When illustrating complex molecular systems, the way you present your data can make a big difference. Whether you’re explaining interactions within a protein or visualizing assembly processes in a material, clarity matters. One common problem modelers face is how to present structures appearing step-by-step, in a way that’s both visually intuitive and scientifically accurate. Adding a reveal effect to specific atom groups helps viewers follow what’s happening—especially in educational or presentation contexts.
This is where SAMSON’s Reveal atoms animation comes in. Unlike animations that rely on transparency, this effect progressively displays atoms (and the bonds between them) based on visibility settings instead. It’s ideal for showing the emergence of a molecular complex, allowing you to control exactly when and how structural components become visible in your animation.
What does the Reveal atoms animation do?
The Reveal atoms animation in SAMSON lets atoms and their connecting bonds gradually appear over a specific range of keyframes. This is not a fade-in effect—transparency isn’t used. Instead, it precisely switches the visibility of structural elements to provide clear visual cues during a transition.
Why use it?
Here are a few use cases where this becomes especially helpful:
- Showing how a ligand binds to a protein by making the ligand appear one part at a time.
- Telling a visual story of molecular assembly, as atoms are added progressively.
- Contrasting before-and-after molecular conformations.
How to use it:
1. Select the atoms and bonds you want to animate.
2. In the Animation panel of the Animator, double-click on Reveal atoms.
3. SAMSON will create an animation block with 4 keyframes:
- Keyframes 1–2: Atoms and bonds are hidden.
- Keyframes 2–3: Atoms and bonds begin to appear gradually, based on their order in the selection.
- Keyframes 3–4: All selected parts are shown.
You can, at any time, adjust the placement of keyframes to fine-tune the timing of each appearance phase.
Fine control with easing curves
The Easing curve parameter determines how fast or slow the appearance progresses. You can modify this in the animation properties to create effects like slow starts or smooth accelerations. This adds subtle but important nuance to your visualizations. For example, you might want atoms to appear slowly at first, then speed up, simulating a more natural formation effect.
Visually, what should you expect?
Below is an example combining both the Conceal atoms and Reveal atoms animations. It highlights how atoms disappear and then reappear in sequence, helping convey molecular changes over time:
In short, the Reveal atoms feature provides a clear, discreet way to guide viewers through structural transitions. Whether you’re preparing teaching material or communicating research results, this animation improves how others understand and follow complex molecular systems step-by-step.
To learn more, visit the Reveal atoms animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.