In molecular modeling and communication, clarity is critical. Whether you’re preparing a presentation for colleagues or publishing a video abstract, showing a complex molecular structure all at once can be overwhelming for your audience. Often, you want to guide the viewer’s attention, gradually building up the structure to tell a story—something that resonates and informs.
This is where progressive atomic visualization through animations becomes useful. Reveal Atoms, one of the available animation effects in SAMSON, offers a practical solution. It lets you make atoms (and the bonds between them) appear gradually across a set of frames. This effectively enables you to reveal structure over time, which can help improve understanding and avoid overwhelming visuals.
Why this matters
Let’s face it—molecular systems are intricate. When showing highly connected atom networks or large biomolecules, viewers can quickly lose focus if all the details pop in at once. Progressive reveal helps put the spotlight on specific parts in a deliberate order. It’s especially helpful in teaching workflows, structure-function analyses, and scientific storytelling.
How Reveal Atoms works
In SAMSON, Reveal Atoms doesn’t rely on transparency; instead, it uses node visibility. You define your atom and bond selection, and the animation gradually makes them visible between chosen frames. Here’s the basic workflow:
- Select the atoms and bonds you want to animate. This could be a specific domain of a protein, a ligand entering a binding site, or a growing molecular chain.
- Open the Animation panel within the Animator.
- Double-click on the Reveal Atoms effect to add it to your animation.
The animation consists of four keyframes:
- From frame 1 to 2: the atoms and bonds are hidden.
- From frame 2 to 3: they progressively appear, depending on their order in the selection.
- From frame 3 to 4: all selected atoms and bonds are visible.
You can adjust the timing or spacing of keyframes to control the pacing. This allows you to synchronize the appearance with narration or other events in your presentation.
Pro tips
- If you want specific atoms to appear earlier, adjust the selection order before starting the animation.
- Use the Easing curve to fine-tune how the animation interpolates between keyframes. A slow-in-ease, for instance, may produce a softer, more natural visual flow.
- Combine Reveal Atoms with Conceal Atoms to build up and then simplify your scenes.
This technique is already used by researchers to highlight binding sites gradually, guide through reactions, or showcase structural features without clutter.
To learn more about the Reveal Atoms animation in SAMSON and its optional settings, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.