Communicating molecular insights visually is one of the most powerful ways to convey structure-function relationships, simulation results, or molecular mechanisms. Yet, some subtle visualization choices can make or break the clarity of your output.
Have you ever tried to make part of your molecular model disappear in an animation by reducing its transparency, only to find that other elements are still visible through it, making the visualization confusing? There’s a simple, overlooked solution in SAMSON: the Hidden animation effect.
Why You Should Consider Hiding, Not Fading
Modelers often rely on transparency to show or conceal molecular components. While transparency has its place, it’s not ideal when you want parts of a model to be completely invisible at specific moments during your animation.
The Hidden animation is SAMSON’s answer to this. Rather than gradually changing an object’s transparency, it controls its visibility directly, meaning it’s either shown or completely hidden between two keyframes.
This is particularly useful in cases where you:
- want to simplify a scene to guide focus to a specific region,
- transition between different functional states, or
- prepare step-by-step assembly or disassembly animations.
How It Works
Using the Hidden animation is straightforward:
- Select the nodes (molecular objects) you want to hide.
- Open the Animation panel in the Animator.
- Double-click on Hidden. This will add a keyframe at the current frame.
- Scrub the timeline and adjust the keyframes to define the visibility change interval.
Need to fine-tune the transition? You can always move or edit keyframes later. While the Hidden effect does not produce a gradual fade, it results in a visually clean switch that can be combined with other effects for maximum impact.
Example: Coordinating Show and Hide Effects
In many cases, hiding works best when combined with Shown effects to create seamless model transitions. Here is an example illustrating how Shown and Hidden work together:
Note that the video uses an older version of the interface where an “Animation” menu was available. As of now, all animations are accessible directly from the Animator via the Animation panel (or with the shortcut Ctrl+7 or Cmd+7).
Want Smoother Transitions?
While Hidden toggles visibility instantly, you can still control how the parameters interpolate by modifying the Easing curve. This is especially useful when you’re layering effects or synchronizing multiple animation sequences.
Carefully choosing when to use visibility toggling vs. continuous transparency gives you more control over the story your molecular animation tells.
To learn more about the Hidden animation effect, check the full documentation here: https://documentation.samson-connect.net/users/latest/animations/hidden/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.