Presenting molecular transitions in a visual and understandable way is one of the common challenges molecular modelers face, especially during presentations or when generating animations for educational and research purposes. Complex structures often clutter the screen, making it hard to emphasize the parts that matter most. In these situations, being able to progressively hide specific atoms and bonds can greatly enhance the clarity of your visual story.
In SAMSON, the Conceal atoms animation offers a clean and controlled way to make selected atoms and their connecting bonds gradually disappear between keyframes. Unlike adjusting transparency, this effect hides elements entirely, offering a clearer view of what remains. Let’s explore how this animation can address one of the most frequent pain points in molecular visualization: managing complexity through simplification over time.
Why it works
Instead of toggling visibility suddenly or fading elements through transparency (which may still leave clutter), the Conceal atoms animation smoothly steps users through a structural change. This is particularly useful for:
- Emphasizing the core structure of large biomolecules by gradually hiding side chains or solvent molecules.
- Creating pedagogical animations that introduce complexity step-by-step, or deconstruct a molecule for better comprehension.
- Generating cleaner visuals in presentations and publications.
How it works
The Conceal atoms animation works via visibility changes, not transparency, and uses a 4-keyframe structure:
- Keyframe 1–2: All selected atoms and bonds are shown.
- Keyframe 2–3: Atoms and related bonds progressively disappear in selection order.
- Keyframe 3–4: All selected atoms and bonds are hidden.
You apply it by double-clicking on the Conceal atoms effect in the Animation panel of the Animator, after selecting the atoms and bonds you want to disappear.
The pace and feel of this transition can be further adjusted by editing the Easing curve, which determines how interpolation occurs between the keyframes. For example, you can accelerate the fade at the beginning and slow it at the end, add bounce effects, or create a smoother gradient.
In Action
Here’s an illustrative example showcasing both the Conceal and Reveal atoms animations:
This technique is a key component of several documents prepared using SAMSON, such as:
By integrating this animation into your workflow, you’ll be able to tell clearer molecular stories, highlight key components, and simplify structure interpretation for audiences.
To learn more, visit the official Conceal atoms documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.