A molecular structure can be difficult to explain when every atom and bond is visible at once. Viewers may struggle to see which part matters first, especially when you are presenting a large assembly or a complex region. One way to make the structure easier to follow is to reveal selected atoms and bonds progressively, so the audience can take in the model in stages.
In SAMSON, the Reveal atoms animation does this by changing node visibility—not by fading atoms through transparency. That distinction is useful: the selected atoms and bonds are hidden, then shown in sequence. The result is a clear transition from an empty region to the complete selected structure.
Plan the reveal around the story
Before adding the animation, decide which atoms and bonds should appear and in what order. The reveal sequence follows the order of the selection, so the selection is not just a way to identify what belongs in the animation; it also helps define how the structure is introduced. For example, you might want viewers to see one part of a selected structure before the next. Arrange the selection with that intended sequence in mind.
This approach can help when you want to focus attention on a particular part of a model without asking viewers to interpret the entire structure at once. It is also useful for building a presentation in which the complete model is eventually shown, but the path to that final view matters.
What the four keyframes do
After selecting the atoms and bonds, double-click Reveal atoms in the Animation panel of the Animator. The animation uses four keyframes:
- Keyframes 1–2: The specified atoms and bonds become hidden.
- Keyframes 2–3: They progressively appear. Atoms are shown according to their order in the selection, along with bonds between atoms that have been shown.
- Keyframes 3–4: All specified atoms and bonds are shown.
This means the animation includes both a setup interval, where the selected content is hidden, and a reveal interval, where it returns progressively. If the timing does not fit your explanation, move the keyframes to adjust when each part happens. You can change the interpolation between frames with the animation’s Easing curve, which affects how the transition progresses over time.
A simple workflow for a clearer presentation
Start by selecting only the atoms and bonds you want to introduce. Consider the sequence a viewer should follow, then make the selection order reflect that plan. Add the animation from the Animation panel and review the transition: first confirm that the selected content is hidden, then check that it appears in the intended order and that the complete selection is visible at the end. Adjust the keyframes if the reveal feels too fast, too slow, or poorly timed for the rest of your presentation.
Because the animation changes visibility rather than transparency, it is suited to a clean, on/off style of reveal. If you need a gradual fade instead, this is not a transparency animation; choose an effect that matches the visual transition you want.
A deliberate reveal can make a complex structure easier to discuss: choose the relevant atoms, use their selection order to guide the sequence, and let the final keyframes show the full selected structure.
For the full procedure and animation details, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.