When preparing molecular animations, every detail can affect clarity and impact. If you’ve ever wanted to make a model gradually appear—rather than just pop into view—the Appear animation in SAMSON can help you do just that. This subtle visual effect can improve storytelling in scientific movies or presentations where molecular transparency dynamics matter. Here’s how.
Why You Might Want to Use the Appear Animation
One common pain for molecular modelers is the sudden, jarring appearance of molecules in animations or presentations. When representing complex systems, especially those involving step-by-step construction or progressive unveiling (e.g., assembly of a protein complex, docking sequence, or visualizing drug-target interactions), you want control over when and how your audience sees parts of your model.
The Appear animation solves this by letting you make nodes progressively transition from transparent to fully visible. The result is smoother and more engaging animations that are easier to follow, especially in educational or exploratory contexts.
What Can You Animate?
The Appear animation is designed to work on any node that has a transparency attribute. This includes:
- Structural models
- Visual models
- Meshes
- Labels
Note: Individual atoms and bonds don’t have a direct transparency attribute. To animate their opacity change, you need to apply the animation to their containing structural model.
How It Works
Once you’ve selected the desired nodes in your scene, adding the Appear animation only takes a couple of clicks within the Animation panel of the Animator. The animation automatically creates 4 keyframes:
- Keyframe 1 to 2: nodes remain fully transparent
- Keyframe 2 to 3: transparency progressively decreases
- Keyframe 3 to 4: nodes become fully opaque
You are free to reposition the keyframes in time to match the pacing of your scene.
Customizing the Transition
The appearance isn’t limited to a linear transition. If you want a smoother or more dramatic fade-in, you can modify how parameters change between keyframes through the Easing curve. Curves let you control acceleration and deceleration of the effect, giving you greater expressive control, whether you’re aiming for realism or highlighting particular moments in the animation.
Practical Tip
In longer movies or presentations, you might want several components to appear at different times. You can apply the Appear animation multiple times to different nodes or create staggered appearances by editing the timing of each animation’s keyframes. This makes animations more dynamic and less overwhelming to the viewer.
Note: The animation shown in the image above used the Animation menu, which has since been replaced with the Animation panel in the Animator. You can open the Animator via Ctrl + 7 (or Cmd + 7 on macOS).
When Not to Use It
If the node you’re trying to animate does not support transparency (e.g., basic atom-level nodes), the Appear animation behaves similarly to the Show animation—nodes simply become visible without gradual transparency. For full control, always target nodes with transparency support.
To learn more or explore related animations like Disappear, Pulse, or Flash, check out the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.