When presenting molecular models, especially in educational or research contexts, clarity and engagement are key. A common challenge is how to show complex molecular structures in a way that guides the viewer’s attention and helps them grasp what’s happening step by step. This is where progressive visualization becomes valuable.
Using SAMSON’s Reveal atoms animation, you can orchestrate the appearance of atoms and their connecting bonds over time within a molecular story. This makes it easier for viewers to focus on the specific elements you’re showcasing, without being overwhelmed by the full structure at once.
Why gradual visibility matters
Imagine narrating the assembly of a protein complex, or explaining binding site accessibility in a ligand-receptor interaction. Showing the entire molecule at once can be visually cluttered. Instead, with the Reveal atoms animation, you can choose which atoms and bonds appear first, and progressively bring others into view as your animation progresses.
How to apply the Reveal atoms animation
To use the feature:
- Select the atoms and bonds you want to animate.
- In the Animation panel of the Animator, double-click on Reveal atoms.
The animation uses four keyframes:
- Keyframe 1 ↔ Keyframe 2: all selected atoms and their bonds are hidden.
- Keyframe 2 ↔ Keyframe 3: atoms (and their associated bonds) start appearing progressively, based on the selection order.
- Keyframe 3 ↔ Keyframe 4: all selected atoms and bonds are now fully visible.
This design lets you emphasize different regions of a molecule across time, improving storytelling in scientific presentations. Plus, since this animation adjusts visibility directly rather than using transparency, it keeps the visual presentation clean and precise, without semi-transparent overlays.
Tweaking your animation
If needed, you can modify how the reveal progresses by tweaking the Easing curve. This affects the timing and smoothness of the transition between visible states.
You can also move the keyframes freely to adjust the timing and duration of each phase in the reveal sequence.
Practical tip
To increase clarity, order your atom selection thoughtfully. For example, select atoms from the exterior to the core, or by functional group. This way, the reveal matches the logic of your explanation.
Combined with other effects like Flash or Pulse, the Reveal atoms animation can help you build modular, sequential tutorials or visual narratives of structural dynamics.
To learn more, visit the full documentation: Reveal atoms – SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.