When presenting molecular systems to colleagues, students, or collaborators, one of the most common goals is to clearly highlight a region of interest or to steer attention gradually from one part of the system to another. Yet, many molecular modelers struggle with presentations in which parts of the model suddenly disappear or clutter the screen during transitions, making it harder to follow the narrative.
Fortunately, SAMSON’s Disappear animation offers a smooth, visually natural solution: gradually fading out models via transparency. This avoids abrupt jumps in visibility and provides better continuity when storytelling through molecular motion or transitions.
Why fade instead of hide?
In molecular animation, using a simple ‘hide’ function often causes structures to vanish instantly. This can be jarring — especially in educational or scientific outreach videos where viewers must follow every detail. The Disappear effect solves this by smoothly increasing the transparency of selected elements over time, helping the audience maintain context.
The animation applies to any object with a transparency property, such as:
- Structural models
- Visual models
- Meshes
- Labels
Since individual atoms and bonds don’t have their own transparency attribute, it’s recommended to apply the effect to the parent structural model instead.
How to add the Disappear effect
Adding the animation is straightforward. In the Animation panel of the Animator, just double-click Disappear after selecting the nodes you want to animate.
This effect consists of 4 keyframes:
- Keyframes 1→2: The model stays fully opaque
- Keyframes 2→3: Transparency gradually increases
- Keyframes 3→4: Model becomes fully transparent
You can move and adjust these keyframes to control precisely when and how fast the fade occurs.
Make it your own with Easing curves
The Easing curve option lets you refine how transparency changes over time. For example, models can fade slowly at the start and quickly disappear at the end—or vice versa. This gives you complete control over the pacing and feel of your animation.
Example in action
Take a look at this example where both appearing and disappearing animations are applied to protein structures. This helps direct attention to specific regions while maintaining visual continuity.
Conclusion
Whether you’re teaching biochemistry, preparing reveals for molecular design projects, or showcasing structural changes in a simulation, fading out parts of a system offers a more polished alternative to hiding. The Disappear animation in SAMSON helps you build visual narratives that remain clear and engaging.
To learn more and see other related animations (such as Appear, Flash, or Hide), visit the Disappear animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.