Molecular modelers sometimes need to visually represent atomic motion in custom ways—for simulations, presentations, or educational purposes. But creating smooth, controllable animations without writing code can be a challenge.
This is where SAMSON’s Move atoms animation comes in handy.
If you’ve ever wanted to interpolate atomic positions over time for a structure, SAMSON’s keyframe-based animation system offers an intuitive, graphical approach. Whether you’re presenting the dynamic behavior of a molecule, twisting a nanotube, or visualizing design changes in real time, the Move atoms feature can help.
What is the Move atoms animation?
This animation makes atoms interpolate between positions defined by keyframes that you manually add. You define the movement at specific frames, and SAMSON takes care of generating the in-between positions for a smooth animation.
Step-by-step animation: move atoms with intent
Here is a basic workflow for using this feature effectively:
- Position and select atoms: Start by placing your atoms where you’d like the motion to begin. Then select them.
- Add the first keyframe: Open the Animator, then double-click on the Move atoms animation effect from the Animation panel. This initializes the animation with a starting keyframe.
- Create movement: Move to a later frame in the animation track, modify the positions of atoms, and another keyframe will reflect the new state. Atoms will now interpolate between those positions over time.
- Adjust interpolation: If you want to control the nature of the transition, tweak the easing curves and smoothing options in the Inspector panel to control acceleration and deceleration.
Refining the animation
You’re not stuck with initial decisions! You can freely move keyframes along the animation timeline, and right-click on them to remove unwanted ones. This makes it easy to experiment and refine animations.
Using custom transformations
Need more complex edits? You can temporarily hide the animation controller and use tools like the Move editors or the Twister editor. These let you apply translations, rotations, or twists to atomic structures, all with visual feedback. When done, simply add a new keyframe to lock in those changes.
Where this helps
Such animations are valuable for communicating concepts: molecular flexibility, changes due to external forces, or simply walking through molecular mechanisms. And with everything controlled through an interface—no programming required—it lets domain experts focus on science, not code.
To explore the Move atoms animation options in depth, including easing curves and controller behavior, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/move-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.