Scientific visualizations are essential to communicating complex molecular structures clearly. But for molecular modelers, a common challenge appears when presenting structures: how to smoothly make elements appear in a scene to emphasize specific spatial or temporal relationships? Sudden pop-ins can be visually jarring and can distract from the message. If you’re using the SAMSON platform for integrative molecular design, there’s a built-in solution for this: the Appear animation.
The Appear animation is particularly useful when you want to stage a step-by-step reveal of molecular models, surfaces, or annotations. It allows selected nodes with a transparency attribute to fade in over time, guiding the viewer’s attention smoothly. This is often used in molecular presentations, education, or dynamic simulations to help explain binding processes, conformational changes, or structural organization.
What is the Appear animation?
In SAMSON, many visual elements—such as structural models, visual models, meshes, and labels—support transparency. The Appear animation progressively decreases their transparency across four keyframes:
- Keyframes 1-2: Nodes are fully transparent.
- Keyframes 2-3: Transparency decreases gradually (nodes fade in).
- Keyframes 3-4: Nodes are fully opaque.
This makes it ideal for highlighting complex structures in phases.
When and why to use it?
Consider a typical scenario where a user wants to introduce multiple components of a protein complex one after the other. Instead of showing everything at once or toggling visibility statically, you can assign an Appear animation to each group of structural models and sequence them. This adds clarity and pacing to the animation without requiring external video editing tools.
How to add the Appear animation
Here’s a quick walkthrough:
- Select the nodes (structural models, meshes, etc.) you want to animate. Note: individual atoms and bonds do not have a transparency setting, so apply the animation to their parent structural model.
- Open the Animator and locate the Animation panel.
- Double-click the Appear animation. It will be added with default keyframes (4 total).
- Adjust the timing by moving keyframes to fit your desired pacing.
You can also adjust how the animation behaves between keyframes using the easing curve, which controls the interpolation speed.
Visual Example
Here’s an illustration of the Appear animation in action, alongside its counterpart, Disappear:
Benefits of using the Appear animation
- Improves the visual flow of your animations.
- Highlights transitions and relationships clearly.
- Reduces cognitive load during presentations.
- Requires no scripting—just a few clicks in the Animator panel.
If you’re manually fading objects using visibility toggles or adjusting transparency values over time, the Appear animation is a faster and more reliable approach. It’s a focused tool that solves a specific but very common presentation need: clear, controlled reveals.
To learn more, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.