One of the most common challenges in molecular modeling is effectively directing attention in a dynamic scene. Whether you’re showcasing ligand binding, conformational changes, or molecular assemblies, clarity is key. Many modelers default to using transparency to hide or reveal elements, but this can create visual noise, especially when transparency levels are subtle or combined with complex backgrounds.
The Shown animation in SAMSON offers a simple alternative: directly toggling the visibility of molecular nodes without using transparency. This makes transitions more immediate and less visually ambiguous, helping your audience focus on what’s important.
Why visibility matters
In molecular animations, timing when an object should appear or disappear can guide viewers through a molecular event step-by-step. But if you rely on semi-transparency for staging, parts of your model remain partially visible, which can distract or confuse viewers. The Shown animation explicitly switches nodes from hidden to shown states, removing ambiguity.
How the Shown animation works
The Shown effect toggles a node’s visibility between keyframes, without changing its transparency. Here’s how to use it:
- Select the nodes you want to show during the animation.
- Open the Animation panel in the Animator.
- Double-click on the Shown animation effect. This creates a keyframe at the current frame, telling SAMSON when the nodes should become visible.
- You can then move the keyframes to control the timing. For example, if you want the node to appear halfway through your animation, just place the keyframe accordingly.
An important note: this is a visibility switch, not an interpolation. The selected nodes will go from completely hidden to fully visible—no in-between states.
In the example above, you can see how the animation synchronizes the appearance of molecular parts at specific moments. This is especially useful in educational and presentation contexts, where each step of a process needs to be clearly seen and understood.
Customizing the transition timeline
While the appearance itself is binary, you still have flexibility in orchestrating your animation using SAMSON’s timeline. If you’re combining multiple animation types—like Appear or Flash—you can coordinate the Shown effect with others to emphasize changes or flow.
You can also modify how parameters interpolate between keyframes using SAMSON’s Easing curves, although this mainly applies to effects that use continuous values (e.g., rotation, scaling).
Things to keep in mind
- Shown toggles visibility only; it doesn’t affect transparency or any material properties.
- Double-check that you’re using the Animation panel in the Animator, not the older Animation menu (which is no longer present).
- Remember to set the begin and end keyframes appropriately—this determines when visibility changes during playback.
Using visibility-based animations like Shown can make your molecular movies cleaner and more focused. It’s a small but impactful tool that helps guide your audience through complex transitions without unnecessary visual clutter.
Learn more about the Shown animation in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.