If you’ve ever struggled to communicate molecular processes clearly in your presentations or publications, you’re not alone. A recurring challenge for molecular modelers is making animations that convey structural changes or molecular assemblies in a smooth and visually intuitive way. Jagged transitions or abrupt atom appearances can confuse viewers, especially those unfamiliar with molecular structures. One effective solution in SAMSON, the integrative molecular design platform, is the Reveal atoms animation.
This animation effect progressively reveals selected atoms and the bonds between them, allowing you to illustrate complex processes — such as self-assembly, molecular evolution, or docking — in a much more digestible way.
What Happens in a Reveal?
Unlike animations that fade molecules in or out through transparency, Reveal atoms works by toggling their visibility. If you want structures to feel like they are forming naturally, atom by atom, this tool offers a better alternative.
Here’s what happens step by step in the animation:
- Keyframes 1 to 2: All selected atoms and relevant bonds are hidden.
- Keyframes 2 to 3: Selected atoms and bonds progressively appear in the order they were selected.
- Keyframes 3 to 4: All selected elements are fully visible.
You can adjust the timing of each keyframe to control how fast (or slow) this reveal occurs. Whether you’re introducing ligands binding to a protein or revealing side chains one by one, this control helps tailor the animation to your message.
How to Add the Effect
Setting this up is straightforward:
- Select the atoms and bonds you want to progressively reveal.
- Double-click the Reveal atoms effect in the Animation panel of the Animator.
- Adjust the keyframes or easing curve as needed for better timing or a more natural pacing.
Why Ordering Matters
The atoms are revealed based on the order of selection. This might sound minor, but it’s quite powerful. For example, if you’re animating a polymer growing from one end to the other, you can ensure that only the next logical atom appears in sequence — rather than an arbitrary appearance across the structure.
To ensure this works as intended, use the Options tab in the Selection Inspector to carefully build and order your selection set.
Fine-Tune with Easing Curves
You can customize how the animation behaves between keyframes using Easing curves. For example, ease-in can create a slower initial reveal that speeds up over time, giving the effect of acceleration as atoms assemble.
This subtle tweak can greatly enhance the professional quality of your presentations. It’s worth experimenting with different curves to get the feel that best matches your scientific story.
Use Case: Conceal and Reveal Together
Often useful in tandem with the Conceal atoms animation, Reveal atoms helps modelers show reversibility, assembly/disassembly cycles, or clear transitions between molecular states. With both, you can illustrate a molecular machine forming, functioning, and then disassembling — making your story much more dynamic and clear.
Whether you’re working on a lecture, a research presentation, or educational content, smooth and logical animation is more than an aesthetic detail — it’s part of scientific clarity. With this tool, communication becomes easier, and your visuals will speak more powerfully.
Learn more about the feature in the Reveal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.