Creating clear and compelling visualizations is one of the ongoing challenges in molecular modeling. Whether you’re preparing a molecular animation for a publication, a presentation, or for educational purposes, making it easier for your audience to follow structural transformations step-by-step can make all the difference.
One particularly useful technique is revealing atoms progressively, allowing parts of a molecule to appear over time instead of showing everything at once. This approach reduces visual clutter, emphasizes key steps, and helps audiences build up an understanding of molecular structures in an intuitive way.
If you use SAMSON, the integrative molecular design platform, this can be done with the Reveal atoms animation effect. This effect gives you control over how atoms and bonds appear from one frame to another—not by adjusting transparency, but through actual visibility changes.
Get Started: Adding the Reveal Atoms Animation
To use this animation, first select the atoms and bonds you want to visualize. In SAMSON, you simply double-click the Reveal atoms animation item in the Animation panel of the Animator. This adds a 4-keyframe sequence to your animation timeline:
- Keyframes 1-2: All selected atoms (and their bonds) are hidden.
- Keyframes 2-3: Atoms start appearing sequentially in the order you selected them, along with the bonds between currently visible atoms.
- Keyframes 3-4: All selected atoms and bonds are fully shown.
This gives you a gradual unveiling effect—ideal for highlighting parts of a molecule or walking through formation steps of complex structures.
Personalize with Easing Curves
Another helpful feature is the ability to control easing curves, which determine how smoothly the animation transitions between frames. This is particularly useful if you want to emphasize suspense or motion continuity when presenting your molecular system.
Tip: You can freely move the keyframes to adjust the reveal duration or sync it with other animation elements.
Why This Matters
Many molecular animations show all atoms at once, making it hard for the viewer to focus on what’s important. Using the Reveal atoms effect allows molecular modelers, educators, and researchers to guide the viewer’s attention and build narrative into their animations. This technique becomes especially valuable when working with large systems, intermediate structures, or when teaching molecular assembly processes.
Here’s an example of the animation in practice:
To learn more, explore the full documentation here: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.