When preparing molecular animations, one common challenge is to selectively emphasize particular components of a system—be it a ligand, a protein domain, or a cofactor—at specific points in time. Traditional methods might rely on changing opacity or tweaking rendering styles. But in SAMSON, there’s a cleaner and more efficient approach: using the Shown animation effect.
The Shown animation allows you to explicitly manage the visibility of molecular nodes between keyframes. This makes it easier to build clear narratives through your animations, particularly when highlighting interactions, mechanisms, or temporal events in simulations.
Why not just change transparency?
It might be tempting to use transparency to illustrate presence or absence visually. However, this approach has two drawbacks:
- It keeps the objects technically visible, which may interfere with interaction clarity in complex systems.
- Managing gradations of transparency over time can quickly become cumbersome and imprecise.
The Shown animation bypasses these issues by toggling visibility directly, giving you more control without visual ambiguity.
How to use the Shown animation
Here’s how to add a Shown animation to emphasize selected nodes at a specific point in your animation sequence:
- Select the nodes you want to make visible at a particular frame.
- Open the Animation panel in the Animator.
- Double-click the Shown animation effect. A keyframe is created at the current frame, setting visibility to visible for the selected nodes.
- You can then move the keyframes along the timeline to control when these nodes become visible during playback.
Note: You can reposition keyframes anytime, allowing flexibility in fine-tuning the moment your components appear.
Where this comes in handy
Whether you’re building a teaching video, preparing a presentation, or simply documenting how a ligand enters a binding pocket, being able to show molecular components at just the right time adds significant clarity and polish to your animations.
In the example below, you can see how the Shown and Hidden animations are used together to manage visibility for different parts of a system.
Tuning the transition
The transition between keyframes can also be adjusted using different easing curves. This allows smooth or stepwise changes in visibility depending on the narrative style you’re aiming for.
Note that the video example included in the documentation uses an older version of the Animation menu. In the current version of SAMSON, you should use the Animator’s Animation panel to access all animation types and presentation features.
Overall, mastering node visibility can drastically improve the visual clarity of your molecular animations by letting you highlight key elements exactly when they’re needed on screen.
To learn more about the Shown animation, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.