Presenting molecular structures effectively is often as important as building them. Whether you’re preparing a lecture, visual abstract, or research video, storytelling through molecule animations can engage your audience in ways static images can’t. But one recurring challenge many molecular modelers face is how to emphasize how structures form or assemble over time—without becoming visually overwhelming.
This is where the Reveal atoms animation effect in SAMSON comes into play. It enables you to show atoms—and the bonds between them—progressively, guiding the viewer step by step through structural formation. This can be helpful for illustrating everything from macromolecular assembly to ligand-binding events or revealing substructures in complex systems.
What is ‘Reveal atoms’?
The Reveal atoms animation does exactly what its name suggests: it progressively makes atoms and their bonds visible between two key animation frames. Importantly, it uses visibility toggling rather than partial transparency. This makes it more distinct and uncluttered, especially when compared to effects that rely on faded visuals.
When to use it?
Consider the following situations where this animation can be especially useful:
- Illustrating the building of a molecule from functional groups or subcomponents
- Animating the progressive appearance of binding pockets or active sites
- Revealing results from dynamic simulations where you want to show emerging molecular structures
- Teaching how structural domains come together in a protein complex
How to apply it?
From your SAMSON project:
- Select the atoms and bonds you want to reveal.
- Open the Animation panel in the Animator.
- Double-click Reveal atoms.
This effect creates four keyframes. Here’s what each set does:
- Keyframes 1 → 2: Atoms and bonds are hidden
- Keyframes 2 → 3: Atoms and bonds progressively appear, based on your selection order
- Keyframes 3 → 4: All chosen atoms and bonds become fully visible
You can move the keyframes around the timeline as needed to adapt the timing. This allows for fine control over pacing, either to speed up or slow down the visual narrative.
Tuning the effect
The interpolation of how atoms become visible can be further customized. To make the transitions smoother or more dynamic, you can adjust the Easing curve. This is especially useful when you’re trying to synchronize the animation with narration, music, or other timed visuals.
Why it’s useful
Unlike transparency-based methods, visibility-based animations like ‘Reveal atoms’ are clearer and less prone to visual clutter. They can also help viewers follow complicated structures more intuitively—useful for both research communication and education.
Ready to try it out? Learn more about the Reveal atoms animation on the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.