When creating molecular animations, it often becomes necessary to shift focus, reduce visual noise, or reveal features step-by-step. Instead of abruptly switching views or hiding atoms instantly, a more refined approach is to progressively hide atoms and bonds over time. This technique provides a smooth, visually intuitive transition that enhances the clarity of a presentation or video, especially when working with large or complex molecular systems.
SAMSON’s Conceal atoms animation effect is designed precisely for this purpose. Unlike adjusting transparency, which may still leave molecules partially visible and visually confusing, the ‘Conceal atoms’ effect fully hides atoms (and the bonds between them) gradually across a defined time span. This feature becomes invaluable when trying to guide your audience through molecular structures smoothly and sequentially.
How It Works
To use this effect, select the atoms and bonds in your molecular system that you want to hide. Then, in the Animation panel of the Animator, double-click on Conceal atoms.
The animation is composed of four keyframes that define the stages of visibility:
- Keyframes 1 to 2: All selected atoms and bonds are shown.
- Keyframes 2 to 3: Atoms and bonds are progressively hidden based on their order in the selection set.
- Keyframes 3 to 4: All the selected atoms and bonds are fully hidden.
This means you can control exactly when atoms begin disappearing and when they become fully hidden. You can also move the keyframes on the timeline to match spatial or temporal cues in your presentation. For instance, this is especially helpful when zooming in on a ligand binding site and gradually hiding parts of the surrounding protein to prevent distraction.
Why Visibility Trumps Transparency
Unlike transparency, which makes atoms semi-visible and may clutter a dense scene with overlapping faded shapes, the conceal animation completely hides parts of the molecule. This creates a clearer visual hierarchy and makes it easier for the viewer to focus on what matters most at any given moment.
Customization and Control
To make the visual progression more natural, you can control the timing and feel of the concealment process using SAMSON’s Easing curve. Easing curves let you accelerate or decelerate the motion between keyframes, giving a more realistic or stylized flow, depending on your preferences.
Example in Action
Here’s an example of a conceal-and-reveal animation in action:
Try It in Your Next Presentation
Use the ‘Conceal atoms’ animation in your next molecular visualization to simplify your scenes, direct attention, and add sophistication to your presentations. Whether you’re preparing a classroom presentation or a video abstract, this technique can help you make your message more effective and concise.
To explore this feature in more detail, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.