Molecular animations can quickly become overwhelming when dealing with complex structures, especially when multiple elements appear and disappear during a presentation or simulation. A frequent challenge for molecular modelers is ensuring clarity in dynamic visualizations: how do you focus attention in a controlled way, without manipulating transparency settings for each object?
The Shown animation in SAMSON is a tool designed exactly for this purpose. Instead of adjusting opacity, it simply makes selected nodes visible between two keyframes and keeps them hidden outside that time interval. This direct control over visibility is often more intuitive and reliable when scripting molecular storytelling inside presentations or simulations.
Simplified Focus on Structure
Whether you’re animating the interaction of a ligand with a protein or showing a step-by-step molecular path, toggling visibility is a simple way to bring attention to the right component at the right time. Unlike transparency, visibility is binary: shown or hidden. That clarity is powerful in presentations or educational material.
How It Works
To use the Shown animation in SAMSON:
- Select the nodes you want to make appear between keyframes.
- Double-click on the “Shown” animation effect in the Animation panel of the Animator. This inserts a “begin” keyframe at the current frame position.
- Then move to the desired time in your timeline and set the “end” keyframe by dragging or adjusting manually.
This animation does not fade objects in. They are either visible or not, making transitions clean and easy to interpret. This is especially useful for educational clips or stage-by-stage renderings of molecular processes where visual clutter can mislead or overwhelm viewers.
Tips to Refine Your Visual Output
Want more control? You can fine-tune the animation timing using SAMSON’s keyframe system. For example:
- Use the easing curve (found under Animation Properties) to introduce non-linear animation timing, like sudden reveals or sustained visibility.
- Combine the “Shown” animation with animations like Flash or Pulse to reinforce emphasis.
- Group related nodes (e.g., a residue chain, surface, and annotation) so that toggling visibility gives the full visual context.
Things to Keep in Mind
- This animation relies on node visibility, not transparency. So even if nodes are set to “transparent” style, they will still become invisible outside defined keyframes.
- Use scenes where fewer visual variables change concurrently. This keeps the visual language of the presentation clean to follow.
- The “Shown” and “Hidden” animations are complementary. Use them together to toggle parts of your molecular model systematically.
Whether you’re preparing a class, a talk, or a research video, using binary visibility through the “Shown” animation can help simplify your storytelling and improve how viewers grasp complex molecular behaviors.
To learn more, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/shown/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.