Molecular modelers often spend hours perfecting animations that communicate complex mechanisms and structures with clarity. When showing a ligand docking process or a protein folding simulation, even a few fast-moving frames can disrupt the viewer’s ability to keep up.
This is where the Pause animation in the SAMSON platform becomes particularly useful. It lets you hold a key frame in your presentation for a specified duration—just enough for your audience to absorb what they’re seeing. No need to artificially stretch out transitions or pause your screen recording manually.
What’s the need for pausing?
Let’s take a typical scenario: you’ve just animated a conformational change in a protein structure, highlighting the transition from inactive to active state. It happens over five seconds, but your audience needs more time to study the activated complex, maybe identify the binding site or observe the electrostatic changes you’ve highlighted.
Instead of rerunning the entire animation or inserting still-frame slides, you can use a Pause animation effect in SAMSON to hold that moment right in your timeline.
How to insert a Pause animation
To add a pause, open the Animation panel available in the Animator workspace. Find the Pause effect and double-click it. This places a Pause keyframe at the current frame of your timeline.
You can drag this keyframe to another frame if needed. The only thing left to do is select the keyframe in the Document view and adjust its duration in the Inspector.
How long should you pause?
This depends on the complexity of your structure and the story you’re telling. Three to five seconds may be sufficient to highlight a ligand binding event or expose a buried cavity. For more detailed moments—such as highlighting multiple interactions—you might pause for ten seconds or more.
Tips for effective use
- Use pauses before transitions. This makes the movement in your animation more understandable.
- Combine with visual markers. Add labels and arrows to highlight active sites while the pause holds.
- Don’t overuse it. Pausing after every frame can make the animation feel disjointed.
Finally, remember that the Pause animation is just one tool in SAMSON’s presentation workflow. It’s designed to keep your audience with you—not behind you.
You can explore more on how to use the Pause animation and integrate it into your workflows at the official documentation: https://documentation.samson-connect.net/users/latest/animations/pause/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.