When working with complex molecular models, clarity is essential. Molecular modelers often face the challenge of communicating dynamic processes, stepwise assemblies, or structural differences — and static images or abrupt transitions are rarely effective. If you’ve struggled to make molecular components gradually appear in your videos or presentations, the Reveal atoms animation in SAMSON offers a clean, frame-by-frame solution.
Unlike changes in transparency — which can be misleading in terms of presence or interaction states — the Reveal atoms animation relies fully on visibility. This makes it an instructive way to guide the audience’s eyes to where atoms (and bonds) progressively emerge, one by one, in an order you control.
Highlighting complexity without overwhelming your viewer
Explaining the binding of a ligand, the assembly of a macromolecular complex, or the unfolding of a molecular interaction often means slowly walking your audience through what’s being revealed. With this animation, you can introduce atoms and bonds stepwise — often more digestible and appealing than an immediate full view.
To apply the Reveal atoms animation, first select the atoms and bonds whose emergence you want to control. Then, double-click Reveal atoms in the Animation panel of the Animator.
What actually happens between the frames?
This animation works with 4 keyframes, and each one helps guide the transition:
- Frames 1–2: All selected atoms and bonds are hidden.
- Frames 2–3: Atoms and bonds progressively appear. This is based on their order in your selection, so you have full control over the reveal path.
- Frames 3–4: All atoms and bonds are fully visible.
You can move the keyframes to control the speed of appearance, or adjust easing using various easing curves to create smooth transitions or more sudden reveals depending on what fits your story best.
When to use this animation
This technique is especially useful for:
- Step-by-step visualization of ligand binding.
- Illustrating dynamic changes in conformation (e.g., folding or assembly).
- Paired visualizations with Conceal atoms to emphasize molecular regions being added or removed.
The visual result is shown below. The atoms are not faded in — they appear clearly, which avoids confusion and makes interpretation easier for your audience.
Learn more about the Reveal atoms animation in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.