When creating molecular animations to explain a mechanism or guide an audience through a complex structural change, timing is everything. One common challenge for molecular modelers and scientific communicators is how to effectively reveal parts of a molecule to focus attention and make transitions more understandable.
Rather than simply showing or hiding everything instantly, what if you could gradually reveal atoms and bonds — as if they’re emerging step by step? This is exactly what the Reveal atoms animation effect in SAMSON solves.
Why gradual appearance matters 🔍
Consider you’re presenting a ligand binding process. If everything appears on-screen at once, your audience may struggle to understand where to look or how the process unfolds. But if atoms and their bonds emerge progressively, spatial and temporal coherence is maintained. It becomes easier to follow structural transformations, especially when combined with narration or other dynamic elements.
How the ‘Reveal atoms’ animation works
The Reveal atoms animation in SAMSON works with 4 keyframes that control visibility — not transparency — of the selected atoms and their connecting bonds:
- Keyframes 1 to 2: the specified atoms and bonds are hidden.
- Keyframes 2 to 3: atoms and bonds are revealed progressively, one after another based on their order in your selection.
- Keyframes 3 to 4: everything is fully visible.
You can always adjust the timing between keyframes to determine how long atoms stay hidden or how quickly they are revealed. This gives you fine-grained control over the visual narrative you’re crafting.
Use case: revealing a binding site
Imagine you’re designing a short animation to highlight a binding site in a protein model. Using the Reveal atoms feature:
- Select the atoms forming the binding site.
- Double-click the Reveal atoms animation effect in the Animator’s Animation panel.
- Position your four keyframes where they best match the timeline of your story.
- Use the Easing curve to fine-tune the interpolations for even smoother transitions. For instance, you may opt for a slow start and fast end to build suspense.
This approach can subtly guide viewers’ attention and enhance comprehension by pacing the exposure of visual information.
Visual example
Quick tip: combine with other effects
You’re not limited to using Reveal atoms alone. For instance, combine it with Flash or Pulse to emphasize specific regions after they appear. This layered approach keeps your animations clear and visually engaging without adding unnecessary complexity.
Interested in exploring further? You’ll find more on how this animation behaves and integrates with other tools in the original documentation page: Reveal atoms documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.