Creating effective molecular animations can be tricky, especially when you want to illustrate how a molecule becomes structured, how atoms bond progressively, or how a system transitions from disorder to order over time. One frequent challenge is controlling the visibility of atoms and bonds over time, without resorting to transparency effects that can be misleading in scientific presentations.
The Reveal atoms animation effect in SAMSON provides a solution to this. Instead of adjusting opacity, it uses visibility to make atoms and their bonds appear gradually, frame by frame―a clear and simple way to help viewers understand molecular assembly or structural transitions.
What the Reveal Atoms Effect Does
The Reveal atoms animation shows selected atoms (and bonds between them) gradually appearing over time. Rather than fading in with transparency, atoms and bonds go from completely hidden to fully visible. This is helpful in contexts where visual precision and clarity are important, such as in educational animations or during scientific communication.
It consists of four keyframes:
- Keyframes 1 → 2: All selected atoms and relevant bonds are hidden.
- Keyframes 2 → 3: Atoms and bonds progressively appear in the order they are selected. This part creates the actual reveal effect.
- Keyframes 3 → 4: All selected atoms and bonds are shown completely.
This setup lets you show how a molecular fragment grows, how a ligand enters a binding site, or even how a full molecule builds up from components―with full control over timing and clarity.
How to Use It
Here’s a step-by-step summary:
- Select the atoms and bonds you want to reveal. Their order in the selection affects the appearance sequence.
- In the Animator, go to the Animation panel and double-click on “Reveal atoms”.
- Adjust keyframes to control when atoms are hidden, when they appear, and when they’re all revealed.
- You can also modify the easing curve to change how smooth or abrupt the animation feels.
Why Visibility Over Transparency?
Transparency effects can sometimes create ambiguity, especially when showing many overlapping atoms. Full visibility toggling is clearer: what’s visible is fully there, and what’s not is completely out of view. It avoids visual clutter and eliminates misinterpretations that could result from half-visible atoms.
When to Use This
- When illustrating how molecules assemble or fold.
- When describing step-by-step bond formation in reaction mechanisms.
- In teaching materials for students at various levels.
- In presentations where clarity and sequence matter more than visual flair.
Here’s what it looks like in a sample animation:
With just a few clicks, you can build orderly, comprehensible animations that support molecular education and presentation goals without confusion. To explore the Reveal atoms animation further, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.