One of the frequent challenges in molecular modeling is presenting trajectories in a way that conveys structural changes clearly and seamlessly. Whether you’re cycling through conformations, visualizing motion along a reaction coordinate, or showing docking sequences, creating a smooth and synchronized animation can make a big difference.
The ‘Play path’ animation in SAMSON addresses this challenge by allowing you to easily animate molecular trajectories stored in path nodes—without writing scripts.
Why Use ‘Play path’?
Path nodes in SAMSON store frames of molecular structures across time, or configuration space. Using the ‘Play path’ animation, you can animate one or more of these paths between two frames in your animation timeline. This is particularly useful when you want to:
- Show a trajectory from atomistic simulations
- Cycle through docking poses or conformations
- Compare different protonation states or isomers using synchronized paths
The ability to synchronize multiple paths makes it powerful for comparative studies and presentations. The animation intuitively interpolates structures across frames, giving the appearance of smooth motion.
How It Works
To use the ‘Play path’ animation:
- Select one or more path nodes in your document. A path typically contains a series of conformations or trajectory frames.
- Open the Animation panel inside the Animator.
- Double-click on Play path. This adds the animation keyframes.
- Move the keyframes on the timeline to control the portion and flow of the animation.
By default, the path is interpolated to match the number of animation frames. This smoothing ensures visual continuity when animation duration doesn’t match trajectory length. However, if you prefer to display the actual sampling (e.g. for highlighting discrete steps), you can turn off smoothing in the Inspector.
Fine-Tuning the Animation
Once your animation is added, you can go further by adjusting interpolation behavior with the Easing curve. The easing curve modifies how quickly or slowly the transition between frames happens, making the animation more natural, or emphasizing particular moments:
Parameters for interpolation can include options like linear, ease-in, or ease-out, giving you control over timing without manually repositioning frames.
When to Avoid Scripting
Many researchers default to scripting to animate trajectories. But for qualitative assessments, quick presentations, or when time is limited, using features like ‘Play path’ is a lightweight and visual alternative. It keeps you close to your structural data, minimizing context-switching between tools.
If you’re publishing molecular videos or teaching molecular concepts, integrating animation directly in your modeling platform can also streamline your workflow dramatically. ‘Play path’ is ideal for that.
To explore the full documentation and other related features (like ‘Play reverse path’), 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.