One of the recurring challenges in molecular modeling and visual communication is directing attention to specific parts of a molecule. Whether you’re preparing a presentation, creating a tutorial, or crafting a demo for students, hiding parts of a structure needs to be handled carefully. Simply fading parts of a molecule via transparency can be visually confusing or feel too artificial—especially when you want to maintain structural clarity.
In SAMSON, the Conceal atoms animation offers an elegant solution: it lets you make atoms and the bonds between them disappear progressively without manipulating transparency. Instead, it hides the elements directly by progressively toggling their visibility. This is especially useful when preparing tutorial videos, step-by-step mechanism visualizations, or just focusing on core structural areas as a story unfolds.
This animation works with a clear logic
When added, the animation inserts four keyframes by default:
- Keyframe 1-2: all selected atoms and bonds are shown;
- Keyframe 2-3: the selected atoms and bonds progressively disappear, following their sequence order in the selection (useful when ordering matters);
- Keyframe 3-4: all selected atoms and bonds are now hidden.
This approach uniquely avoids the limitations of transparency, which can result in unwanted overlaps or mixed visibility effects, especially during transitions. Instead, the element is either fully visible or hidden, which keeps visual interpretations clean and unambiguous.
Use cases beyond the obvious
This animation suits more than just walkthroughs. In educational videos, it can support progressive learning — beginning with a full view before gradually focusing only on the most crucial parts. In collaboration meetings, it can help highlight specific residues or substructures by removing surrounding visual clutter.
How to get started
- Select the atoms and bonds you want to hide.
- Double-click on the Conceal atoms effect in the Animation panel.
- Adjust the positions of the 4 keyframes to match the timing of your presentation.
Don’t forget, the order in which atoms disappear during the transition depends on their order in the atom selection. You can control this to achieve the flow that best communicates your story.
Customize the transition
The animation’s flow between frames can be fine-tuned using different easing curves—whether you prefer a linear reveal or something more dynamic. This level of control helps better reflect the mood or intent of your presentation.
Want to see it in context?
There are a couple of public presentations on SAMSON Connect using this effect effectively:
This feature is a good fit for modelers, educators, and science communicators seeking cleaner, distraction-free focus areas when telling molecular stories.
To learn more about this animation in SAMSON, visit the documentation page here: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net