In many fields of molecular modeling and structural biology, clear visual storytelling is essential to communicate ideas, mechanisms, and results. Whether you’re preparing for a presentation, creating an educational video, or crafting a visual for publication, controlling what appears—and disappears—in your molecular scene can make all the difference.
One challenge that some SAMSON users face is removing elements from a scene gradually, instead of making them vanish abruptly. This is especially helpful when you want to guide attention or highlight specific transitions in dynamic processes.
Fortunately, SAMSON’s Disappear animation function provides an elegant way to make selected molecular elements fade away progressively. This simple effect helps direct viewers’ focus more smoothly and professionally. Here’s a guide on how to use it effectively.
Why use the Disappear animation?
Imagine you’re visualizing a large protein complex and want to gradually fade out part of it to highlight an active binding site. Or maybe you’re showing multiple conformations of a molecule and need to transition between them smoothly. Using the Disappear animation makes these transitions more comprehensible and visually clean, instead of jarringly hiding elements from the viewer.
What can be made to disappear?
The Disappear effect works on any nodes that have a transparency attribute. These include:
- Structural models (e.g., atoms and bonds via their container)
- Visual models (e.g., surfaces)
- Meshes
- Labels
Important detail: you can’t apply the transparency effect directly to individual atoms or bonds. Instead, apply the Disappear animation to the structural model they belong to.
How to apply the effect
- Select the node(s) in your SAMSON document that you want to fade out.
- Go to the Animator and double-click on the Disappear animation in the Animation panel.
- The animation will automatically add four keyframes:
- Keyframes 1–2: Full opacity
- Keyframes 2–3: Gradual transparency increase
- Keyframes 3–4: Full transparency
- Adjust the keyframe positions to control the timing of the fade.
You can also adjust how the transparency parameter changes between these frames by choosing an Easing curve that best suits the rhythm of your animation.
When is it useful?
This feature can be particularly useful in:
- Step-by-step mechanism animations (e.g., showing only catalytic residues)
- Zooming into specific domains or subunits while fading out non-essential elements
- Teaching transitions by layering fading models in and out
Final thoughts
The Disappear animation is a small but powerful tool that can improve how you share and explain molecular structures. Whether you’re creating animations for research, education, or outreach, using transparency for emphasis often communicates better than simply hiding structures.
You can explore the full documentation on the Disappear animation feature here:
https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.