A dense molecular structure can be difficult to explain all at once. When every atom is visible from the beginning, viewers may struggle to follow which part matters or how the structure is being introduced. A progressive reveal can make a presentation easier to track by showing selected atoms and their bonds over time.
In SAMSON, the Reveal atoms animation gradually makes selected atoms—and bonds between them—visible. It changes node visibility rather than transparency. In other words, atoms are hidden or shown; they are not simply faded in. That distinction is useful when you want a clear, staged introduction instead of a translucent structure that remains visible throughout.
Plan what the audience should notice
Before adding the animation, decide which atoms and bonds belong in the reveal. The selection is important because the animation uses the order of the selection to determine which atoms appear during the progressive section. If the order is meaningful to your explanation, arrange the selection accordingly before creating the animation.
For example, you might want to introduce one portion of a structure before another, or guide attention through a sequence of selected atoms. The animation does not decide what is scientifically important; that comes from your choice of atoms and their order. Thinking through that sequence first can help prevent a reveal that feels arbitrary.
What happens across the four keyframes
After selecting the atoms and bonds, double-click Reveal atoms in the Animation panel of the Animator. The animation has four keyframes, which create three stages:
- Between keyframes 1 and 2: the specified atoms and bonds are hidden.
- Between keyframes 2 and 3: atoms appear progressively, following their order in the selection. Bonds between atoms that have appeared are shown as well.
- Between keyframes 3 and 4: all specified atoms and bonds are shown.
This structure gives you a useful presentation rhythm: establish the hidden state, reveal the selection progressively, then allow the complete selected set to remain visible. The keyframes can be moved, so you can adjust when each stage occurs to fit the pace of your explanation.
Adjust the timing to suit the explanation
If the reveal feels too rushed or too slow, move the animation’s keyframes. You can also change how parameters are interpolated between frames using the Easing curve. This provides a way to adjust the character of the transition without changing which atoms were selected.
A practical approach is to preview the animation while asking a simple question: can someone watching understand what is appearing, and in what order? If not, revisit the selection order or the placement of the keyframes. These adjustments address two different issues: selection order shapes the reveal sequence, while keyframe placement shapes its timing.
Use this animation when a structure is easier to understand in stages than as a complete image from the outset. For related visibility effects, SAMSON also documents animations such as Conceal atoms, Appear, Disappear, and Show.
For the full instructions, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.