When you’re preparing molecular animations for presentations, publications, or educational purposes, the goal is often to guide attention without overwhelming your audience. A common frustration for molecular modelers is the crude nature of traditional atom or structure removal — objects just snap out of view, interrupting the flow of a sequence and breaking visual continuity.
Instead of a sudden disappearance, what if your molecules could gently fade away? In SAMSON, the Disappear animation effect does just that — smoothly increasing node transparency across keyframes, allowing for more natural narrative transitions in molecular presentations.
Why this matters
In structural biology or materials science animations, you’re often shifting focus between different molecular subsystems, regions, or functional sites. Using Hide can make these changes too abrupt. The Disappear animation offers:
- Visual continuity: Fade out parts of a model gradually as the camera reveals finer details elsewhere.
- Clarity: Help your viewers clearly distinguish transient elements and avoid visual clutter.
- More expressive storytelling: Communicate conformational shifts, binding events, or component removal while maintaining immersion.
How it works
The Disappear animation in SAMSON can be applied to all nodes that support transparency: structural models, visual models, meshes, and labels. This includes macromolecules, surfaces, EM maps, and more. However, individual atoms and bonds don’t support transparency — to animate them, you apply the effect to their structural model.
Once applied via the Animation panel in the Animator, the Disappear animation spans four keyframes:
- Keyframes 1–2: Fully opaque
- Keyframes 2–3: Gradual increase in transparency
- Keyframes 3–4: Fully transparent
You can drag keyframe positions on your timeline to synchronize disappearance with other scene events — camera movements, label introduction, subsystem highlighting, and more.
Tip: Make it smooth
The Disappear animation also supports easing curves. This means you can fine-tune how fast or slow the transparency interpolation occurs across frames. Want your molecule to linger slightly, then dissolve quickly? Adjusting the easing curve lets you do this precisely — no need for video post-processing software.
An example in action
In the animation below, a molecule uses both the Appear and Disappear effects — first emerging from transparency, then fading away to reveal another structure beneath:
Final thoughts
For molecular modelers looking to improve the quality of their visualizations without additional software or complex pipelines, Disappear is a simple but powerful tool inside SAMSON. It offers greater narrative control, especially when preparing compelling molecular demonstrations or explanatory videos.
Learn more about the Disappear animation in SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.