Communicating complex molecular processes often requires showing how a molecule forms or changes over time. But static images — or even basic animations — can fall short when you’re trying to illustrate a structural assembly or interaction step-by-step. One of the challenges molecular modelers face is how to clearly and progressively show components appearing in a meaningful way during a presentation or recorded animation. This is where SAMSON’s Reveal atoms animation effect becomes especially helpful.
Why gradual appearance matters
Imagine you’re presenting a protein-ligand binding process, or explaining how a macromolecule assembles. Revealing all atoms at once doesn’t convey the order of assembly — and using transparency blurs the distinction between what’s already assembled and what’s about to appear.
The Reveal atoms feature takes a clear and instructive approach. It shows atoms and bonds actually appear in between frames, based on visibility rather than transparency. This makes it an excellent choice for creating instructive animations that walk your audience through construction or interaction processes.
How it works
Once you’ve selected the atoms and bonds to include in the animation, all you need to do is double-click Reveal atoms in the Animation panel of the Animator in SAMSON. The feature inserts four keyframes into your animation timeline:
- Keyframes 1 → 2: The specified atoms and bonds are hidden.
- Keyframes 2 → 3: Atoms and bonds progressively appear based on their position in your original selection.
- Keyframes 3 → 4: All specified atoms and bonds are fully visible.
During the progressive reveal, only atoms (and the bonds between visible atoms) are made visible — providing a meaningful sequence that depends on how you’ve sorted your selection.
A tip: your selection order matters
SAMSON uses the order of your selected nodes to determine which atoms appear first. So if you want the molecule to build up in a specific way (e.g., central to peripheral, or residue by residue), be deliberate in your selection. This gives you control over the narrative of your structural assembly.
Refining the feel with easing curves
You can also control how smoothly the reveal progresses, using the easing curve. This adjusts the interpolation between frames to create effects like slow starts, accelerations, or smooth finishes — giving your animation a more natural feel.
Try combining it with Conceal for a full cycle
To make assembly-disassembly cycles, try pairing Reveal atoms with the Conceal atoms animation. This makes your animations loop-friendly for embedded demos or educational footage.
Explore the full documentation on the Reveal atoms animation to learn more.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.