For molecular modelers and structural biologists working with complex molecular systems, presenting molecules in a clear and digestible way can be a real challenge—especially when you’re trying to guide an audience through a process, a mechanism, or a sequence of molecular events. If everything shows up at once, your viewers may miss important context or feel overwhelmed.
This is where the Appear animation in SAMSON comes in. It’s a simple but highly effective tool for improving clarity and flow when introducing molecular structures or highlighting transitions in a story. With the Appear animation, models don’t just pop into view suddenly—they are smoothly revealed in a controlled way, allowing you to guide attention exactly where it’s needed.
Why use the Appear animation?
There are many cases where progressive reveal is helpful:
- Introducing a complex assembly step-by-step
- Revealing a binding site after showing the environment
- Transitioning from abstract shapes to atomic details
With Appear, models become visible through a change in transparency, giving viewers time to process what’s happening. This creates smoother visual transitions and a more professional presentation—without requiring any scripting.
How it works
The Appear animation is applied to nodes in your scene that have a transparency attribute. This includes structural models, visual models, meshes, and labels. Nodes without transparency support (such as individual atoms or bonds) can’t be directly animated this way—but their parent structural models can.
Adding the animation
Just follow these steps:
- Select the nodes that you want to appear.
- Open the Animator and go to the Animation panel.
- Double-click the Appear effect to apply it.
The animation consists of 4 keyframes:
- Between keyframes 1 and 2: nodes are fully transparent.
- Between keyframes 2 and 3: nodes progressively reduce transparency.
- Between keyframes 3 and 4: nodes are fully visible (opaque).
You can move these keyframes to control timing, and also customize the transition using easing curves in the animation’s properties. This makes it easy to create synchronized reveals or coordinate multiple animations.
Tips for smooth transitions
- Apply Appear to grouped nodes to control multiple elements together.
- Combine Appear with camera animations for cinematic introductions.
- Use easing curves to match the pacing of narration or text overlays.
And remember: even if you’ve already applied animations, they are fully editable—keyframes can be moved at any time.
When your visualization needs clarity at the very first frame, Appear helps set the stage without overwhelming your viewers. To learn how to apply it in more detail, see the full documentation page: https://documentation.samson-connect.net/users/latest/animations/appear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net