Whether you’re preparing a presentation for a paper, teaching structural biology, or simply clarifying a dense molecular system to collaborators, one challenge often arises: how do you remove visual clutter from complex molecular structures without completely deleting parts of your model?
This is a common hurdle in molecular modeling—particularly when presenting large biomolecular systems such as proteins, DNA, or ligand-receptor complexes. Full visibility is often overwhelming, yet hiding atoms abruptly can look jarring and confusing in an animation. The Conceal atoms animation feature in SAMSON offers a useful alternative: progressive disappearance of selected atoms and bonds, smoothly transitioning between visible and invisible states.
Progressive concealment, not transparency
Unlike transparency effects, which can still contribute to on-screen clutter and may require additional color-coding to clarify, Conceal atoms works through node visibility. That means atoms and the bonds between them are hidden step-by-step based on their selection order—making it easy to guide attention without overwhelming the viewer.
How it works
To use this animation in SAMSON, follow these steps:
- Select the atoms and bonds you want to disappear over time.
- Open the Animator via the Animation panel.
- Double-click the Conceal atoms effect.
This effect creates four keyframes by default:
- Frames 1–2: All selected atoms and connecting bonds are shown.
- Frames 2–3: The selected components begin disappearing gradually, based on their selection order.
- Frames 3–4: All selected atoms and bonds are hidden.
This structured fading helps illustrate mechanisms like ligand binding, site mutations, or even allosteric transitions by eliminating parts of the structure step by step, leaving only key elements visible.
Customization options
Need to adjust the animation’s timing or pacing? You can reposition any keyframe or modify how the concealment progresses using an easing curve. This way, the fade-out can accelerate, slow down, or even follow a non-linear rhythm by simply tweaking interpolation settings.
See it in action
This example of a fly-around of 1AF6 demonstrates how Conceal atoms makes it easier to guide the viewer through a molecular structure without distraction—especially when combined with reveal effects or viewpoint transitions.
When to use this
If you’re:
- Preparing educational animations to show structure-function relationships,
- Trying to highlight a binding pocket inside a dense morphology,
- Or setting up a clear visual path for your audience to follow within a molecular system,
then Conceal atoms may save you significant time and help keep your visuals clear and effective.
To learn more, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net