When communicating complex molecular behavior, nothing beats a well-crafted animation. Whether you’re illustrating ligand dynamics, protein flexibility, or simply aligning datasets for a presentation, conveying atomic motion in an intuitive way matters. Many molecular modelers, however, still rely on tedious scripting or third-party tools to animate molecular movement—often leading to errors, time sinks, and steep learning curves.
If you’re looking to animate atoms directly in your visualizing environment, SAMSON‘s Move atoms animation functionality offers a streamlined solution: visually-driven, keyframe-based motion—no scripting required.
What does ‘Move atoms’ do exactly?
The Move atoms animation in SAMSON lets atoms gradually transition between user-defined positions. Instead of hard-cut transitions or complicated trajectory files, you can visually interpolate positions through keyframes right within the SAMSON interface.
This method is easy to use and well-suited for creating animations that communicate conformational changes, molecular transitions, or pathways—without requiring any programming knowledge.
How it works: a step-by-step overview
1. Select Atoms: Start by positioning and selecting the atoms you want to animate. Selection tools in SAMSON make this straightforward.
2. Add Starting Keyframe: Double-click “Move atoms” in the Animation panel to set the first position (i.e., the starting keyframe).
3. Add New Position via Keyframe: Move the timeline to a desired frame, reposition atoms in the 3D workspace, and a new keyframe will appear. SAMSON visually interpolates the transition.
Here’s what this looks like in motion:
4. Fine-Tune the Movement: Modify movement behavior with an Easing curve to control acceleration/deceleration, or toggle smoothing effects to improve visual continuity.
Advanced Use: Mix with Other Editors
The real flexibility comes when combining Move atoms with SAMSON’s other transformation tools, such as the Move editors or the Twister editor. Simply hide the animation’s transformation controls temporarily using the Document view, apply new transformations using the desired tool, then return to animation mode and add fresh keyframes.
This makes it possible to integrate complex deformations or rotations while still tracking everything through keyframes.
Why this matters
This visually driven technique is ideal for modelers who:
- Don’t have time to code animation scripts
- Need precise control over molecular transformations
- Want instant visual feedback while editing animations
- Create educational materials or scientific presentations
From visualizing nanotube deformations to modeling complex molecular machines, the Move atoms feature removes technical hurdles and gives back creative control—right inside the environment you’re already working in.
To learn more and explore detailed examples, check out the official documentation: Move Atoms Animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download them from SAMSON Connect.