When creating molecular animations, many researchers and educators face a common challenge: controlling the visibility of individual atoms without relying on transparency settings, which can lead to cluttered visuals and overlapping structures. Whether you’re preparing a molecular dynamics presentation or just trying to communicate structural insights clearly, being able to progressively hide parts of a molecule in a clean and structured way can make a real difference.
The Conceal atoms animation in SAMSON provides a straightforward way to progressively make atoms (and the bonds between them) disappear between animation frames. This avoids manipulating transparency and instead uses visibility toggling—which is both computationally lighter and visually cleaner. Here is how it works and how you can make the most of it in your own projects.
What Does It Do?
The Conceal atoms effect works with visibility—atoms and their connecting bonds are hidden over time between user-defined keyframes. This is especially useful when you want to highlight or isolate a substructure, show active sites, or transition between different representations of a molecule while keeping the presentation focused.
How It Works
In SAMSON, this animation consists of four keyframes, each serving a specific purpose:
- Between keyframes 1 and 2: All selected atoms and their bonds are visible.
- Between keyframes 2 and 3: These atoms progressively disappear, based on their order in the selection.
- Between keyframes 3 and 4: All selected atoms and bonds are hidden.
This step-wise disappearance offers precision, and it avoids abrupt visual changes in your animation. You can rearrange the keyframes freely to control the timing and duration of each stage—a useful feature when synchronizing visibility with other motions or narrative elements.
When to Use It
This animation is particularly useful in scenarios where:
- You want to reveal the inner structure of a macromolecule by peeling off external layers.
- You aim to gradually expose or hide ligands, channels, or subunits to explain function.
- You need consistent and clean visuals for comparative animations—without visual noise from semi-transparent objects.
Enhancing Your Animation
You can further control the animation by adjusting the easing curve that interpolates between frames. Whether you prefer linear transitions or more natural acceleration/deceleration curves, this control helps fine-tune how atoms are concealed over time.
Real-World Examples
SAMSON users can draw inspiration from available public presentations that use this technique. For instance:
Both use steps of conceal and reveal to focus viewer attention on different structural parts during the animation, achieving a concise visual storytelling flow.
To learn more about the Conceal atoms animation and how to implement it in your own projects, visit the full documentation: 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.