When presenting molecular structures or simulating molecular processes, clarity is often key. Complex molecules with hundreds—or thousands—of atoms can easily overwhelm your audience and obscure the insights you want to share. Whether you’re preparing a lecture, building an educational video, or creating a scientific presentation, being able to emphasize or isolate specific parts of a molecule matters.
This is where progressive atom concealment in SAMSON can help. Instead of simply deleting parts of the structure or using transparency (which can become visually chaotic), SAMSON allows you to gradually make atoms and bonds invisible with an animation effect called Conceal atoms. This technique offers a precise, frame-by-frame control over visual emphasis—without altering molecular integrity.
What is Conceal atoms?
The Conceal atoms animation lets you progressively hide selected atoms and the bonds between them over a defined time sequence. Unlike lowering opacity, this method works directly on the visibility of nodes and their connections. The atoms don’t fade—they disappear, enabling you to control what is in view at each phase of your molecular story.
When would you use it?
- You want to draw attention to the core of a protein by gradually hiding surface residues
- You need to isolate and explain a ligand-interaction site
- You want to focus your viewer’s attention as a molecular mechanism unfolds
This animation effect can be especially helpful for educators who want to take students step-by-step through complex structural movements without making them feel lost.
How it works
Once you’ve selected the atoms and bonds you want to hide, simply double-click the Conceal atoms effect inside the Animation panel. Behind the scenes, this triggers a 4-keyframe animation:
- Keyframes 1 → 2: all selected atoms and bonds are shown
- Keyframes 2 → 3: atoms and bonds progressively disappear in the order defined by your selection
- Keyframes 3 → 4: everything specified becomes fully hidden
This offers both flexibility and control. You can move the keyframes to adapt the timing, and adjust the easing curve to create smooth or abrupt transitions depending on visual preference.
Visual example
Here’s an example of what that looks like in action:
Interested in applications?
SAMSON Connect provides a few ready-made documents using this animation, such as:
The Conceal atoms animation is one of multiple visibility-based tools in SAMSON designed to give you non-intrusive, reversible control over molecular visualization—perfect for educators, students, and scientists alike who want to tell clearer molecular stories.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.