A molecular model can contain far more detail than an audience can take in at once. When every atom and bond is visible from the beginning, it may be difficult to focus attention on a particular region or follow how parts of a structure are being introduced. A progressive reveal can make that presentation easier to follow without changing the molecular structure itself.
In SAMSON, the Reveal atoms animation makes selected atoms and the bonds between them appear progressively between two frames. It works through node visibility, not transparency: atoms are hidden or shown rather than gradually made more opaque. That distinction helps set expectations for the effect—you are controlling when selected nodes become visible, not fading their color or opacity.
Plan the reveal around the story
Imagine presenting a large molecular assembly and wanting viewers to notice one selected group before seeing the rest of the chosen atoms. You can select the atoms and bonds to include, then add Reveal atoms from the Animation panel in the Animator. The animation has four keyframes, which define the progression:
- Keyframes 1–2: The specified atoms and bonds are hidden.
- Keyframes 2–3: They progressively appear. The order follows the selection, with atoms and bonds between atoms that have appeared being shown along the way.
- Keyframes 3–4: All specified atoms and bonds are shown.
This makes the selection itself an important part of preparing the animation. If the reveal should move through a structure in a particular order, arrange the selection accordingly before creating the effect. For example, you might choose atoms in a sequence that helps an audience track a region from one end to another. The animation follows that order; it does not infer a scientific narrative or decide which atoms should be introduced first.
Use timing to make the sequence readable
The four keyframes establish the stages, and you can move them as needed. Their placement gives you control over how much of the timeline is devoted to the hidden state, the progressive reveal, and the fully visible state. If the appearance happens too quickly for viewers to follow, adjusting the keyframes can give the reveal more time. If the animation needs to move briskly, the keyframes can be placed closer together.
You can also change how parameters are interpolated between frames by modifying the easing curve. This is useful when the transition’s pacing should feel different, while keeping the same basic reveal sequence. Preview the result and check whether the order and timing support the point you want to make.
A practical preparation checklist
- Select the atoms and bonds that should participate in the reveal.
- Check the selection order, especially if the audience should follow a particular progression.
- Double-click Reveal atoms in the Animator’s Animation panel to add the effect.
- Review the four-keyframe progression and move keyframes to suit the presentation’s timing.
- Adjust the easing curve if you want to change the interpolation between frames.
One helpful way to think about this animation is as a visual cue for attention: the structure is introduced in stages, while the chosen atoms and bonds remain the same. It can help reduce the initial visual load of a dense model, provided the reveal order is deliberate and the timing gives viewers a chance to follow it.
For the complete instructions, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.