Molecular animations are powerful tools for communicating complex structural and dynamic concepts. Whether you’re presenting a conformational change, a docking event, or an interactive walkthrough of biomolecular interactions, every frame matters. But there’s a challenge many molecular modelers face: giving the viewer enough time to absorb what’s on screen without disrupting the flow of the animation. This is where the Pause animation in SAMSON can make a difference.
Why Introduce Pauses?
Visualizations often move quickly from one molecular event to the next. However, key moments — such as the formation of a hydrogen bond, a conformational switch, or a ligand entering an active site — can benefit from a short pause. These pauses allow viewers, especially those unfamiliar with the molecular system, to comprehend what’s happening.
Instead of manually editing your timeline to duplicate frames or render slower transitions, SAMSON offers a more elegant solution: the Pause animation effect.
What the Pause Animation Does
In short, the Pause animation freezes the current frame for a specified number of seconds. It’s placed like any other keyframe in the timeline and adds no interruption to the current action; it simply gives the viewer time to focus.
For instance, you might pause after a molecular alignment or prior to the start of a reaction mechanism to ensure the audience is following along.
How to Add a Pause
Adding a pause animation in SAMSON is straightforward:
- Open the Animation panel in the Animator.
- Double-click on the Pause effect. This inserts it at the current frame in your timeline.
- You can always move the keyframe to the precise moment you want to introduce the pause.
This action adds a visual marker in your timeline corresponding to the pause effect.
Setting the Pause Duration
Once you’ve inserted the pause, you can control how long it lasts:
- Go to the Document view and select the pause animation node.
- Open the Inspector to reveal its properties.
- Specify the pause duration in seconds. It’s that easy.
The interface is designed to be intuitive, minimizing the time needed to add these kinds of refinements.
Suggested Uses
Here are a few effective moments to insert a pause in a molecular animation:
- After zooming in on a binding site.
- When switching from one conformation to another.
- Before a major transformation or simulation step.
These pauses can improve clarity without altering your story’s flow, making them highly useful for tutorials, research presentations, and even teaching materials.
Conclusion
Small adjustments like well-placed pauses can dramatically enhance a viewer’s understanding of complex molecular animations. If you haven’t tried using the Pause animation in your SAMSON presentations yet, now is a good time to give your audience a moment to breathe and reflect — one frame at a time.
You can learn more on the original documentation page about the Pause animation here: https://documentation.samson-connect.net/users/latest/animations/pause/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.