In molecular modeling, visual clarity is essential when communicating complex structures and mechanisms. Whether you’re showcasing a protein-ligand interaction or preparing an educational molecular scene, the way elements appear and disappear can greatly influence how well your audience understands molecular behavior.
One common frustration for modelers is that sudden disappearances of atoms during an animation can look jarring and inorganic. A smoother, more natural progression from visibility to invisibility is often more useful, especially when comparing conformations or emphasizing interesting regions.
Enter the Conceal atoms animation in SAMSON, a tool made to gently remove atoms and bonds from your scene — not by tweaking transparency but through progressive visibility changes. This animation lets atoms disappear in a controlled, frame-based way, helping you direct attention while maintaining a smooth visual flow.
Why conceal instead of fade?
Fading usually involves altering the opacity of atoms, which can be visually noisy and hard to interpret in dense molecular assemblies. Concealing works by manipulating the visibility of nodes (atoms and their bonds), avoiding semi-transparent clutter while keeping the scene clean and precise.
How it works within SAMSON
To use the Conceal atoms animated effect:
- Select the atoms and bonds you want to make disappear.
- Open the Animation panel in the Animator.
- Double-click on Conceal atoms.
The animation includes 4 keyframes:
- Keyframes 1 → 2: All selected atoms and bonds are fully visible.
- Keyframes 2 → 3: The system progressively hides atoms and their connecting bonds, depending on the selection order.
- Keyframes 3 → 4: Everything selected becomes invisible.
As with all animations in SAMSON, you can rearrange the keyframes on the timeline to fit the pacing of your presentation.
Customization and Interpolation
You can adjust how gradually visibility changes occur using the Easing curve properties. This feature defines the acceleration of the disappearance, whether it’s linear, accelerating, or easing smoothly.
Examples in Use
To see the Conceal atoms animation in a real setting, explore these presentations on SAMSON Connect:
These demonstrations show how concealing atoms in stages makes a difference when illustrating internal regions or transitioning between molecular states.
Final Thoughts
The Conceal atoms animation provides a subtle yet effective way to manage visibility in molecular presentations. Instead of simply hiding structures instantly, you can now ease them out of view, guiding the viewer’s attention with more refinement. Consider combining it with the Reveal atoms animation to alternate focus between regions of interest.
To learn more, visit the SAMSON documentation page on this topic: 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.