When you’re creating molecular animations, there are moments when simply making an atom vanish instantly feels abrupt or visually jarring. Whether you’re teaching, presenting, or designing a publication-ready visual, gradual transitions can significantly improve clarity and storytelling. One frequently encountered challenge among molecular modelers is how to create clean, intuitive transitions in animations — especially when specific atoms or groups need to be subtly removed from view to guide attention elsewhere.
To address this, SAMSON includes a useful animation effect called Conceal atoms. This effect lets atoms (and their bonds) disappear progressively across an animation timeline. The transition doesn’t rely on transparency but instead uses visibility — a cleaner, computationally lighter solution that’s often preferable, especially when rendering complex scenes.
Why Use Conceal Instead of Instant Hiding?
Progressive concealment is helpful to:
- Allow viewers to track atom removals smoothly during structural transitions
- Avoid visual confusion during rapid scene changes
- Guide audience attention dynamically
How It Works
You can add the Conceal atoms effect by selecting atoms and bonds in your molecular structure, then double-clicking on the effect in the Animation panel of the Animator. Once added, the animation uses 4 keyframes to define different stages:
- Keyframes 1–2: All selected atoms and bonds remain visible.
- Keyframes 2–3: Atoms and bonds progressively disappear, in the order they were selected.
- Keyframes 3–4: All selected atoms and bonds are fully concealed.
These frames can be repositioned along the timeline to match the pacing of your presentation or animation.
Example in Action
Here’s what the conceal effect looks like when combined with its complement (Reveal atoms):
As you can see, the fading out of specific atoms helps to cleanly transition the visual focus, which can be particularly helpful during fly-throughs or molecular docking visualizations.
Fine-Tuning Transitions
To modify how quickly or smoothly atoms are hidden across keyframes 2 and 3, you can adjust the easing curve. This changes the interpolation between frames, allowing for either very sharp or gradually accelerating/disappearing motions depending on your visual goals.
Try Existing Examples
Want to see how others use the Conceal animation? Explore these examples on SAMSON Connect:
These can provide a starting point or inspiration for incorporating subtle structural changes into your own animations.
To learn more, 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 get SAMSON at https://www.samson-connect.net