In molecular modeling, there’s often a need to highlight a specific region of a structure, demonstrate the dynamic progression of a process, or quite simply avoid overwhelming the viewer with too much visual complexity. If you’ve ever faced the challenge of focusing your audience’s attention during a presentation or a video, the Conceal atoms animation in SAMSON might be a tool worth exploring.
This animation effect allows you to make atoms — and the bonds between them — disappear progressively over time, across multiple keyframes. Unlike changes in transparency, this effect modifies the node visibility directly, providing a crisp and clear removal without ghost-like remnants. The result is a clean visual cue that an atom is no longer present or is being de-emphasized.
When could molecular modelers use this?
Here are a few common scenarios where Conceal atoms becomes extremely useful:
- Zooming into a reaction site: Remove peripheral atoms to bring a pocket site closer to view.
- Step-by-step mechanism explanation: Conceal parts of a molecule between animation segments to isolate the components involved in each step.
- Comparative visualization: Toggle between two structures or mutants by hiding parts of one variant as the animation progresses.
How the animation works
The Conceal atoms animation functions with 4 keyframes:
- Between keyframes 1 and 2, the selected atoms and bonds are fully visible.
- Between keyframes 2 and 3, the atoms progressively disappear based on their order in the selection. Bonds between atoms are hidden only if both bonded atoms are also hidden.
- Between keyframes 3 and 4, all selected atoms are fully hidden.
You can flexibly reposition any of these keyframes to suit your storyboard, thanks to SAMSON’s user-friendly animator interface.
Customizing the transition
To make the concealment feel smoother or snappier depending on your narrative intentions, you can tweak the easing curve. This affects how quickly or slowly the atoms appear to fade from view between keyframes. Whether you want a linear fade, an ease-in, or a dramatic acceleration toward the end — it’s your choice.
Real-world examples
Several presentations created in SAMSON Connect already use this animation effectively. For instance:
- 1AF6 – Fly around: atoms phase in and out to create an elegant molecular flythrough.
- 1AF6 – Fly around – 2: a slightly different take, with subtle conceal-reveal transitions to emphasize molecular interaction sites.
Visual example
Here’s a visual demonstration of atoms progressively disappearing and reappearing using the Conceal atoms and Reveal atoms effects in sequence:
Whether you’re building an educational video, a research presentation, or simply documenting your molecule, the ability to control what is seen or hidden in time is a small but powerful way to enhance clarity.
To learn more and explore the full guide to using Conceal atoms, 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 the platform at https://www.samson-connect.net