When preparing molecular animations, one common frustration for researchers and educators is visual clutter. Large molecules display countless atoms and bonds, making it hard to direct attention to specific structural changes, active sites, or interactions. If you’re working with biomolecules, this can be especially challenging when you simply want to emphasize a domain, ligand, or localized region without overwhelming your viewer.
To address this, SAMSON provides a useful animation effect: Conceal atoms. Rather than using transparency — which often leaves visual traces — this effect makes atoms and bonds progressively disappear from the scene by adjusting their visibility. The result is a much cleaner and more focused animation stream, ideal for storytelling around molecular mechanisms or highlighting transformations over time.
What does ‘Conceal atoms’ do?
The Conceal atoms animation creates a smooth transition where atoms and the bonds connecting them vanish progressively between specified frames. This concealing is done using node visibility rather than transparency. It is particularly helpful when you want to highlight a specific part of a complex molecule by reducing visual distractions.
How it works
To use this effect in SAMSON, you need to:
- Select the atoms and bonds you want to hide.
- Double-click the Conceal atoms animation in the Animation panel of the Animator.
The animation is structured around four keyframes:
- Frame 1 to Frame 2: All selected atoms and their bonds are shown.
- Frame 2 to Frame 3: Atoms and bonds progressively disappear, one after the other, based on selection order.
- Frame 3 to Frame 4: All selected atoms and corresponding bonds are hidden entirely.
This keyframing approach lets you control precisely when and how elements disappear, giving you flexibility to adjust timing and focus.
Customization and control
To further fine-tune how atoms are concealed over time, SAMSON offers Easing curves, which let you adjust the interpolation speed between frames. For example, you can make atoms disappear slowly at first, then more rapidly, or vice-versa.
Example in action
Here’s what the Conceal and Reveal atoms animations look like in motion:
Why this matters
With the Conceal atoms effect, you gain a simple but effective way to manage visual complexity. Whether you’re preparing teaching material, a scientific presentation, or even just trying to visualize a specific molecular pathway, having this kind of control over what is and isn’t visible at a given time helps your audience stay focused on the story you want to tell.
You can explore example presentations using this animation within SAMSON Connect – Documents, such as:
To learn more, visit the Conceal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.