Creating engaging molecular animations is essential for presentations, teaching, or visually exploring structural transformations. But here’s a common challenge molecular modelers face: how to precisely control the motion of atoms over time without writing complex scripts or using several disconnected tools?
In SAMSON, the Move atoms animation provides a clean and intuitive solution. With this animation effect, you can define specific positions for atoms at different frames and let SAMSON interpolate the motion in between. It’s a keyframing-based system, where users visually program motion in a timeline, much like animating in video or 3D software.
Why would you want to animate atoms this way?
Let’s say you’re modeling a deformation of a carbon nanotube, folding of a nanostructure, or any transformation between molecular states. Using Move atoms allows you to:
- Illustrate molecular events clearly over time, frame by frame
- Focus viewer attention on specific atomic trajectories
- Avoid scripting or keying positions manually via code
How to use the Move atoms animation
In your Animator panel in SAMSON, double-clicking on the Move atoms animation effect adds your first keyframe. Position the atoms where you want them at the beginning of the animation. Then, at another frame on the animation timeline, move the atoms to their next intended position (either by dragging directly or using editors like the Twister or Move editors), and insert a new keyframe. SAMSON handles the smooth interpolation between these positions.
For instance, you might start with a nanotube in its relaxed state and apply transformations frame by frame to create a bending or twisting animation. Here’s what that might look like:
Tip: Temporarily hiding animation controllers
If you’re using editors like Twister to apply non-linear deformations, you might want to temporarily hide the Move atoms controllers. Head to the Document view and uncheck the controllers to keep the view clean. When you’re done, just switch back to the Select editor.
Controlling animation smoothness
Need finer timing control? You can adjust interpolation behavior between keyframes using the Easing curve and toggle smoothing in the Inspector. This lets you speed up or slow down transitions as desired—useful for emphasizing moments in your animation.
Examples in action
Some public SAMSON documents show these techniques applied in real cases, like:
If you’re frequently preparing visuals or teaching materials in molecular sciences, mastering the Move atoms animation can save lots of time while producing clear, frame-accurate results.
To learn more about the Move atoms animation in SAMSON and explore detailed steps, visit the official documentation here: Move atoms – Animation documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.