When creating molecular animations to present simulations or structural analyses, clarity is often a challenge. Whether you’re building an educational visualization or prepping a presentation for collaborators, simply switching atoms on or off rarely provides the nuance needed to communicate your message effectively.
One helpful solution when transitioning between molecular states is the subtle step-by-step appearance of atoms. This is where the “Reveal atoms” animation in SAMSON can make a big difference. This animation effect lets you control when atoms and bonds progressively appear between two frames—based on their selection order—offering a much more controlled and polished transition.
Why use progressive reveal?
Progressive atom reveal can be useful for:
- Demonstrating the assembly of molecular systems
- Highlighting differences between conformations or time steps
- Directing your audience’s attention to specific structural components
- Improving clarity in complex systems by reducing visual clutter
This animation is based on binary visibility (not transparency), allowing atoms and bonds to stay either visible or hidden. This makes it ideal for building comparisons, educational content, or visual storytelling with maximum control.
How to set it up in SAMSON
To use the animation, follow these simple steps:
- Select the atoms and bonds you want to reveal progressively. Selection order matters—atoms will appear in this sequence.
- Open the Animator and go to the Animation panel.
- Double-click on the Reveal atoms effect.
Keyframe guide:
- Keyframes 1–2: All selected atoms and bonds are hidden.
- Keyframes 2–3: Atoms and bonds progressively appear based on selection order. Bonds between visible atoms also appear progressively.
- Keyframes 3–4: The full selection is now visible.
You can adjust the timing of each part of this progression by moving the keyframes as needed. This makes it easy to pace your animations according to the narrative you’re building.
Fine-tuning using Easing Curves
To smooth your animations even further, explore the Easing curve options. These give you control over how the animation accelerates or decelerates between frames, making the transitions feel more natural and dynamic.
When to consider Reveal over Appear
Although Appear and Reveal atoms might seem similar, they function differently. The “Appear” animation generally applies transparency-based changes, while “Reveal atoms” is purely about visibility states. If you want atoms to fade in, “Appear” is your go-to. But if you want atoms to pop into visibility one-by-one or in a certain sequence, “Reveal atoms” gives you greater control.
Example in Action
Below is a GIF showing a combination of the Conceal and Reveal atoms animations, demonstrating how atoms can be hidden and then revealed in a clean and visually informative way:
By using Reveal atoms thoughtfully, you can simplify what may otherwise be complex structural presentations, making your analyses clearer and more accessible to collaborators, students, or a broader audience.
To learn more and explore advanced animation options, check out the official documentation: 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 here: https://www.samson-connect.net