Visualizing molecular structures over time is vital for understanding dynamic processes such as protein folding, ligand binding, or complex formation. Yet molecular modelers often face a challenge: how to create clear and engaging animations that communicate these transitions without overwhelming the viewer with sudden visual changes.
This is where the Appear animation effect in SAMSON, the integrative platform for molecular design, can help. This animation makes selected molecular components (or nodes) gradually emerge through transparency, guiding the viewer’s attention and improving visual clarity.
When and Why to Use the Appear Animation
Sometimes, you want part of your structure to unfold or become visible step-by-step – for example, to introduce a newly formed complex or a portion of a protein that’s transitioning into view. If you apply the Appear animation to nodes that support transparency (like structural models, visual models, meshes, or labels), those parts will emerge progressively over time.
This is especially useful when creating presentations, teaching materials, or explanatory visualizations for publications or collaborative discussions. Sudden jumps often force viewers to re-adjust focus; gradual transparency changes can ease comprehension significantly.
How It Works
Here’s how the Appear animation unfolds:
- Keyframes 1 & 2: objects are fully transparent.
- Keyframes 2 & 3: transparency is progressively decreased – the object starts appearing.
- Keyframes 3 & 4: object is fully visible (opaque).
You can insert the Appear animation by double-clicking on the Appear effect within the Animation panel of the Animator. Make sure you’ve selected the appropriate nodes first.
Because individual atoms or bonds don’t have transparency attributes, you should apply this animation at the structural model level. If you’re trying to make specific atoms gradually appear, include them as part of a larger transparent model.
Fine-Tuning the Animation
One of the strengths of this feature is flexibility. You can:
- Move the keyframes to synchronize with other presentation elements.
- Adjust the Easing curve to control how quickly the transparency changes over time. For instance, a slow start and fast finish might create a subtle “materializing” effect.
For example, in the animation below, two molecular structures gradually appear over time. This helps direct attention without abrupt changes:
Keeping Up with SAMSON
Note that the older Animation menu shown in some tutorials has been replaced by the Animation panel and Animator controls. Use these tools to access all your animation features in the current version of SAMSON.
To learn more and go deeper into animation features, explore the complete 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.