When preparing molecular animations, one common challenge for modelers is to highlight changes — whether it’s a reaction step or a conformational switch — without confusing the viewer. Too many rapid visual transformations or sudden structure appearances can overwhelm audiences unfamiliar with atomic detail.
This is where the Reveal atoms animation in SAMSON makes a difference.
Rather than fading in atoms through transparency (which can create misleading depth perception), the Reveal atoms animation effect gradually makes atoms and their bonds visible between two frames. This subtle progressive reveal creates a clear and controlled storytelling sequence in molecular animations. It draws attention to structure emergence, step-by-step, helping your audience follow the science.
Why Use This Instead of a Fade In?
There’s a subtle, but important, distinction.
- Transparency suggests atoms are still present, just less visible, which may not match the intended molecular mechanism.
- Visibility communicates appearance or disappearance — perfect for showing bond formation, nucleation, or complex assembly.
This method is especially helpful when explaining mechanisms like drug binding, molecular self-assembly, or material growth processes.
How to Use Reveal Atoms in SAMSON
Using the Reveal atoms animation consists of selecting the atoms and bonds that should appear progressively, and positioning keyframes in the Animator.
- Select the atoms and bonds you want to progressively reveal.
- Open the Animation panel in the Animator.
- Double-click on the Reveal atoms animation effect.
You will now see 4 keyframes:
- Keyframes 1 ➝ 2: Atoms are hidden.
- Keyframes 2 ➝ 3: Atoms appear progressively in the selection order. Bonds are shown only between atoms already shown.
- Keyframes 3 ➝ 4: All specified atoms and bonds are fully visible.
You can move the position of keyframes along the timeline, making the transition longer or shorter. You can also fine-tune the pace using easing curves to test various acceleration effects for a more organic or mechanical feel.
Here is an example of how it looks in action:
Animating Molecular Growth or Complex Assembly
This animation is particularly suited for educational materials or scenario demonstrations where molecular structures are built progressively. You can even synchronize narration or text annotations alongside the animation, creating layered insights for students or stakeholders.
Finally, animations based on visibility rather than object transformation often lead to straight-forward rendering, reducing confusion in scenes with multiple overlapping effects.
To learn more about the Reveal atoms animation and how to use it effectively, visit the SAMSON documentation here: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.