When preparing molecular presentations or animations, one common goal is to highlight a specific part of a structure. Whether introducing a binding site, focusing on a key residue, or guiding attention across a molecular assembly, modelers often look for ways to de-emphasize parts of the system without cluttering the visual story.
Transparency is frequently used for this purpose. However, gradually hiding atoms entirely—rather than adjusting their opacity—can sometimes be the more effective strategy. In SAMSON, the “Conceal atoms” animation offers a simple way to progressively make atoms and bonds disappear over time, helping users communicate molecular transformations or stepwise simplifications clearly and smoothly.
What problem does “concealment” solve?
Imagine explaining a complex molecular scene in which certain atoms are not relevant for the point you’re trying to make. While transparency might still show distracting details in the background, concealing atoms removes them entirely from view. This focused visualization is especially helpful during animations in talks or demonstrations when controlling the viewer’s attention is critical.
How it works in SAMSON
The Conceal atoms animation is easy to set up from the animation panel in SAMSON’s Animator. To use it:
- Select the atoms and bonds you want to gradually hide.
- Double-click on the Conceal atoms entry in the animation panel.
The animation inserts 4 keyframes by default:
- Keyframes 1–2: atoms are fully visible
- Keyframes 2–3: atoms progressively disappear (concealment depends on their order in the selection)
- Keyframes 3–4: atoms are fully hidden
With this setup, parts of your molecule vanish in a controlled, staged fashion, without relying on visual transparency effects—ideal for clarity and seamless transitions.
Why order matters
During the concealment phase (keyframes 2–3), the atoms are hidden one after another based on their order in the selection. This gives you fine-grained control over the animation’s flow. Want a central region to disappear last? Select those atoms last. You can also move the keyframes to control the duration of each phase.
Customize with easing curves
The animation’s timing and feel can be refined by adjusting the easing curve, allowing for smooth or abrupt transitions depending on your presentation style.
See it in action
Here’s an example of the “Conceal atoms” animation used alongside a reveal effect to guide viewer focus:
Try it on your own models
Two example documents using this technique can be found on SAMSON Connect:
They show how this animation helps guide the audience through complex molecular trajectories without overwhelming the visual field.
Learn more about the Conceal atoms animation in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.