Creating molecular presentations that feel clean and professional takes more than accurate models—it requires thoughtful visual storytelling. One common challenge for molecular modelers and educators alike is managing visual complexity in dense molecular scenes. Sometimes, key structures are hidden behind others, or you want to emphasize a subset of atoms without deleting or permanently altering your model.
This is exactly where SAMSON’s Conceal atoms animation comes in. Rather than relying on transparency or removing elements, this animation progressively hides selected atoms and their bonds over a period of time, using discrete visibility changes. And because this is done through animation keyframes, it’s fully reversible and easy to reconfigure.
What is “Conceal atoms”?
Conceal atoms is an animation effect in SAMSON that makes selected atoms and the bonds between them disappear smoothly over a defined animation timeline. Unlike transparency, this method ensures clean occlusion—hidden atoms don’t just fade but are removed from view altogether based on your selection and frame settings.
Use cases
- Focus on active sites: Hide surrounding atoms to isolate and present a catalytic site.
- Step-by-step storytelling: Gradually remove parts of a structure to walk an audience through the molecular architecture.
- Create space: Improve clarity in educational videos by removing non-essential elements during key narrative moments.
How it works
To apply the concealment effect:
- Select the atoms and bonds you want to hide over time.
- Open the Animator and find the Animation panel.
- Double-click on Conceal atoms to add the effect to your selection.
The animation is built with four keyframes:
- Keyframes 1–2: All selected atoms and bonds are visible.
- Keyframes 2–3: Atoms and bonds disappear progressively based on their order in the original selection.
- Keyframes 3–4: All selected atoms and bonds are hidden.
You can rearrange these keyframes to speed up or slow down the effect, and adjust the transition smoothness using an Easing curve. This allows for more organic or technical transitions depending on your style.
Real example
One of the cleanest uses of “Conceal atoms” can be found in SAMSON Connect documents like 1AF6 – Fly around. In these examples, concealed atoms allow the viewer to fly through complex assemblies without unnecessary visual clutter or occlusion.
Tips and considerations
- Combine Conceal atoms with Reveal atoms for a complete show/hide cycle.
- Prepare your selection order with care—the sequence of disappearance follows this order.
- Use the Hide and Show animations for simpler visibility toggles when you don’t need progressive transitions.
To learn more details about how to add and configure the concealment effect, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.