When preparing molecular animations, showing only the most relevant parts of a structure at the right time can help you tell a compelling scientific story. A common challenge in molecular modeling is how to guide your audience’s attention to specific atoms or bonds as your animation progresses—without overwhelming them with clutter.
If you’ve ever tried to simulate the progressive build-up of a molecular structure or illustrate a reaction mechanism step by step, then you’ve likely encountered this issue. Fortunately, SAMSON’s Reveal atoms animation provides a streamlined and interactive way to control which atoms appear and when, helping you focus on clarity and precision.
What is the ‘Reveal atoms’ animation?
The Reveal atoms animation in SAMSON lets you gradually show atoms and the bonds between them over time. Unlike changing transparency, this tool works through visibility toggling, which means atoms are either shown or hidden—nothing in-between. This makes it especially helpful for focusing audience attention without visual distractions.
Key use case: Step-by-step structural assembly
Let’s say you’re presenting a complex biomolecule and only want to introduce key residues at certain stages. By applying the Reveal atoms animation, you can define a group of atoms and progressively show them across keyframes.
How it works
Once you’ve selected the atoms and bonds you want to gradually unveil, follow these steps:
- Open the Animation panel from the Animator workspace.
- Double-click the Reveal atoms effect.
- The animation will automatically include 4 keyframes:
- Between keyframes 1 and 2: all selected atoms and their bonds remain hidden.
- Between keyframes 2 and 3: atoms and their interconnecting bonds begin to appear in order.
- Between keyframes 3 and 4: all selected atoms and their bonds are fully visible.
- You can drag the keyframes independently to fine-tune timing.
Tip: Choose which atoms to reveal first
The order in which atoms appear is linked to the order of your selection. By carefully selecting atoms in a meaningful sequence (e.g., from active site outward), you control the narrative flow of your animation.
Customize the pace with easing curves
If you need the animation to accelerate or decelerate, modify the Easing curve. This changes the rate at which atoms are revealed for a smoother or more dynamic presentation.
This feature is ideal for:
- Teaching molecular biology or chemistry concepts.
- Illustrating drug-binding sites step by step.
- Building up large molecules piece by piece for presentations or publications.
To learn more and try it yourself, visit the original documentation page: Reveal atoms – SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.