When creating animations of molecular processes, clarity and timing can make all the difference. Whether you’re showing molecular assembly, drug docking, or simply highlighting part of a structure, there’s often a need to make specific groups of atoms appear progressively to tell your story in a clear, engaging way. But how can you do that without suddenly flashing atoms into view, which can confuse non-expert viewers?
This is where SAMSON’s Reveal atoms animation comes in handy. It allows you to introduce atoms (and the bonds between them) gradually over time by adjusting their visibility—without relying on transparency. This method ensures that attention is focused precisely where and when you need it and that changes to the molecular structure are easy to follow.
One animation, four stages
The Reveal atoms animation effect works across four keyframes:
- Keyframes 1 to 2: The chosen atoms are fully hidden.
- Keyframes 2 to 3: The atoms appear progressively based on their order in your selection. Bonds between visible atoms are shown too.
- Keyframes 3 to 4: All specified atoms are now fully visible.
This setup gives you precise control over the timing and sequence of visualization. It’s particularly useful when you want to show how a ligand or functional group enters a binding site, or when walking the viewer through a molecular structure step by step.
How to add the effect
Adding the Reveal atoms effect to your animation is simple:
- Select the atoms and bonds you want to reveal.
- In the Animation panel, double-click on Reveal atoms.
- Adjust the keyframes to control the duration of each phase.
You can modify how quickly atoms appear by editing the Easing curve. This gives you control over the pacing of the animation—for instance, whether atoms appear linearly over time or accelerate into view.
When to use it
The Reveal atoms effect isn’t just cosmetic. It’s a storytelling tool.
- Want to focus attention on a protein active site? Hide the rest and reveal it gradually.
- Explaining a molecular construction or experiment timeline? Highlight each part over time.
- Need to simplify the visual complexity of a dense structure? Use Reveal atoms to introduce only the relevant components.
By improving the intelligibility of your molecular animations, this effect helps make your work more accessible to colleagues, students, and interdisciplinary teams.
Learn more about the Reveal atoms animation in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at https://www.samson-connect.net.