When preparing molecular animations, it can be tricky to control how atoms appear and disappear without overwhelming your audience. In many visualization tools, fading atoms using transparency can cause visual clutter, making it hard to follow the structural changes you want to highlight. This is where the Conceal Atoms animation in SAMSON can offer a distinct and useful alternative.
Conceal Atoms is an animation effect in SAMSON that hides atoms and the bonds between them progressively between keyframes — not by making them semi-transparent, but by changing their visibility. This can help you craft clearer and more focused animations that communicate structural changes or isolate key regions of interest.
Why this matters for molecular modelers
When presenting molecular mechanisms, such as a ligand entering a protein binding site or a conformational shift, you often want to direct the viewer’s attention to specific atoms or domains. Fading things out with transparency adds visual noise, especially when surfaces, labels, or densities are involved. Hiding atoms cleanly avoids these issues and allows you to construct uncluttered sequences.
How the Conceal Atoms animation works
After selecting the atoms and bonds you want to hide:
- Open the Animation panel in SAMSON’s Animator.
- Double-click on Conceal Atoms to add the animation.
The effect introduces 4 keyframes:
- Keyframes 1-2: All selected atoms and connecting bonds are visible.
- Keyframes 2-3: Atoms and bonds progressively disappear following their order in the selection.
- Keyframes 3-4: The selected elements are fully hidden.
You can move these keyframes to fine-tune animation timing. With the Easing curve control, you also have precise control over the interpolation behavior between frames — for example, making the hiding accelerate or decelerate smoothly.
Practical uses
This animation works well when combined with Reveal Atoms, letting atoms disappear and reappear in sequence for emphasis. Examples on SAMSON Connect show how this is used in action:
Using Conceal Atoms creates a precise storytelling tool: show a molecular component, then remove it seamlessly to unveil internal interaction sites, tunnels, or buried residues.
Visual example
This GIF demonstrates the synchronized conceal and reveal of atoms during a fly-around, guiding the viewer through the structure step by step.
Learn more about Conceal Atoms animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.