In molecular modeling, one of the persistent challenges is how to clearly communicate complex structural changes or highlight specific atoms during a presentation or video. A static model often fails to deliver the impact of a dynamic transition, especially when demonstrating processes like ligand binding, conformational changes, or molecular assembly.
Fortunately, SAMSON provides a useful way to guide the viewer’s attention visually: the Reveal Atoms animation. This built-in animation tool allows you to progressively show selected atoms and bonds over time, giving you fine control over how molecular structures are introduced.
Why Use Reveal Atoms?
Rather than making atoms simply fade in via transparency, the Reveal Atoms animation works by toggling node visibility. This results in clean visual steps where individual atoms or groups appear one after the other, perfect for storytelling in scientific presentations. It can be used to:
- Dramatize the emergence of a protein’s active site
- Highlight a bound ligand or key residue
- Gradually introduce multiple molecules in an assembly
How It Works
To apply the Reveal Atoms animation in SAMSON:
- Select the atoms and any connecting bonds you want to progressively show.
- Double-click the Reveal atoms animation effect from the Animation panel within the Animator.
The animation has 4 keyframes:
- Keyframes 1-2: All selected atoms and bonds are hidden.
- Keyframes 2-3: Atoms and bonds start to appear based on their order in the selection.
- Keyframes 3-4: Everything is fully visible.
The order in which atoms appear is determined by the selection order. This small detail gives you flexibility to tell your molecular story in a particular rhythm. For example, you could first reveal a binding pocket before showing the ligand, guiding your audience’s attention to what matters most.
Customization Options
To adjust the timing or add dramatic pauses, simply move the keyframes within the Animator timeline. You can also change the way atoms appear over time by modifying the Easing curve. This gives you additional control in how gradual or sudden the transitions occur. A linear easing feels clinical and even, while smoother curves can make the transitions feel more organic.
Example in Action
Below is a GIF showing the conceal and reveal animations applied to a molecular structure. This kind of visual storytelling can make your presentation both clearer and more engaging:
Whether you’re preparing a talk, building an educational video, or explaining a simulation workflow, this simple yet powerful animation effect can make your molecular scenes more intuitive.
To learn more about the Reveal Atoms animation and how to use it effectively, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net