Creating molecular animations is a powerful way to communicate structural changes, reaction mechanisms, or simply highlight important features in a model. But if you’ve ever tried synchronizing object appearances in time during an animation, you know it can get messy. Many modelers use transparency to simulate visibility, but this often leads to unintended overlaps, sluggish playback, or inconsistent rendering during presentations.
Instead of tweaking transparencies and fine-tuning material settings frame-by-frame, you can use a more straightforward trick in SAMSON: the dedicated Shown animation effect. This approach is cleaner—it toggles actual visibility status of nodes in an animation, without modifying transparency. In short, it’s a true visibility switch designed for clarity and control. Let’s walk through how to use it effectively.
Why this is useful
Molecular modelers often need to:
- Temporarily hide or reveal molecules or molecular groups during transitions
- Simplify visual storytelling without dealing with overlapping transparencies
- Ensure clarity when showing complex assemblies step by step
Using the Shown animation effect means you can keep your transparency settings untouched, while maintaining full control over which nodes appear and when.
How it works
To use the Shown animation:
- Select the nodes (e.g., atoms, molecules, groups) you want to animate.
- Open the Animator panel.
- Double-click the Shown animation effect from the Animation panel. This action adds a keyframe at the current timeline position.
- Move the keyframes to align transitions with the desired timing in your animation.
This approach contrasts with older workflows, like using the Animation menu (now deprecated in SAMSON), which introduced more complexity and limited flexibility. Now, everything goes through the Animator panel—a more intuitive and streamlined interface.
Fine-tuning the animation
You can further improve your animations by adjusting the Easing curve. This defines how the animation transitions between keyframes—useful if you’re sequencing visibility with motion or other visual effects.
Quick tip
The Shown animation works by toggling the visibility status, not adjusting transparency percentages. This ensures that hidden nodes don’t interfere with rendering performance or distract viewers with ghost-like overlays—it’s all about precision and visual clarity.
Combined with the complementary Hidden, Appear, and Flash animations, you can choreograph truly engaging molecular walkthroughs.
Animated visibility in SAMSON is structured, non-destructive, and efficient. Whether you’re building a video lecture or preparing figures for a paper, the Shown animation gives you a practical edge.
To learn more about the Shown animation, visit the original documentation page here: https://documentation.samson-connect.net/users/latest/animations/shown/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net