When creating molecular presentations, showing everything at once can lead to visual overload — especially for larger molecules. Sometimes all you want is to walk your audience through a part of a structure, one piece at a time. Whether you’re preparing a lecture or illustrating a discovery, smoothly introducing atoms adds clarity and keeps your viewer engaged.
This is where the Reveal atoms animation in SAMSON comes into play. It allows you to progressively make atoms and bonds appear between two frames, helping you narrate your molecular stories more clearly. Unlike fading effects which use transparency, this animation modifies visibility for a cleaner, crisper transition.
Why Use Reveal Atoms?
Imagine you’re trying to explain a new ligand binding site or a step-by-step assembly of a macromolecular complex. If the entire model is shown simultaneously, detailing stages of interaction or emphasizing specific residues becomes cognitively harder for the viewer to process. Using Reveal Atoms, you can easily guide your audience through each part of the structure, focusing their attention while maintaining control over what is shown and when.
How It Works
The animation works across four keyframes:
- Keyframes 1 to 2: The chosen atoms and bonds are hidden completely.
- Keyframes 2 to 3: The atoms and bonds progressively appear, ordered according to your selection order. This allows for stepwise reveal.
- Keyframes 3 to 4: All specified atoms and bonds are fully shown.
You can move the keyframes freely along the timeline, allowing control of the reveal speed. This means the same animation effect can be used to match both quick overviews and slow, detailed introductions depending on the scenario.
Using It in Practice
To start using this animation:
- First, select the atoms and bonds you want to reveal. Make sure the selection order reflects the order you want them to appear.
- Then, double-click the “Reveal atoms” animation effect in the Animation panel inside the Animator.
- Adjust the timing and easing curves if needed for a smoother reveal motion. You can modify interpolation through the Easing curve options.
Here’s an example combining Reveal Atoms with its counterpart, Conceal Atoms:
Tips & Best Practices
- For best effect, use consistent selection order when revealing groups of atoms (e.g., start from residues close to binding sites).
- Use Reveal Atoms in reverse (by reordering your timeline) for a “conceal” effect to close your animation loops.
- Combine Reveal with highlights and labeling steps to create guided educational segments.
Progressively revealing atoms isn’t just visually appealing — it brings clarity to molecular presentations. Whether you’re explaining a gradual assembly process or building up a story atom by atom, this animation gives you the visual control needed for effective communication.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.