring conformational ensembles.
Where Paths Come From
Paths in SAMSON usually result from sampling algorithms or simulations and are stored within Path nodes. If you’re running your own path-generating process (e.g., morphing or enhanced sampling), the results can be directly visualized using Play path.
To learn more, consult the official documentation on Play path.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.