When creating molecular animations for presentations, publications, or educational videos, one of the simplest but often underestimated challenges is managing which elements of the model the audience sees — and when. If you’ve ever wanted to reveal specific molecules or structures at the right moment without overcomplicating your animation timeline, the Shown animation in SAMSON provides a practical solution.
Unlike transparency-based animations, Shown directly manipulates the visibility of nodes (e.g., atoms, molecules, proteins, or any other structural elements) to make them visible between chosen keyframes. This ensures clarity and avoids the visual ambiguity that partial transparency can introduce.
Why Visibility Control Matters
In molecular modeling, overwhelming your audience with too much visual information can reduce the impact of your work. Sometimes, the best way to keep a viewer focused is by revealing components sequentially. For example, imagine explaining a protein-ligand interaction—starting with the empty pocket, then showing the ligand appear exactly when needed. The Shown animation enables this clarity of storytelling with just a few clicks.
How the Shown Animation Works
Here’s how to get started:
- Select the nodes you want to show at a specific time in your animation timeline.
- Navigate to the Animation panel in the Animator.
- Double-click the Shown animation effect.
This sets the current frame as the beginning of the shown time interval. You can then move the keyframes along your timeline as needed to define precisely when the nodes should appear. This gives you direct control over the visibility of parts of your structure across time.
Adjusting the Transition
While the Shown effect is discrete (elements are visible or not, without gradual change), you still have access to animation timing tools like the Easing curve. These allow you to adjust how keyframes interpolate over time—useful when combining Shown with other effects like Appear or Flash.
Notes on the UI
If you come across older tutorials or videos, they might mention an Animation menu that no longer exists. Don’t worry—all animations are now accessible via the Animation panel in the Animator. This centralizes animation control and streamlines the experience.
When to Use Shown Instead of Other Visibility Effects
The key distinction is that Shown is an explicit visibility toggle—not a fade, glow, or pulse. Choose it when your animation needs absolute visual clarity about what is and isn’t present. It’s especially useful when combined with effects like Hidden, so you can control exactly which parts of a molecular system are visible during specific timeframes.
For more details and step-by-step instructions, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON from https://www.samson-connect.net.