A molecular structure can be difficult to explain when every atom is visible at once. A gradual reveal can help viewers follow the structure as it builds, rather than asking them to take in the whole model immediately. In SAMSON, the Reveal atoms animation progressively shows selected atoms and the bonds between them across an animation timeline.
This is useful when preparing a presentation, teaching a structural feature, or guiding attention through a complex model. Instead of fading atoms through transparency, the effect changes their visibility: atoms are hidden or shown. That distinction matters when you want a clear, stepwise appearance rather than a translucent overlay.
Plan the reveal before adding the effect
Begin by choosing the atoms and bonds you want the animation to reveal. Think about what the viewer should notice first and what should come later. The animation’s progressive phase follows the order of the selection, so the selection order is part of the visual story. A useful way to plan is to divide the structure into meaningful groups—for example, the parts you want viewers to notice earlier and the parts you want them to notice later—then make the selection accordingly.
Once the atoms and bonds are selected, double-click Reveal atoms in the Animation panel of the Animator. The effect is created with four keyframes, which divide the animation into three stages:
- Keyframes 1–2: the specified atoms and bonds are hidden.
- Keyframes 2–3: atoms and bonds appear progressively, according to the selection order. Bonds between atoms that have appeared are shown as the reveal advances.
- Keyframes 3–4: all specified atoms and bonds are shown.
This structure gives you a hidden starting point, a progressive reveal, and a fully visible ending. It can make an animation easier to follow because viewers can focus on the changing portion of the structure instead of trying to track every component at once.
Use timing to make the sequence readable
After adding the animation, move its keyframes to adjust how much time each stage occupies. For example, you might allow more time for the progressive interval if the selection contains many atoms, or shorten the lead-in if viewers do not need to pause on the hidden state. These are presentation choices: the documentation does not prescribe a single ideal timing, so preview the sequence and choose a pace that suits the amount of information being revealed.
You can also change how parameters are interpolated between frames by adjusting the easing curve. This affects the character of the transition between keyframes. If the reveal feels too abrupt or too gradual, review the easing curve as well as the keyframe spacing; both contribute to how the animation plays.
A quick check before presenting
- Confirm that the selected atoms and bonds are the ones you intend to reveal.
- Check that the selection order supports the sequence you want viewers to follow.
- Preview the transition from hidden to progressively shown to fully visible.
- Adjust keyframe positions and easing if the sequence is hard to follow.
The example below shows the related conceal-and-reveal animation effects in action.
For the complete procedure and details, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.