Creating animations of molecular behavior can be essential for illustrating dynamics, conformational changes, or transformations in chemical systems. However, many molecular modelers find this process time-consuming or difficult to control precisely. If you’re looking for a straightforward way to animate changes in molecular structures over time, the Move atoms animation feature in SAMSON provides a practical solution using keyframes.
The Move atoms animation interpolates atom positions between keyframes, creating smooth transitions that can help explain a wide range of molecular phenomena—without the need to script or simulate. This can be useful in educational settings, molecular storytelling, or visual exploration of mechanisms.
What Problem Does It Solve?
Let’s say you’re working on a presentation or video and want to show a molecule twisting or moving between conformations you’ve defined. You want to communicate an idea visually without running a full dynamics simulation. Manually positioning atoms for each frame is tedious, and relying solely on simulation often lacks control or reproducibility for visual storytelling.
This is where keyframed animation becomes useful—especially using SAMSON’s Move atoms animation with its built-in controllers and timeline interface.
Getting Started
- First, select the atoms you want to animate.
- Open the Animator, go to the Animation panel, and double-click on Move atoms. This adds the initial keyframe with the current atom positions.
- Next, move the timeline slider to a new frame, use the on-screen controllers or external editors to reposition the atoms where you want them to appear at that moment in time, and a second keyframe will be added.
This creates a smooth interpolation between the two atom positions—essentially making the atoms move. You can repeat the process to build a full motion sequence.
Tips for More Control
- You can move keyframes to adjust timing by dragging them along the timeline.
- To remove a keyframe, right-click on it in the Animator’s Track view and choose “Remove keyframe.”
- If the default animation curves feel unnatural, you can modify the interpolation by adjusting the easing curve and switching smoothing on or off.
Working with Advanced Transforms
Sometimes you may want to use specific motion editors (like a twisting editor) instead of the built-in Move atoms animation controllers. This is possible: just hide the Move atoms animation controllers from the Document view, apply your transformations using the preferred editor, and add a new keyframe. After editing, return to the Select editor to continue building your animation.
When to Use This
This feature is especially useful when you’re working on demonstrations of molecular movement, nanostructure transformations, or even hybrid animations that combine conformational changes with structural mechanics (e.g., twisting nanotubes). You stay in full control of the key steps while leveraging automatic interpolation.
To learn more and explore additional options for customizing your molecular animations, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Discover more and download at https://www.samson-connect.net.