In scientific visualization, clarity is key. Molecular modelers often struggle to convey transitions over time—such as decay, motion, or a process that reveals structures progressively—while maintaining visual coherence. If you’ve ever needed to make parts of your molecular model fade out smoothly instead of disappearing abruptly, SAMSON’s Disappear animation might be exactly what you’ve been missing.
The Disappear animation in SAMSON is designed to progressively alter the transparency of nodes to create a fading effect. Unlike a simple hide/show animation, Disappear allows for a smooth visual transition that can enhance presentations, teaching materials, and molecular movies. This is especially helpful when trying to draw attention to a specific part of a complex molecular system or when communicating a simulation flow without visual jumps.
Why Use Disappear Instead of Just Hiding Elements?
When you hide nodes abruptly, it can be jarring for the viewer. For complex models—like structural assemblies, protein-ligand complexes, or annotated meshes—sudden disappearances can interrupt the visual narrative. The Disappear animation introduces smooth transparency transitions where models gradually fade out, making the experience more transparent (pun intended).
How It Works
The Disappear animation works on nodes that feature a transparency attribute. These include:
- Structural models
- Visual models
- Meshes
- Labels
It cannot be applied directly to individual atoms and bonds (as these don’t have an opacity property), so users should apply the fade effect to their parent structural model to achieve the desired result.
Quick Walkthrough
- Choose the nodes you want to make disappear.
- Open the Animation panel in the Animator.
- Double-click on the “Disappear” animation effect.
- Four keyframes are added automatically:
- Between keyframes 1 and 2: the nodes are fully opaque.
- Between keyframes 2 and 3: nodes transition to being transparent.
- Between keyframes 3 and 4: the nodes stay fully transparent.
- Adjust keyframe positions and timing using the Animator timeline to control exactly when the disappearing should occur.
Tip: Customize the Easing
To make the transition from opaque to transparent feel more natural, adjust the easing curve. This controls how the opacity changes over time—whether it eases in slowly, accelerates, or behaves linearly.
Presentation Ready
Disappearing parts of a molecule can signify degradation, molecular exit, or focus shift. When combined with the corresponding Appear animation, users can design complex sequences that tell stories about molecular mechanisms, biochemical pathways, or material transformations.
This example GIF shows a model gradually becoming transparent. It’s much easier on the eyes—and minds—than a sudden vanishing act.
Learn more about the Disappear animation in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.