One of the most common challenges in molecular modeling is maintaining clarity in complex scenes. When visualizing large biomolecular systems—like proteins, nucleic acids, or ligands in crowded environments—researchers often find themselves overwhelmed with visual clutter that can obscure important details.
This is where selective concealment becomes a useful tool. The Conceal atoms animation effect in SAMSON provides a straightforward but effective solution: progressively hiding atoms and the bonds between them across frames, helping you and your audience focus only on what’s relevant.
Why use concealment instead of transparency?
Transparency is often the default choice when trying to reduce the visual weight of certain parts of a molecular system. However, transparency can still leave distracting visual noise in dense models. With the Conceal atoms animation, atoms aren’t just made semi-transparent—they are completely hidden, helping ensure a cleaner, more focused visualization.
How the animation works
The animation is based on adjusting the visibility of nodes (atoms and the bonds between them). It uses 4 keyframes:
- Between keyframes 1 and 2: all selected atoms and bonds are visible.
- Between keyframes 2 and 3: atoms and bonds progressively disappear based on their order in the selection.
- Between keyframes 3 and 4: all specified atoms and bonds are hidden.
You define which atoms and bonds are affected simply via selection. SAMSON then takes care of animating their visibility with no scripting needed.
Controlling the effect
To fine-tune the appearance or disappearance behavior, SAMSON allows you to change the Easing curve. This controls how the visibility transitions happen across time—making the change feel more natural or dramatic, depending on your presentation.
When to use this
- If you’re preparing pedagogical content where focus needs to shift from the whole structure to a binding pocket.
- If you want to reduce complexity progressively to reveal a reaction site more clearly.
- Or if you’re simply trying to draw attention to conformational changes by hiding static components.
Visual example
Here’s a short example of the Conceal and Reveal animations in action, applied to a flyaround animation of the 1AF6 protein:
Getting started
To add the Conceal atoms effect, select the atoms and bonds you want to hide. Then, double-click on the Conceal atoms effect in the Animation panel of the SAMSON Animator. Move and adjust the keyframes as needed to fit your narrative. That’s it. Your animation is now focused, clearer, and more effective.
To learn more about this effect—or to see other related animations like Reveal, Pulse, or Flash—visit the official documentation page: 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.