One common challenge faced by molecular modelers is how to effectively communicate structural changes or visual transitions in a clear and engaging way. Whether you’re building an educational video or preparing a research presentation, presenting molecules in a visually coherent sequence can dramatically improve understanding of structural contexts.
In SAMSON, the Appear animation makes it easier to gradually introduce models by modulating their transparency across time. Unlike an abrupt ‘Show’ action, ‘Appear’ provides a smooth transition, ideal for narration, progressive reveals, or highlighting specific molecular regions.
When gradual is better
There are times when instantly revealing an entire molecular structure is overwhelming. For large biomolecules, or scenes composed of multiple model types (e.g., structural models, meshes, labels), viewers might benefit from a step-by-step unveiling. The Appear animation does just this by smoothly decreasing transparency from fully transparent to fully opaque.
What it works with
This animation can be applied to any node that has a transparency attribute:
- Structural models
- Visual models
- Meshes
- Labels
A key detail is that individual atoms or bonds do not have their own transparency attributes—their parent structural models do. So, if your goal is to animate atoms gradually appearing, make sure to apply the animation to the structural model(s) they belong to.
How it works
To use the Appear animation:
- Select the nodes you want to reveal gradually.
- Open the Animation panel via the Animator.
- Double-click Appear to add the animation to your timeline.
This animation includes 4 customizable keyframes:
- Keyframes 1–2: The nodes remain fully transparent.
- Keyframes 2–3: Transparency gradually decreases—models begin to appear.
- Keyframes 3–4: Nodes are fully visible with zero transparency.
You are free to move these keyframes to adjust timing and align with other animated events in your presentation. You can also tweak the interpolation of the transparency using the easing curve feature, adjusting the acceleration of the changes for added visual control.
A helpful trick for highlighting components
You can use multiple layered ‘Appear’ animations with different start times to introduce various molecular parts in a sequence, such as ligands, cofactors, or functional domains. This is especially helpful for complex systems or when working on educational materials that require scaffolding concepts gradually.
Visual example
The GIF above shows a practical application of the Appear (and Disappear) animation in action: smooth transitions, transparent starts, and layered visuals that result in an engaging molecular presentation. Note that the user interface has since been updated—the Animation menu has been replaced by a centralized Animation panel, accessible directly via the Animator.
Learn more about the Appear animation and how it fits into your molecular animation workflow.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.