In molecular modeling, clear communication is essential—especially when presenting molecular interactions in animations. A common challenge arises when trying to control when parts of a model, such as ligands or cofactors, appear during an animation. This is vital for storytelling in education, research visualization, or scientific publishing.
SAMSON’s Show animation solves this in a simple yet powerful way. It allows you to make nodes (which can be atoms, molecules, or any molecular structure) appear precisely at a designated keyframe and remain visible afterward. This means you can introduce parts of a complex model exactly when needed—such as showing a ligand only when a binding pocket is ready—without manually juggling visibility parameters.
How it Works
The Show animation combines the flexibility of two other effects—Hidden and Shown—but packages them into a single, intuitive animation.
- From keyframe 1 to keyframe 2: the selected nodes remain hidden.
- At keyframe 2: the nodes appear instantly.
- From keyframe 2 to keyframe 3: the nodes stay visible.
This setup is handy when you want to focus your viewer’s attention on certain events in a complex dynamic system, such as ligand binding or conformational changes, without gradually changing transparency or using more complex fade effects.
Practical Example
Let’s say you’re creating an animation to explain how a small molecule inhibitor binds to a kinase. Early in the animation, you explore structural rearrangements of the kinase. Only when the pocket is open do you want to display the ligand. Follow these steps:
- Select the ligand node (or any nodes you want to appear).
- Open the Animation panel in the Animator.
- Double-click on the Show animation effect.
- Three keyframes are created; by default, the ligand appears at keyframe 2 and stays visible after.
- Slide these keyframes as needed to match your animation timing.
The simplicity of this setup avoids the need to manually use multiple visibility or transparency effects. This not only saves time, but reduces errors when assembling your final animation.
Adjusting the Animation Flow
Sometimes, a sudden appearance might be too abrupt. In such cases, you can customize how parameters evolve between frames using the Easing curve. Though the Show animation toggles visibility based on keyframes (not gradual transparency), understanding and combining easing curves with subsequent animations can refine your visual storytelling.
Accessibility
If you’ve seen older tutorials using the Animation menu, note that the current version of SAMSON uses the Animation panel instead. You can access it via Ctrl+7 (or Cmd+7 on macOS).
This quick but versatile animation is ideal for educators, structure viewers, or anyone showcasing dynamic models. Making parts of your system appear at key moments helps focus attention and better convey mechanisms or events.
Want to try it out or learn more? See the full documentation page on the Show animation here: https://documentation.samson-connect.net/users/latest/animations/show/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.