Complex molecular structures often overwhelm audiences when presenting biochemical mechanisms or molecular simulations. Showing every atom and bond might be accurate, but it quickly becomes counterproductive if the viewer can’t follow what’s happening.
This is a challenge many molecular modelers face: how to draw attention to what’s essential, without discarding the rest of the structure. One solution built right into SAMSON is the Conceal atoms animation effect, which enables you to hide atoms and bonds gradually over time. This method maintains scientific integrity while improving clarity and storytelling in molecular visualizations.
Why conceal atoms instead of deleting them?
Deleting parts of a structure is not only irreversible during a presentation, but also misleading. Concealing, on the other hand, allows modelers to maintain the full structure while adjusting visibility over specific time frames — and doing so progressively. This subtle yet powerful tool can help demonstrate concepts like ligand binding, conformational changes, or focus on active sites without discarding structural context.
How it works in SAMSON
To add the Conceal atoms animation effect in SAMSON:
- Select the atoms and bonds you want to progressively hide.
- In the Animation panel of the Animator, double-click the Conceal atoms animation.
This effect introduces 4 keyframes by default:
- Keyframes 1-2: All selected atoms and bonds are visible.
- Keyframes 2-3: The atoms and bonds progressively disappear, in the order defined by the current selection.
- Keyframes 3-4: All selected atoms and bonds are fully hidden.
You can freely move the keyframes to adjust timing. Additionally, you can tweak how the animation behaves using different easing curves for more natural motion.
Real examples in molecular presentations
Here’s how this effect works in action:
This GIF shows a molecule in which parts of the structure are concealed or revealed over time — helping focus the viewer on the regions of interest. The invisibility isn’t achieved through transparency, but actual visibility toggling of nodes, which makes it lighter computationally and avoids rendering issues in some styles.
Want to try it?
SAMSON Connect provides presentation examples using this technique, including:
Whether you’re communicating with collaborators or preparing teaching material, learning to conceal atoms smartly can drastically improve the clarity of your molecular animations without losing scientific detail.
To learn more, visit the full documentation page on Conceal atoms here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.