Visual presentation is a critical aspect of molecular modeling, especially when preparing demonstrations, tutorials, or research presentations. One common challenge faced by molecular modelers is how to control the visibility of atoms, molecules, or annotations in a smooth and convincing manner—especially when transitioning between different structural states or simulating molecular events.
In SAMSON, the integrative molecular design platform, the Disappear animation offers a streamlined way to handle this. Unlike abrupt hiding effects, the Disappear animation increases the transparency of nodes over time, resulting in smooth, professional-looking transitions that can significantly enhance your visual storytelling during presentations and recorded videos.
When and Why to Fade Out a Structure
Imagine showcasing a reaction mechanism and wanting to fade out intermediate states as the reaction progresses. Or maybe you want to abstract certain molecular layers to focus on annotations or more critical substructures. The Disappear animation can help with all of this by making selected elements gradually vanish, giving your audience space and time to shift their attention.
The key benefit? It’s not just about making things invisible—it’s about how they disappear.
What Can Disappear
Not all elements in a molecular model respond the same way to animations. The Disappear effect specifically requires that a node has transparency capabilities. These include:
- Structural models (which encompass atoms and bonds)
- Visual models
- Meshes
- Labels
It’s important to note that individual atoms and bonds are not natively transparent, but their structural model containers are. So, if you want to fade out a selection of atoms, apply the animation to the structural model that holds them.
How the Animation Works
Here’s how the Disappear animation is structured within SAMSON’s Animator panel:
- Keyframe 1 – 2: Selected nodes remain fully opaque
- Keyframe 2 – 3: Transparency is gradually increased (nodes begin to disappear)
- Keyframe 3 – 4: Nodes become fully transparent
You can reposition keyframes to control timing and combine them with other animations for more complex visual effects. For example, you might synchronize a Disappear effect with an Appear or Flash animation on another group of nodes.
Fine-Tuning Transitions
SAMSON provides an Easing curve option to tailor how parameters transition between frames. Want your molecules to disappear slowly at first and then quickly fade? Adjust the curve accordingly to fit the rhythm of your presentation.
Accessing the Animation
To apply the Disappear animation:
- Select the nodes you wish to fade out
- Double-click the Disappear effect in the Animation panel
- Adjust keyframes as needed using the Animator
It’s worth noting that earlier versions of SAMSON featured an Animation menu—which has since been replaced with the Animation panel in the Animator workspace.
To learn more about how the Disappear animation works and how it integrates with other effects, check out the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.