In molecular modeling and structural biology, clear visual communication can be just as important as accuracy. When presenting molecular processes or dynamic events—whether in a team meeting, educational video, or scientific conference—there are moments when you want part of the structure to step aside, so your audience can focus on what truly matters.
For these situations, animating the progressive disappearance of atoms and the bonds between them can be useful. Rather than instantaneously hiding elements, a gradual vanishing effect naturally guides viewers’ attention and makes transitions easier to follow. In SAMSON, this is possible through the Conceal atoms animation tool.
What is the Conceal Atoms Animation?
The Conceal atoms animation in SAMSON progressively hides user-defined atoms and the bonds between them between two animation frames. This is achieved by controlling node visibility (as opposed to changing transparency), which tends to make transitions visually cleaner and computationally lighter.
Importantly, this effect is not just an on-off toggle. It includes four keyframes to represent a full animation cycle:
- Frames 1-2: Selected atoms and bonds are fully visible.
- Frames 2-3: Selected atoms and their associated bonds are hidden progressively, one after another, based on their order in your selection list.
- Frames 3-4: All specified atoms and bonds are completely hidden.
By adjusting the positions of these keyframes in the timeline, you can control how fast or slow the concealment occurs. This offers flexibility, whether you’re designing a fast visual transition or a detailed, pedagogical breakdown of a molecular process.
When and Why to Use It
If you’re dealing with a molecule where certain chains, residues, or ligands obstruct the region of interest—perhaps an active site or a binding pocket—the Conceal atoms animation allows you to create space and remove distractions dynamically. Viewers don’t just “see” the final structure; they understand what’s being hidden and why, which improves the overall clarity of the presentation.
Additionally, this effect pairs well with the Reveal atoms animation to create intro-outro effects or looping molecular transformations.
How to Add the Animation
- Start by selecting the atoms and bonds you want to be progressively hidden. You can use selection tools in SAMSON for this.
- Open the Animation panel in the Animator.
- Double-click on the Conceal atoms animation effect to apply it to your selection.
- Fine-tune the effect using the keyframes and adjust the easing curve to modify how quickly or slowly items fade out.
Presentation Examples
Want to see it in action? These publicly available examples on SAMSON Connect showcase the Conceal atoms effect:
To learn more about how to configure this effect, including modifying easing curves and other animation properties, visit the original 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.