One of the recurring challenges in molecular modeling is how to clearly present only the relevant parts of a complex system in an animation. Whether you’re working on a protein-ligand interaction, a nanostructure, or a drug design simulation, the clarity of your presentation can make a big difference—especially when you’re sharing your results in a paper, a class, or a lab meeting.
Enter the Shown animation in SAMSON. This feature lets you control when certain nodes (like atoms, molecules, or groups) are made visible during an animation, which can help reduce clutter and focus your audience on what really matters.
Unlike the Appear or Disappear effects, which can adjust the transparency of nodes, or the Flash and Pulse animations that add temporal emphasis, the Shown animation allows for a cleaner visual break: a node is either visible or it isn’t, at specific times. This is especially helpful when you want to avoid the visual noise introduced by partially transparent structures, which can sometimes make interpreting a molecular scene harder rather than easier.
How It Works
To apply the Shown animation:
- Select the nodes (for example, a ligand or side chain) that you want to become visible at some point in the animation.
- Open the Animator panel by clicking on the Animation panel.
- Double-click on the Shown effect in the panel. This sets the initial keyframe at the current frame.
- Move the animation slider to the frame where you want the visibility to change, and adjust keyframes accordingly.
If you want a cleaner visualization that draws attention to new components step-by-step—like introducing atoms only when they interact or showing solvent molecules after a solute is in place—this feature is a great solution.
Refining with Easing Curves
For more control over how your animation timing feels, you can tweak the Easing curve. While Shown is a binary effect (visible / not visible), adjusting the curve allows you to control the animation’s pacing in synchrony with other timed changes—like camera movements or structural deformations.
Example in Action
Here’s a simple visual showing the Shown effect in combination with the Hidden animation. By toggling visibility across keyframes, the animation adds clarity by restricting the viewer’s attention to the parts of the system that matter at each point in the sequence.
Whether you’re making educational videos, preparing a research talk, or trying to explain a concept to a colleague, reducing visual noise with targeted visibility can help your audience understand and retain the message more easily. For more information, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.