Communicating molecular complexity in an engaging and understandable way is one of the longstanding challenges in molecular modeling. Whether you are preparing an animation for teaching, a presentation for a research project, or simply trying to highlight a structural transformation in a simulation, being able to control how and when parts of a molecular system appear on screen can make a significant difference.
This is exactly where the Reveal atoms animation in SAMSON proves useful. Instead of adjusting transparency to fade in atoms, this feature gradually toggles their visibility, giving you precise control over the timing of molecular appearances. The result is a clean and focused visualization – for example, you can first hide everything, and then guide the viewer’s attention by revealing atoms progressively, according to your selection order.
Why this matters
Consider a scenario where you’re presenting a ligand binding event. Simply showing the final pose of a molecule within a binding pocket might be effective, but animating the appearance of the binding residues, or the ligand itself, can add clarity and narrative flow. A progressive reveal helps emphasize structural hierarchy or sequence, and keeps the viewer focused.
The Reveal atoms animation is built around four keyframes:
- Keyframes 1 → 2: Selected atoms are completely hidden.
- Keyframes 2 → 3: Atoms begin to appear progressively, based on their order in the selection.
- Keyframes 3 → 4: All atoms are fully visible.
You can move the keyframes freely to match the timing of your visualization goals. If you want atoms to remain hidden for longer or reveal faster, adjust accordingly. For more control, tweak the motion between keyframes using easing curves.
How to add the animation
To use this animation in SAMSON:
- Select the atoms and bonds you want to reveal.
- Open the Animation panel in the Animator.
- Double-click the Reveal atoms animation effect.
- Fine-tune keyframes and easing curves as needed.
This feature bypasses transparency altogether, which is especially helpful when working with complex models where overlapping semitransparent atoms can create visual clutter or confusion. Visibility toggles provide cleaner visual segmentation.
Selection order matters
One subtle but important feature: the order in which atoms are selected determines how they’re revealed in the animation. So, if you want the active site to appear first, followed by the rest of the structure, simply select in that order before applying the animation. This offers a straightforward way to script a visual narrative without writing any code.
To learn more, visit the full documentation: Reveal atoms animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.