When presenting molecular simulations or designing compelling molecular animations, controlling the visibility of specific molecular components becomes essential. Whether you’re showcasing the stepwise assembly of a macromolecular complex or highlighting a structural subunit midway through a simulation, managing how and when molecules become visible can clarify your messaging and sharpen your story. This is where SAMSON’s Shown animation plays a key role.
One common frustration among molecular modelers is the abruptness or opacity of transitions. For instance, setting the transparency of objects often results in less-than-satisfactory visual clarity, especially when rendering videos for presentations or publication. What many don’t realize is that visibility and transparency are not the same thing — and for emphasis and clarity in academic or research settings, simple visibility changes can be far more effective.
What is the Shown Animation?
The Shown animation in SAMSON makes selected nodes appear (i.e., become visible) between keyframes in your animation. This is fundamentally different from altering transparency: the node is either visible or not, and fades/transparency effects are not involved.
This is ideal when you want elements of your system—such as specific residues, ligands, or structural motifs—to suddenly appear at predefined steps in your animation timeline. The result is a crisp, intentional visualization that audiences can easily follow.
How to Use the Shown Animation in SAMSON
- Select the node(s) (e.g., atoms, molecules, molecular groups) that you want to be shown.
- Open the Animation panel in the Animator.
- Double-click on the Shown animation effect.
- SAMSON will automatically insert a begin keyframe at the current animation frame. You can move this keyframe to the specific time you want the node to appear.
Tip: You can always adjust the keyframes later — so don’t worry about getting it perfect in the first go. Fine-tuning is part of the process!
It’s worth noting that the tutorial video linked from the documentation might show an outdated interface with an Animation menu. In the current version of SAMSON, all animation tools and effects are accessible through the Animator panel directly. For quick access, you can also press Ctrl+7 (on Windows/Linux) or Cmd+7 (on macOS) to open the Animator.
Smooth Transitions with Easing Curves
Another powerful feature you might want to explore is how the parameters of animations like Shown can be interpolated. In SAMSON, this is achieved by customizing the Easing curve. While the visibility in Shown is binary, using easing curves in combination with other effects (like camera motion or object translation) allows for a polished, dynamic animation style.
When to Use “Shown” Instead of Alternatives
The Shown effect is particularly useful when:
- You want an object to become visible without changing its transparency.
- You are scripting an assembly process or molecular growth simulation.
- You want to emphasize contrast — for example, a hidden receptor domain that becomes visible upon ligand binding.
Consider pairing Shown with its counterpart, Hidden, for toggling visibility states.
Effective animations tell a story. The Shown effect helps modelers and educators pace that story thoughtfully.
To learn more about the Shown animation and visibility controls in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/shown/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.