When designing molecular presentations, clarity often hinges on what you choose to show—and just as importantly, what you choose to hide. The Conceal atoms animation in SAMSON offers a simple way to make atoms—and the bonds between them—disappear progressively. This is especially useful when you want to focus the viewer’s attention on specific molecular substructures without abrupt visual transitions.
Rather than adjusting transparency, this feature works by changing the visibility of atoms and bonds between defined keyframes. Let’s take a closer look at how this animation adds value to your presentations and how you can integrate it effectively.
Why Conceal Atoms?
Whether you’re preparing a molecular dynamics presentation or crafting a tutorial, you may need to guide your audience’s eyes. Perhaps there’s a ligand in a protein pocket you wish to highlight, or maybe you’re trying to walk a viewer through a reaction center. Concealing atoms over time provides a smooth and intuitive way to shift attention—no sudden jumps, no visual clutter.
This animation proves especially useful in dynamic visualizations, where transitions matter. Unlike toggling visibility or using fading transparency (which could conflict with lighting or rendering artifacts), the Conceal animation removes atoms step-by-step based on the order of your selection.
How It Works
To apply the Conceal atoms animation:
- Select the atoms and bonds you want to gradually hide.
- Open the Animation panel in the Animator.
- Double-click the Conceal atoms animation effect.
This adds an animated sequence with four keyframes:
- Keyframe 1 to 2: Atoms and bonds are fully visible.
- Keyframe 2 to 3: Atoms and bonds progressively disappear depending on their position in the selection.
- Keyframe 3 to 4: Everything you selected is hidden.
This four-step structure gives you granular control. For example, you can delay the start of the concealment phase, or stretch the transition to fit the rhythm of your presentation.
The concealment behavior is non-destructive and reversible. You can always move the keyframes later to align better with other transitions or camera movements.
Tapping Into Selection Order
The selection order determines which atoms disappear first. This allows interesting storytelling opportunities: hide peripheral groups first, and keep central atoms visible a little longer for focus. The animation is especially powerful when combined with the Reveal atoms animation, enabling objects to appear and disappear in tandem.
Controlling the Speed
You can fine-tune the visual tempo of the conceal effect using the Easing curve. Choose linear for uniform pacing, or try an ease-in curve to accelerate the fading at the start. These curves affect how quickly atoms disappear between keyframes 2 and 3.
See It in Action
Here’s an example showing atoms being concealed step-by-step. This type of visual cue can help instructors, researchers, or students better follow complex molecular changes.
Explore Sample Documents
For presentations that incorporate this animation, check out the following examples on SAMSON Connect:
Learn more about the Conceal atoms animation and its features in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.