When preparing scientific presentations or molecular animations, one common frustration faced by structural biologists and molecular modelers is presenting complex atomic transformations in a clear, smooth, and repeatable way. Often, the motion of molecules is illustrated frame-by-frame, requiring tedious positional updates that are hard to manage as animation complexity increases. Fortunately, SAMSON offers a solution with the Move atoms animation effect, simplifying this process through intuitive keyframe-based transformations.
This blog post focuses on the practical use of the Move atoms animation in SAMSON to create seamless and controlled molecular motions. This technique is ideal for researchers and students who want to visually communicate concepts such as conformational changes, docking processes, or nanostructure formation — without diving into complicated scripting.
Animating Atom Positions with Keyframes
The Move atoms animation effect allows you to interpolate the positions of selected atoms between keyframes. This means you can define the start and end positions of a group of atoms and SAMSON will automatically generate the intermediate frames, making the motion appear continuous and smooth.
Here’s how you can add and edit motion in SAMSON using this feature:
- Select the atoms you want to animate. You can position them manually or using the built-in Move editors.
- Double-click on the Move atoms animation effect in the Animation panel. This adds the first keyframe.
- Move forward in the animation timeline, reposition the atoms, and insert another keyframe. SAMSON will interpolate the motion.
This process reduces the cognitive load of managing dozens of frames manually and allows scientific communicators to focus more on clarity of visuals rather than technical animation details.
Visual Editing & Flexibility
Once keyframes are placed, you can modify them in several ways:
- Drag keyframes along the animation track to adjust timing
- Use animation controllers to manipulate atom positions directly in the viewport
- For custom transformations like twisting, temporarily hide the Move atoms controllers and use other editors (e.g., Twister editor)
Adding Smoothing and Custom Interpolation
Flexibility in presentation is essential, and that’s where SAMSON gives you full control over how atoms move between frames. In the Inspector, you can enable smoothing and adjust interpolation using easing curves. This allows you to give a more natural feel to motion — for example, ensuring that atoms accelerate at the start and decelerate at the end, mimicking real-world dynamics.
Efficient Edits and Keyframe Control
If you need to change part of the animation later, there’s no need to redo everything. Just move the atoms at a given frame and the changes are reflected immediately. Redundant or misplaced keyframes can be removed with a simple right-click in the Animator’s track view.
Try it With Real Examples
Several interactive documents using the Move atoms effect are available through SAMSON Connect, such as:
Whether you need to explain nanoscale motions or simulate a molecular assembly process for a lecture or research presentation, this animation technique provides clarity and saves time.
To learn more, visit the full documentation page on the Move atoms animation effect: https://documentation.samson-connect.net/users/latest/animations/move-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net