Creating scientific animations that are both informative and visually clear can present unexpected challenges, especially when depicting molecular structures that evolve or transition over time. One frequent issue molecular modelers face is how to gradually remove atoms or bonds in a scene without inducing visual clutter or unwanted transparency artifacts.
This is particularly relevant when preparing educational content, collaboration materials, or presentations where the audience may not be familiar with interpreting translucent or complex overlapping structures. In these cases, clarity is key—sometimes it’s not about showing more, but showing less, effectively. That’s where the Conceal atoms animation in SAMSON can help.
What does “Conceal atoms” do?
The Conceal atoms animation allows you to progressively make selected atoms and their connecting bonds disappear without changing their transparency. Instead, this effect works by altering the visibility of the nodes (atoms and bonds) across four keyframes:
- Keyframes 1 → 2: atoms and bonds are fully visible
- Keyframes 2 → 3: atoms and bonds are gradually hidden, following the order of selection
- Keyframes 3 → 4: all selected atoms and bonds remain hidden
This makes the animation especially useful for directing attention in molecular presentations, giving viewers a more digestible visual experience as structural elements ‘exit’ the frame cleanly.
Why use visibility instead of transparency?
Transparency might seem like a natural solution at first, but rendering transparent objects in a 3D environment can sometimes lead to unintended layering issues, decreased performance, or simply confusing visuals—especially in dense molecular models. Hiding elements outright makes for a clean and unambiguous visualization.
How to add this animation in SAMSON
To apply the Conceal atoms animation:
- Select the atoms and bonds you want to gradually hide.
- In the Animation panel of the Animator, double-click on Conceal atoms.
- Move the keyframes as needed to adjust the timing of the animation.
- If desired, customize the interpolation using easing curves for a smoother or punchier transition.
When to use it
This animation is especially effective when:
- You want to simplify a complex scene progressively
- Focusing attention by introducing or removing atoms in a particular order
- Making step-by-step walkthroughs in reaction mechanisms or molecular configurations
Here’s an example presentation where this animation is used to create a clean, informative visualization of a fly-around of molecule 1AF6. A second version is also available here.
By removing rather than fading out atoms, this animation style supports precision and visual clarity—two crucial goals in scientific communication.
To explore the full documentation of the Conceal atoms animation, 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.