Creating scientific animations of molecular systems can be time-consuming, and even experienced modelers sometimes face challenges with accurately communicating dynamic behaviors. One common pain point many encounter is smoothly moving atoms or molecular fragments across frames without introducing artifacts or abrupt transitions.
The Move atoms animation feature in SAMSON provides a flexible way to animate molecular systems by interpolating atom positions between defined states—keyframes—within a timeline. If you’ve ever found yourself repeatedly repositioning molecules frame-by-frame, trying to simulate a conformational change or molecular assembly process, this tool can save you valuable time.
Fine-Tuning Molecular Motion with Keyframes
After selecting the atoms you want to move, insert the Move atoms animation by double-clicking it in the Animation panel of the Animator. This sets your first keyframe. You can then insert new keyframes at different frames of the timeline and manipulate the atoms’ positions at each of these points. SAMSON will handle the interpolation, smoothly transitioning the molecule from one state to another between keyframes.
Using External Editors for More Precise Transformations
Sometimes the built-in Move atoms controllers may not offer the specific manipulation tools you need—for example, if you want to rotate a section of a molecule using a dedicated editor. You can disable the Move atoms controllers through the Document view and instead switch to an appropriate transformation tool, such as the Twister editor. Apply your transformation, then add a new keyframe.
Managing the Animation Timeline
Animations are rarely correct on the first try. The Animator allows you to adjust timing by moving keyframes in the track view. If you need to remove a keyframe entirely, just right-click on it and select “Remove keyframe.”
Smoothness and Timing: The Easing Curve
You can refine how atoms accelerate and decelerate between keyframes by modifying the easing curve. This is especially useful for showcasing molecular interactions that require naturalistic motion instead of linear transitions. You can enable or disable smoothing effects depending on the level of realism you want.
Why This Matters
Scientists often need to communicate structural transitions, reaction mechanisms, or pathway behaviors in a way that is visually intuitive. Instead of relying on static snapshots or struggle with external graphics tools, SAMSON’s Move atoms animation gives molecular modelers and educators a straightforward way to visualize dynamics directly from their working environment.
If you’re animating molecular processes or protein-ligand docking sequences, this approach will help ensure clarity of presentation and reduce the effort involved in producing useful visuals for presentations or publications.
Learn more about the Move atoms animation in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.