A molecular structure can be difficult to explain when every atom is visible at once. A dense region may hide the part you want people to notice, while a static image gives no sense of how that region relates to the rest of the model. A progressive reveal can help: it lets viewers follow the appearance of selected atoms and bonds over time.
In SAMSON, the Reveal atoms animation changes node visibility, rather than gradually changing transparency. That distinction matters when planning a sequence: the atoms are hidden or shown, not faded in as translucent objects. The effect is useful when you want a clear, staged introduction to a selected part of a molecular model.
Plan the selection before animating
Start by choosing the atoms and bonds you want the animation to affect. The reveal order depends on the order of items in the selection, so treat selection order as part of the presentation—not just a preliminary step. Consider what viewers should see first and what should follow. For example, you might want to guide attention through a region in a deliberate sequence rather than reveal all selected items at once.
The documentation does not describe an automatic spatial or chemical ordering. If a particular order matters to your story, make your selection with that in mind and check the resulting animation. The selected set also defines the scope of the effect: atoms outside it are not the targets of this reveal animation.
What the four keyframes do
After selecting the targets, double-click Reveal atoms in the Animation panel of the Animator. The animation has four keyframes, which divide the effect into three stages:
- Keyframes 1–2: the specified atoms and bonds between them become hidden.
- Keyframes 2–3: the selected atoms progressively appear. Bonds between atoms that have appeared are shown as well. The sequence follows the order of the selection.
- Keyframes 3–4: all specified atoms and bonds are shown.
This structure gives you a useful way to think about timing. The first interval establishes the hidden starting state, the middle interval carries the reveal, and the final interval completes it. Move the keyframes as needed to adjust where those stages fall in your animation. If the reveal feels too fast or too slow for your explanation, changing keyframe positions is the documented way to adjust its timing.
Use easing to shape the transition
Keyframe placement controls when the stages occur; the easing curve controls how parameters are interpolated between frames. Adjusting the easing curve can change the character of the transition without changing which atoms are selected or their selection order. This is worth checking when a sequence is technically correct but does not feel easy to follow.
A practical review is to play the animation and ask three questions: Does the reveal begin at the right moment? Is the selected order understandable? Does the completed structure appear by the final keyframe? If not, revisit the selection, keyframe positions, or easing curve. These checks help keep the animation focused on the molecular explanation rather than on the effect itself.
For the full procedure and related details, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.