When presenting molecular mechanisms or simulating transitions in a complex system, clarity and pacing can often make or break the message you aim to deliver. Molecular modelers frequently struggle to communicate intricate step-by-step behaviors within molecules—especially when animations move too quickly or overlook moments that need emphasis. Fortunately, the Animator in SAMSON provides a simple but efficient solution: the Pause animation effect.
This feature might seem modest at first glance, but in molecular storytelling, it can dramatically improve your audience’s understanding. Let’s explore what it is and how it can help you better communicate your work.
Why use pause in molecular animations?
Many scientific animations are rich in data but poor in pacing. Without intentional pauses, essential steps in ligand binding, conformational changes, or electron transfers might blur into one another. Viewers—particularly those unfamiliar with the system—can miss critical mechanistic details. By strategically placing pauses, you allow your audience the time they need to mentally process what is being shown.
How the Pause animation works in SAMSON
The Pause animation effect in SAMSON temporarily freezes an animation at a selected frame for a specified number of seconds. This doesn’t permanently alter your model or scene—it simply tells the Animator to hold at that moment, enabling clearer storytelling.
To add a Pause to your animation:
- Open the Animation panel of the Animator.
- Locate the Pause animation effect and double-click it. This will insert a keyframe at the current animation frame.
- The keyframe can then be moved to any desired frame where a pause is needed.
Note
You can always reposition keyframes later on if your pause needs adjustment.
Customizing pause duration
Once the Pause effect is inserted, its duration is fully configurable:
- Select the Pause animation node in the Document view.
- Use the Inspector to adjust how many seconds the pause should last.
Here is how it looks in the Inspector panel:
Practical applications
Here are some ways we’ve seen users apply pauses effectively:
- To highlight a molecular docking pose before transition to a new conformation.
- To gently pace the animation of reaction steps or catalytic cycles.
- To allow non-specialist viewers to observe molecular changes frame by frame.
The result is smoother communication and a more viewer-friendly animation experience. The Pause effect gives you control over the tempo of knowledge transfer—something often overlooked in modeling.
You can learn more about the Pause animation effect in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.