Molecular modeling projects often involve creating visual presentations to highlight specific interactions, regions of interest, or structural changes. But when a model is too complex, clutter from surrounding atoms can obscure what really matters. If you’ve ever struggled to focus your audience’s attention during a presentation, you’re not alone.
This is where the Conceal atoms animation effect in SAMSON offers a handy solution. It allows you to progressively hide atoms and their bonds over time—helping you create focused, step-by-step stories without overloading the viewer with visual information.
What is ‘Conceal atoms’?
‘Conceal atoms’ is one of the animation effects available in SAMSON’s Animator tool. It doesn’t rely on transparency like some other visual effects—instead, it controls visibility strictly by hiding atoms and the bonds between them.
This is particularly useful for modelers who want to:
- Draw attention to a binding pocket or active site without the distraction of the full molecule.
- Show dynamic behavior in a staged manner—first showing a region, then revealing it layer by layer.
- Prepare educational content with gradual visual explanations.
How to add the effect
Here’s how to set up the Conceal atoms animation in SAMSON:
- Select the atoms and bonds you would like to hide progressively.
- In the Animation panel of the Animator, double-click on the Conceal atoms effect.
The animation is automatically set with 4 keyframes:
- Keyframes 1–2: The selected atoms and bonds are fully visible.
- Keyframes 2–3: Atoms and their bonds disappear progressively depending on their order in the selection.
- Keyframes 3–4: All selected atoms and bonds are fully hidden.
You can drag and reposition these keyframes to control the timing. Want the hiding effect to happen more quickly or more slowly? Just adjust the spacing between frames.
Refine with easing curves
To create smoother or more dynamic animations, you can modify the Easing curve. This gives you control over the interpolation between keyframes—for example, accelerating the concealment at the beginning or slowing it at the end for dramatic effect.
In action
The gif below shows the Conceal (and Reveal) atoms effects in action:
These animations can greatly improve clarity for walk-through presentations, tutorials, or molecular storytelling. For example, both 1AF6 – Fly around and its sequel use this effect to manage visual complexity while flying over molecular surfaces.
To learn more or start applying ‘Conceal atoms’ in your own presentations, visit the official documentation at https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.