When presenting molecular models, transitions can be just as important as the models themselves. Animating what appears or disappears — and how — can help deliver clearer, more focused presentations. One common challenge in dynamic molecular visualization is how to elegantly hide specific atoms or regions over time without losing context or overwhelming the viewer with abrupt changes.
The Conceal atoms animation effect in SAMSON offers a solution to this problem by progressively hiding selected atoms (and their bonds) over time in a smooth, frame-based transition. Unlike changes in transparency, which might keep atoms physically visible but less prominent, the ‘Conceal’ feature truly makes atoms and bonds disappear by toggling their visibility — thus reducing visual noise in a scene.
Why this matters
In many molecular animations, especially when highlighting mechanisms like ligand binding, protein folding, or docking, you don’t want everything visible at once. Specific areas may need to fade out gradually to emphasize what’s important. Viewers benefit from a sequential reveal or disappearance of details rather than a sudden switch, which can be jarring or confusing. This is where ‘Conceal atoms’ comes in handy.
How it works
The animation is applied by choosing the atoms and bonds you want to hide, then double-clicking the Conceal atoms animation effect from the Animation panel in SAMSON’s Animator.
Here’s how the four defined keyframes function in sequence:
- Keyframes 1–2: All selected atoms and bonds are completely visible.
- Keyframes 2–3: Atoms and their bonds gradually disappear, following their order in the selection.
- Keyframes 3–4: All selected atoms and bonds are now hidden.
This system allows for a customizable transition pace between frames. You control both timing and order, depending on how you organize your selections. And if things don’t look quite right at first, you can always reposition the keyframes to adjust the timing.
Making the most of your transitions
To improve the feel of the animation, you can also change the easing curve, which adjusts how the interpolation between keyframes behaves. This may make certain parts of the transition feel quicker or slower, helping you match the animation to your narration or presentation tempo.
Examples to explore
If you’re wondering how this might look in practice, here are a few sample SAMSON document presentations that utilize this animation effect:
These examples show how ‘Conceal atoms’ can help simplify complex molecular environments and direct attention where it matters.
To learn more about how to use this animation in your projects, visit the official documentation page for the Conceal atoms animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.