One of the recurring challenges in molecular modeling is conveying motion—especially when creating educational or presentation materials about dynamic systems. Whether you’re illustrating a conformational transition, animating a simulation step, or presenting a mechanical movement inside a nanosystem, static images often fall short. That’s where animation with keyframes becomes essential.
In SAMSON, the molecular design platform, the Move atoms animation lets users interpolate the positions of selected atoms over time, facilitating smooth and precise molecular motion animations using keyframes. Here’s how (and why) this can solve a common pain point: showing meaningful transitions in molecular structures in a flexible yet intuitive way.
Why Animation with Keyframes Helps
When presenting molecular mechanisms—think conformational changes, atom displacements, or nanostructure motions—it’s often necessary to show how specific parts of a system move from one place to another. Manually creating images for every frame is time-consuming and hard to tune. Using keyframe animation solves this by letting you define critical frames between which the system transitions automatically.
Let’s walk through how to use SAMSON’s Move atoms animation to do this effectively.
Setting Up: Adding the Animation
Before animating, select the atoms you want to move. Then, simply double-click the Move atoms effect in the Animation panel in the Animator. This sets your first keyframe.
Add another keyframe wherever you’d like the atoms to end up. On the animation timeline, click at the desired frame, reposition your atoms, and the platform will automatically interpolate motion between your keyframes.
Advanced Editors and Keyframe Control
If you want to use more advanced motion tools, disable the Move atoms animation controllers in the Document view. You can then use editors like the Twister or other Move editors, apply detailed transformations, and insert a keyframe after each transformation. This toggling flexibility makes complex molecular animations much easier to manage and fine-tune.
Fine-Tune Your Molecular Motion
Once your keyframes are in place, you can refine motion through the Inspector. Options include modifying the easing curve (how motion behaves over time), and enabling or disabling smoothing.
This gives you nuanced control over how your system appears to move—linear, ease-in, ease-out, or custom transitions.
What If You Make a Mistake?
Don’t worry—keyframes are not permanent. To remove any keyframe, just right-click on it in the Animator's Track view and choose Remove keyframe. This editability encourages experimentation.
Applications and Examples
You can find real-world examples of the Move atoms animation inside downloadable presentations on SAMSON Connect:
These are excellent starting points for those wanting to see examples of clean atomic motion in practice.
Conclusion
Animating atom motion through keyframes inside SAMSON turns complex molecular interactions into clear, visual stories. Whether you’re demonstrating folding mechanics, illustrating material deformation, or just want to bring a model to life, the Move atoms animation is a practical, easy-to-use tool for molecular modelers who need more than static images.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.