Molecular modelers often face a common challenge when presenting their work: how to visually communicate the dynamic process of molecular assembly or structural evolution across frames. Whether you’re demonstrating the progressive construction of a biomolecular complex or tracking which atoms become involved during a binding event, conveying this visually—especially to a general audience or collaborators outside your field—can be hard.
Simply fading elements in and out may not provide the clarity needed. Transparency is helpful for many illustrations, but sometimes, what you really need is a clean, stepwise reveal: atoms and bonds appearing progressively, following an order as they become relevant in your story. This is where the Reveal Atoms animation in SAMSON can help.
What Does the “Reveal Atoms” Animation Do?
The Reveal atoms animation is designed specifically to make atoms (and bonds between them) appear progressively, between two frames. Think of a molecular model slowly coming to life—atom by atom, bond by bond—without relying on opacity changes. It provides an intuitive, non-distracting way to visualize which parts of a structure are being introduced at each stage of your animation.
This animation works by adjusting the visibility of molecular entities, not their transparency. The result is a crisp and distraction-free focus on what’s new or important in your frame.
How to Set It Up
Here’s a step-by-step guide to using the Reveal Atoms animation in SAMSON:
- Select the atoms and the bonds between them that you wish to animate.
- Double-click the Reveal atoms effect in the Animation panel of the Animator.
Once added, you’ll see that the animation includes four keyframes:
- Keyframes 1 → 2: all the selected atoms and bonds are hidden.
- Keyframes 2 → 3: atoms and their connecting bonds progressively appear, in order of selection.
- Keyframes 3 → 4: all specified atoms and bonds are fully revealed.
The reveal is ordered, meaning if you’ve selected atoms in a logical or spatial sequence (e.g., N-to-C terminal or from core outwards), the animation will follow that order—perfect for illustrating pathways or synthesis steps.
Visual Example: Building a Molecule
In this example, the atoms and bonds gradually materialize, clearly communicating the growth or exploration of a structure. This creates a cleaner and more engaging visual narrative, especially useful in presentations, educational material, or video abstracts.
Tips and Customization
You can adjust the timing by moving the animation’s keyframes along the timeline. Additionally, SAMSON allows you to define the easing curve, so you can fine-tune the motion speed—make it linear, ease-in, ease-out, or use more advanced curves for complex timing profiles.
Because the reveal depends on the order of selection, you can craft stories by carefully choosing which atoms are revealed first. For example, highlight functional groups, active sites, or important mutations in a relevant sequence.
When to Use This
The Reveal atoms tool is ideal when you need to:
- Illustrate the structural formation of molecules or complexes step-by-step
- Emphasize which atoms or groups become involved during a certain reaction or binding event
- Create educational animations that need clarity and focus over flashy effects
If you’re leading a workshop, teaching, or simply want your molecular story to be more accessible, this feature offers a simple solution to a common communication problem in molecular modeling.
Learn more about the Reveal atoms animation 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.