Creating compelling molecular animations often involves more than just rotating models or showing structural transitions. For many molecular modelers, a key challenge is effectively controlling what is visible and when during an animation. Whether you’re assembling a step-by-step enzyme mechanism, showing conformational changes, or simply introducing parts of a molecular complex gradually, timing visibility is critical to clear communication.
SAMSON, the integrative platform for molecular design, offers a variety of animation effects to help with this. One useful yet sometimes underused effect is the ‘Shown’ animation. Unlike effects that manage transparency (which can leave elements barely visible and ambiguous), the Shown animation emphasizes clean visibility toggling — either a node appears or it doesn’t.
Why Use the Shown Animation?
Use cases for the Shown animation are numerous:
- Highlighting how different domains or subunits appear in an assembly process.
- Showing how ligands bind and unbind by making them appear/disappear at specific timepoints.
- Creating clear step-by-step molecular tutorials for students or presentations.
For example, if you’re visualizing the formation of a protein-ligand complex, you might start with just the protein, and then use the Shown animation to reveal the ligand as it binds — without the visual confusion of gradually increasing transparency.
How to Apply the Shown Animation Effect
To use the Shown animation in SAMSON:
- Select the nodes (e.g., atoms, molecules, or groups) you want to appear during your animation.
- Open the Animator and locate the Animation panel.
- Double-click on the ‘Shown’ animation effect.
- The current frame will be marked as the begin keyframe (where visibility begins).
- Adjust the keyframes as needed along the timeline to control exactly when the nodes will appear.
Behind the scenes, SAMSON uses node visibility (not transparency), so nodes are either fully shown or completely hidden — helping you maintain visual clarity.
Pro Tips for Smoother Presentations
Consider combining the Shown animation with logical naming and grouping of nodes, so you can control visibility in batches. For instance, group residues or ligands involved in a specific functional site and animate their appearance together.
You can also modify the easing curve to adjust how rapidly the visibility change feels. While the change is immediate (on/off), you can use easing to time related animations for a more polished storytelling experience.
What about the Other Visibility Tools?
It’s worth noting that the Shown animation is complementary to others available in SAMSON, such as:
Each has a slightly different use case — where Shown emphasizes visual transitions into the scene, Hidden governs disappearance. Chaining them carefully can result in well-crafted educational or scientific videos.
Example
Here’s what a combined Shown and Hidden animation effect can look like in action:
To get started with the Shown animation in your own molecular visualizations, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/shown/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.