In molecular modeling, clarity is often more valuable than completeness. When preparing scientific presentations or instructional materials using complex biomolecular structures, showing every atom at once can be overwhelming—and, more importantly, unnecessary. Sometimes, emphasizing certain atoms and hiding others can help communicate a message more effectively.
This is where SAMSON’s Conceal atoms animation effect can be useful. Available in the Animation panel of the Animator, it allows users to progressively make atoms and the bonds between them disappear between two timepoints. Unlike modifying transparency, this animation directly toggles visibility, completely hiding selected nodes rather than just making them semi-transparent.
Why conceal atoms?
Researchers and educators often use molecule animations to demonstrate mechanisms such as ligand binding, conformational changes, or active site exposure. But full atomic detail may draw attention away from areas of interest. Concealing atoms can help focus the viewer’s eye exactly where it needs to be, cleaning up the noise and improving comprehension.
This animation also helps during workflows that transition between high-level overviews and detailed views. For example, you might initially show a protein’s overall shape and then hide less relevant parts to zoom in on a catalytic site.
How does it work?
To apply the Conceal atoms animation:
- Select atoms and bonds that you want to progressively hide.
- Double-click on Conceal atoms inside the Animation panel.
- The animation will insert 4 keyframes into your Animation timeline:
- Frames 1–2: All selected atoms (and connected bonds) are visible.
- Frames 2–3: A progressive disappearance of atoms based on their order in the selection.
- Frames 3–4: All selected atoms are completely hidden.
- You can reposition these keyframes to control the speed of the disappearance.
Customization tips
Want smoother transitions? The animation supports easing curves, which control the interpolation of parameters between keyframes. Adjusting the curve shape changes the pacing—gradual fades or sudden drops—letting you match the animation style to the context of your message.
Try it with real data
Still not sure how “concealing atoms” might look in your own project? Check out these example presentations available on SAMSON Connect:
In these examples, you’ll see how structure-guided storytelling becomes easier when supported by purposeful visibility transitions.
To learn more about using this tool, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON from https://www.samson-connect.net.