One recurring challenge in molecular modeling is how to build better visual narratives when presenting mechanisms, processes, or molecular structures. Whether you’re preparing for a lecture, scientific presentation, or simply want to communicate structural insight more clearly, animated transitions help guide your audience step by step. A common pain: atoms and bonds appearing all at once can overwhelm the viewer, making it harder to highlight what matters over time.
In SAMSON, the integrative molecular design platform, there’s a lesser-known but useful animation effect you can apply to address this issue: Reveal atoms.
What does “Reveal atoms” do?
As its name suggests, this animation progressively makes atoms and their bonds appear between two points in time. But importantly, it’s not just a fade-in — the atoms are actually shown one after another, based on the order you selected them. This adds a controlled pacing to your animation and focuses the viewer’s attention.
And here’s a key point: this effect doesn’t rely on adjusting transparency. Instead, atoms and bonds are toggled more dramatically using visibility, so they’re either there or not — no distractions or half-visible noise on screen.
How to add the effect
To try it out in SAMSON:
- Select the atoms (and any connecting bonds) that you want to appear over time. You can determine the reveal order by how you select them — first to last.
- Open the Animation panel inside the Animator.
- Double-click on the Reveal atoms animation effect.
How the keyframes work
The animation uses four keyframes to control visibility over time:
- Keyframe 1 to 2: All selected atoms and bonds are hidden.
- Keyframe 2 to 3: Atoms and their connecting bonds are revealed progressively, following the selection order.
- Keyframe 3 to 4: Full visibility — all atoms and bonds are shown.
Don’t forget, you can move these keyframes to change when each part occurs.
Tuning the animation pace
This is where things get interesting. By adjusting the Easing curve, you can control how smoothly (or suddenly) the reveal happens. Want to slow down the start and speed up at the end? Or vice versa? The Easing curve lets you tweak timing until the motion fits your story.
Where this helps
The Reveal atoms effect is especially useful in situations such as:
- Demonstrating molecular assembly mechanisms
- Explaining how ligands approach binding pockets
- Highlighting structural components progressively (e.g., amino acids in an active site)
- Walking audiences through large molecular architectures one region at a time
This small animation detail can enhance clarity and improve audience retention — especially when presenting to people without a molecular background.
For more guidance and examples, visit the Reveal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.