When working in molecular modeling, clear visual communication is just as important as robust computational results. For example, when you’re preparing a presentation or video to explain the structure or function of a molecule, it’s important to guide the viewer’s attention deliberately. One subtle but useful technique is to make molecular elements progressively appear in the scene, rather than having them pop in all at once.
If you’re using SAMSON, you can achieve this using the Appear animation. This effect helps models gracefully fade in using transparency keyframes and is ideal for emphasizing components one step at a time during a presentation. Whether you’re showing protein domains, highlighting mesh boundaries, or introducing visual labels one after another, the Appear animation gives you control over how and when elements come into focus.
When to Use the Appear Animation
The Appear animation is specifically designed to work with nodes that support transparency. These include:
- Structural models
- Visual models
- Meshes
- Labels
Note that individual atoms and bonds do not support transparency directly. Instead, their parent structural models do. If you want atoms and bonds to appear gradually, you should apply the animation to the structural model containing them.
How It Works
Unlike a simple visibility toggle, the Appear animation uses four keyframes to control transparency over time:
- Keyframes 1-2: The object remains fully transparent.
- Keyframes 2-3: Transparency gradually decreases (the model fades in).
- Keyframes 3-4: The object is fully opaque.
This approach ensures a smooth fade-in effect that feels natural and non-disruptive, helping keep your audience focused.
Adding the Animation in SAMSON
- Select the nodes you want to appear.
- In the Animation panel (found under the Animator), double-click the Appear effect.
- Adjust the timing of keyframes as needed by dragging them on the timeline.
Tips to Customize the Visual Feel
For advanced users, you can modify how the transparency changes between frames using an Easing curve. This lets you control whether the transition feels smooth, abrupt, or follows a custom curve. For example, using an ease-in-out curve will make the appearance start slowly, speed up at the midpoint, and slow down again before completing.
Recommendation: Combine with Labels and Meshes
Many researchers use the Appear animation not just on molecular structures but also to fade in labels and supplementary geometry. This makes it ideal for step-by-step interactive animations that walk through molecular functions, binding mechanisms, or system setups.
To learn more about the Appear animation and see the complete documentation, visit the original page at 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.