When molecular models become dense or structurally complex, it’s easy to lose track of key regions in your presentation. Whether you’re demonstrating binding interactions, structural differences, or pathway progression, isolating areas of interest can be crucial for communication.
The Conceal atoms animation in SAMSON offers a helpful solution: it lets you progressively hide atoms and the bonds between them over time, using visibility (not transparency). This makes molecules disappear in a clean, non-intrusive way and is especially useful when creating animations for presentations or publications.
What it does (and what it doesn’t)
Rather than making atoms semi-transparent, the Conceal atoms animation turns them completely invisible step-by-step between specified keyframes. This helps highlight important molecular regions by letting others recede naturally from view.
This effect uses visibility toggling based on the atom selection you specify, offering a crisp and discrete modification of your scene.
Why it matters
Imagine you’re visualizing a protein-ligand complex and want to focus solely on the binding pocket as the rest of the molecule fades away. Or maybe you’re showing a mutation site but want the surrounding chain to disappear, helping your audience remain oriented without feeling overwhelmed. The Conceal atoms effect accomplishes this without distracting fade transitions, frame clutter, or having to manually hide models.
How it works
The process is straightforward:
- Select the atoms and bonds you want to hide progressively.
- Open the Animation panel of the Animator in SAMSON.
- Double-click on the Conceal atoms effect.
The animation introduces four keyframes:
- Between keyframes 1 and 2: All selected atoms and bonds are shown.
- Between keyframes 2 and 3: Atoms and bonds progressively disappear, in the order specified by the selection.
- Between keyframes 3 and 4: All selected atoms and bonds are fully hidden.
You can move these keyframes to control timing and rhythm. For example, a longer delay between keyframes 2 and 3 will create a slower disappearing effect, revealing structural context more gradually.
Customizing your effect
Using the Easing curve, you can choose how the visibility transition occurs — linearly, exponentially, or using other interpolation patterns. This subtle tweak can significantly affect how smooth and natural your animations feel during playback.
Where you’ve seen this in action
Examples of the Conceal atoms animation in public sessions include:
This capability may seem minor, but for molecular modelers aiming to tell clear and engaging stories with their models, any control over structural visibility is highly valuable. With a few clicks, Conceal atoms helps you focus attention, reduce visual clutter, and keep viewers engaged.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.