If you’ve ever prepared a molecular animation to communicate a structural change, a docking process, or a molecular interaction, you’ve probably faced the question: How do I control the visual impact of when atoms appear or disappear? Smooth transitions can make your work easier to follow — and more engaging.
The Reveal atoms animation in SAMSON is designed exactly for this need. Instead of instantly changing the visibility of all atoms at once, you can create a progressive reveal that guides the viewer through your structure, step by step. This is particularly useful when visualizing complex systems, where overwhelming the audience with too many details at once could hinder understanding.
What is the “Reveal atoms” animation effect?
Unlike effects that rely on transparency, the Reveal atoms animation lets atoms (and the bonds between them) transition from invisible to visible across multiple frames, based on visibility states set over time.
In practice, this means your audience won’t suddenly see an entire molecule pop into existence. Instead, they’ll watch it materialize logically, frame by frame, which helps retain attention and emphasize the story you’re trying to tell with the model.
How does it work?
To use the animation:
- Select the atoms and bonds you want to animate.
- Double-click the Reveal atoms animation from the Animation panel in the Animator.
The animation includes four keyframes:
- Between keyframes 1 and 2: All selected atoms and their bonds are hidden.
- Between keyframes 2 and 3: The atoms progressively become visible, following their sequence in the current selection.
- Between keyframes 3 and 4: All targeted atoms and bonds are fully shown.
This precise control of atom visibility can help:
- Emphasize the construction of a biomolecular complex.
- Reveal points of contact or structural components during binding simulations.
- Visually narrate a conformational change.
Customize the Reveal
If you wish to further fine-tune how gradually or abruptly atoms fade into view, you can tweak the easing curve. Slower reveals can build suspense or simulate step-by-step experimental discovery. Faster transitions can be used in spots where you’re aligning with narration or user attention spans.
Why this matters for molecular modelers
Too often, viewers lose track of what’s being shown when animations are too abrupt or complex. By using a structured reveal, you can direct attention and improve clarity — whether you’re publishing a scientific video clip or explaining a mechanism to collaborators.
Used wisely, the Reveal atoms animation becomes a storytelling tool. It helps you pace the delivery of content, which makes your animations not just scientifically correct, but also visually digestible.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.