Animating molecular scenes can help communicate complex ideas clearly—but presenting *everything* at once can create overwhelming visuals. This is a common challenge in molecular modeling, especially when presenting structures to students, collaborators, or during publication preparation. One useful technique to guide your viewer’s attention is progressive disappearance.
In this post, we’ll look at the Disappear animation in SAMSON, which enables you to slowly fade out selected elements in a molecular scene. Whether you want to remove solvent to reveal the active site or hide parts of a protein to focus on specific domains, this animation gives you control over what stays visible—and when.
Why fade instead of cut?
Hard transitions like sudden hiding of parts of a molecule can feel abrupt and disorienting to the viewer. A progressive disappearance, where parts of your molecular model gradually become transparent, creates a much smoother visual break. It helps maintain spatial context as details fade away rather than vanish instantly. This subtlety often makes animations look more polished and intuitive.
What can you animate with Disappear?
The Disappear animation affects nodes with transparency attributes. These include:
- Structural models
- Visual models
- Meshes
- Labels
It’s worth noting that individual atoms and bonds don’t have opacity themselves—their visibility is defined by the structural models they belong to. So if you’re trying to fade individual atoms, make sure to apply the animation to the model as a whole.
How does it work?
After selecting the nodes you want to progressively disappear, here’s how you apply it:
- Open the Animator.
- In the Animation panel, double-click on Disappear.
The animation comes with four keyframes:
- Keyframes 1 → 2: full opacity
- Keyframes 2 → 3: smooth transparency transition (the fade)
- Keyframes 3 → 4: full transparency
You can always reposition the keyframes depending on how quickly (or slowly) you’d like the fade to happen. For example, a slower fade might be useful when breaking down a large complex, while quick fades work better when transitioning between related scenes.
Fine-tuning the effect
To tailor the feel of the fade, you can experiment with the easing curve associated with the animation. Easing curves let you control the speed of the transition between frames. For instance, using a cubic curve can make the fade start slowly and finish quickly, while a linear easing will keep the transparency change constant throughout.
One example, many applications
Need a concrete use case? In the animation below, the Disappear effect is used to smoothly remove a surface representation, allowing focus on the underlying residues and labeled atoms. Notice how the fade maintains spatial continuity while transitioning emphasis:
Conclusion
In scientific communication, visual clarity matters. The Disappear animation in SAMSON provides a simple yet powerful tool to structure what your audience sees—and when—by leveraging transparency. Whether you’re preparing an educational video or a presentation for a research meeting, it can help convey your message more clearly and smoothly.
To explore more about the Disappear animation, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.