Presenting molecular processes to diverse audiences — from researchers to students — often requires more than static snapshots. Animations play a key role in making molecular simulations more comprehensible and visually intuitive. One common challenge for many molecular modelers is how to effectively illustrate the gradual formation or appearance of complex molecular structures. This is where the Reveal atoms animation effect in the SAMSON platform can be especially helpful.
Instead of a sudden appearance of atoms, which can be visually overwhelming or confusing, the “Reveal atoms” animation in SAMSON makes atoms (and the bonds between them) progressively appear between frames without relying on transparency. This provides a clean and controlled way to visualize molecular assembly, complex formation, or even docking simulations.
What Problem Does It Solve?
If you’ve ever attempted to animate molecules building up or forming interactions with sudden shows and hides, you may have gotten feedback that it looks unnatural or hard to follow. Even if you’ve tried using transparency effects, these can often muddy the visuals, especially in complex structures. What you need is precise per-atom control of visibility: exactly what the “Reveal atoms” effect does.
How It Works
To apply the Reveal atoms animation in SAMSON:
- Select the atoms and bonds you want to reveal gradually.
- Double-click on the “Reveal atoms” effect from the Animation panel in the Animator.
The animation breaks down into 4 keyframes:
- Keyframes 1–2: All selected atoms and bonds are hidden.
- Keyframes 2–3: Atoms and bonds begin to appear one by one, in the order specified by the selection.
- Keyframes 3–4: All selected atoms and bonds are visible.
You can move keyframes to control the pacing of each part of the animation. For example, if you want atoms to appear very slowly after an initial delay, increase the time between keyframes 2 and 3.
Customization Tips
One powerful feature of the animation system in SAMSON is the support for easing curves. These allow you to fine-tune how the reveal speed accelerates or decelerates over time. By modifying the easing curve, you can make atoms appear with a burst at the beginning and slow at the end, or vice versa. This brings more nuance to visual storytelling in molecular modeling.
When To Use It?
The Reveal atoms animation is especially useful when:
- Visualizing docking of a ligand into a protein binding site.
- Animating the self-assembly of molecular structures.
- Showing the formation of a supramolecular complex.
- Creating step-by-step educational videos.
Reveal vs Appear
Some users might wonder how “Reveal atoms” differs from the “Appear” animation effect. While both result in atoms becoming visible, “Reveal atoms” works through progressive visibility based on atom order, whereas “Appear” often applies to all at once becoming visible, possibly via transparency.
To learn more and explore this feature in detail, visit the original documentation page: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.