In molecular modeling, clarity is everything. When working with complex molecular systems, it’s often necessary to focus your audience’s attention on specific regions or simplify the visual burden by removing certain atoms or bonds from view. However, simply hiding atoms abruptly can feel jarring or make transitions harder to follow—especially in dynamic presentations shared with teams or shown in educational or research settings.
This is where the Conceal atoms animation effect in SAMSON becomes a practical solution. Instead of instant disappearance, this feature introduces a progressive vanishing of atoms (and the bonds connecting them) between two frames. The effect is immediate: smoother storytelling, cleaner transitions, and clearer focus.
Why not just make atoms transparent?
Unlike many graphical platforms that rely on toggling transparency, SAMSON uses the actual visibility state of nodes. This means the atoms and bonds are either present or not, without the performance cost or visual ambiguity sometimes caused by making things semi-transparent. This categorically improves rendering performance and avoids unintended overlaps in dense molecular structures.
How the animation works
To apply the Conceal atoms animation:
- Select the atoms and bonds you want to progressively hide.
- Open the Animation panel in the Animator.
- Double-click on the Conceal atoms animation.
The animation introduces four keyframes:
- Keyframes 1-2: All selected atoms and bonds are shown.
- Keyframes 2-3: Atoms and bonds progressively disappear based on their order in the selection.
- Keyframes 3-4: All selected atoms and bonds become hidden.
Need to adjust timing? You can freely move keyframes to fit your animation sequence. To control the pace of the transition, use the Easing curve to fine-tune interpolation between frames.
Use cases in focus
This animation is particularly useful when:
- Explaining a nested structure like a binding pocket inside a protein.
- Gradually isolating regions of interest in an interactive molecular model.
- Presenting sequential edits, such as ligand modifications or mutations.
Two example presentations that use this effect are available on SAMSON Connect:
By using the Conceal atoms animation, molecular modelers can produce more polished, informative, and visually coherent animations that guide viewers through the structural layers of complex molecules without distractions.
To learn more about this animation, visit the official 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.