When building molecular presentations, clarity often depends on more than just content—it depends on pacing and focus. One challenge modelers frequently encounter is how to transition parts of a molecule out of view without causing visual clutter or confusion. Fading elements using transparency or abrupt cuts can be distracting or ambiguous for viewers. In SAMSON, the Conceal atoms animation offers an elegant solution to this issue by progressively hiding atoms (and their bonds) with precision and control.
Why hiding atoms matters
Molecular presentations often involve complex structures with thousands of atoms. Highlighting a central zone, a binding site, or transitions in conformation typically means reducing visual noise. Instead of abruptly removing atoms or fading them gradually through transparency—both of which can distract or confuse—concealing atoms progressively simplifies the visual field in a clear and interpretable way.
What the Conceal Atoms animation does
The Conceal atoms animation makes selected atoms (and the bonds between them) progressively disappear between two frames. What makes it effective is that it does this by altering visibility, not transparency. This leads to a more definitive, controlled removal of visual elements, which reinforces the message you want to convey.
The animation creates a logical storytelling flow across 4 keyframes:
- Keyframe 1 to 2: All selected atoms and bonds are visible.
- Keyframe 2 to 3: The atoms and bonds start disappearing progressively based on their selection order.
- Keyframe 3 to 4: All specified atoms and bonds are hidden.
This model supports more nuanced visual storytelling, for instance, by beginning with the aggregate structure and smoothly drawing attention inward by removing outer layers step-by-step.
How to use it effectively
1. Select the atoms and bonds you want to remove gradually.
2. In the Animation panel, double click on the Conceal atoms effect. This adds the animation with its 4 pre-defined keyframes.
3. Adjust the timing by moving the keyframes to match your intended pacing.
4. You can also adjust the easing (interpolation of the transition) using the Easing curve settings if you want a smoother or snappier transition.
Examples and visual illustration
A visual example is provided below, showing how Conceal atoms works alongside its counterpart, Reveal atoms. Notice how atoms are cleanly hidden, layering the presentation in a readable and structured way:
If you want ready-to-use demonstrations, the following documents on SAMSON Connect include conceal animations:
This technique is especially useful in educational walkthroughs or when preparing scientific presentations that require precision and clarity in molecule transitions.
Learn more about Conceal atoms and related animations in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.