When creating visually engaging molecular animations, it’s often important to guide your audience’s attention in a deliberate way. Maybe you want to zoom into the active site of a protein or gradually hide peripheral atoms as you move through a conformational change. Simply cutting atoms out of view can feel sudden or jarring. This is where the Conceal atoms animation in SAMSON offers an elegant solution: a smooth, progressive disappearance of atoms and bonds, all controlled with just a few keyframes.
This blog post is for those who want a more refined storytelling tool when creating molecular animations. Instead of making atoms transparent or instantly removing them, the Conceal atoms effect hides elements gradually based on their order in a selection. It’s a subtle difference that makes a big visual impact for presentations, animations, or videos.
When and why to use Conceal atoms
The Conceal atoms animation is useful any time you want to:
- Direct focus to a region of interest inside a large structure
- Transition from full molecular context to a simplified view
- Create smooth transitions that match other timed animation effects
- Reveal internal components (by concealing outer ones first)
How it works
To add the effect, first select the atoms and bonds you want to hide. Then, double-click the Conceal atoms effect from the Animation panel of the Animator. This inserts a four-keyframe animation with the following behavior:
- Keyframes 1 to 2: All selected atoms and bonds are visible.
- Keyframes 2 to 3: Atoms and bonds progressively disappear in the order they were selected.
- Keyframes 3 to 4: All selected atoms and bonds are fully hidden.
You can drag and adjust these keyframes in the timeline to control the speed and timing of the animation. To fine-tune the interpolation between states, you can also use different easing curves.
Tips for selection and sequencing
The order of selection matters — the concealment follows this order. Selecting atoms from surface inward, or in a chain-based pattern, might produce a more natural peeling effect. Experiment with selection techniques in SAMSON’s Selection filter to get desired results.
Example in action
Imagine fading away the protein shell to reveal a ligand, or hiding neighboring residues to emphasize a metal center coordination. The Conceal atoms animation offers both scientific clarity and aesthetic improvement.
Putting it together
Combine Conceal atoms with other effects like Reveal atoms or Fly around to build layered animations that tell a molecular story. This is especially helpful when presenting to non-experts or when preparing educational videos where visual clarity helps in explanation.
You can explore examples such as 1AF6 – Fly around and its variations, where the Conceal atoms effect is used to fade molecular surroundings elegantly.
Learn more about this animation effect and its properties in the official Conceal Atoms documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.