Controlling the visual introduction of molecular elements in a scene can make a major difference when presenting complex biomolecular data. Whether you’re making a video to share your results or building an interactive animation to highlight dynamic features of a molecule, the way models transition into view matters.
One challenge often faced by molecular modelers is how to avoid abrupt on-screen appearances that distract from the scientific story being told. Fortunately, the Appear animation in SAMSON offers a simple way to make molecular objects fade into visibility gradually, producing a smoother, more polished visual experience.
Why Use the Appear Animation?
The Appear animation lets you progressively display molecular nodes — such as structural models, visual models, meshes, or labels — over time by adjusting their transparency. This is particularly helpful when:
- You want your viewers to focus on specific parts of the model as you introduce them.
- You are layering visual information and want to step your audience through it gradually.
- You are building tutorial or educational material that benefits from well-paced visual cues.
When Does It Work?
The Appear animation can only be applied to nodes that possess a transparency attribute. These typically include:
- Structural models
- Visual models
- Meshes
- Labels
It’s important to note that atoms and bonds themselves do not have an opacity property that you can animate independently. Instead, apply the Appear animation to their parent structural model.
Setting Up the Appear Animation
1. Select the nodes you’d like to fade into view.
2. Open the Animation panel in the Animator.
3. Double-click on the Appear effect to add it to your animation timeline.
The Appear animation includes four keyframes by default:
- Keyframe 1 to Keyframe 2: objects are fully transparent
- Keyframe 2 to Keyframe 3: objects fade in
- Keyframe 3 to Keyframe 4: objects are fully visible
You can adjust the timing between keyframes to control the speed of the appearance. The transparency interpolation between frames is customizable using the Easing curve setting, helping you to fine-tune the pacing for different presentation needs.
A Quick Example
Below is an example from the documentation where structural models are faded into view using the Appear animation in combination with its inverse, the Disappear animation:
Tips
- Use the Appear animation when you want your audience to intuitively follow the flow of added molecular components.
- Combine with other animations like Disappear or Pulse for dynamic presentations.
- You can move keyframes freely to tailor the effect to your sequence’s rhythm.
To learn more, visit the Appear animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.