Visual storytelling is an essential part of molecular modeling, especially when presenting complex interactions in proteins, DNA, or materials. A common challenge faced by molecular modelers is how to ensure a viewer’s attention stays focused on the relevant part of a structure, without overwhelming them with unnecessary atomic detail. The eye can only process so much at once—and that’s where the Conceal atoms animation in SAMSON comes in.
This feature allows you to smoothly hide atoms and their connecting bonds from a molecular scene over time. It’s particularly useful when you want to shift focus from one region to another or introduce a structure progressively. If you’ve struggled with viewers being distracted by side chains, solvent shells, or other components, this subtle yet powerful animation effect can help bring clarity to your presentations.
What Does ‘Conceal Atoms’ Actually Do?
Instead of simply toggling atom visibility on or off, this animation effect lets atoms and their bonds disappear progressively. That progression happens across four keyframes, and not through transparency, but by hiding atoms step-by-step:
- Keyframes 1 to 2: All selected atoms and their bonds are visible.
- Keyframes 2 to 3: Atoms are concealed one-by-one, in the order you selected them, and the bonds between hidden atoms are removed as well.
- Keyframes 3 to 4: All selected atoms and corresponding bonds are hidden.
This technique is distinct from transparency and has practical advantages—especially when working on large biomolecules or assemblies where hidden atoms don’t clutter the scene and reduce rendering overhead.
How To Use It
Using the ‘Conceal atoms’ animation in SAMSON is straightforward:
- Select the atoms and bonds you want to progressively hide. The order of selection matters.
- Open the Animation panel in SAMSON’s Animator.
- Double-click on the Conceal atoms animation to apply it to the selection.
- Adjust the four keyframes along the timeline to control the timing of appearance, disappearance, and stillness.
If needed, you can fine-tune the flow of the animation using the Easing curve, modifying how the transition progresses between frames—from linear fades to more dramatic acceleration and deceleration effects.
When To Use ‘Conceal Atoms’
This animation is especially helpful when:
- You’re presenting a drug binding to a receptor and want to remove water molecules gradually for clarity.
- You want to isolate a functional group’s movement by concealing background chains.
- You’re teaching structural biology and want to move from an entire molecule view to a localized domain.
Importantly, the selection’s order matters for the way atoms disappear. You can precisely control where the animation begins and ends spatially, leading to smooth and professional transitions through complex molecular scenes.
Real Examples
If you’d like to see this technique in action, take a look at the following presentations from the SAMSON community:
To learn more about the Conceal atoms animation, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.