In molecular modeling and dynamics, visual clarity is essential. Whether you are preparing a scientific presentation, illustrating a complex conformational change in a biomolecule, or creating an educational video, the ability to orchestrate what appears—and when—can mean the difference between confusion and insight.
Many molecular modelers use transparency effects to hide parts of a structure, but this often leads to ambiguities in dense visual scenes. In SAMSON, the Hidden animation solves this problem by allowing you to completely hide selected nodes between two keyframes—without relying on transparency.
Why use the Hidden animation?
The Hidden animation is useful when you want to:
- Focus attention on a specific region, such as an active site, by removing surrounding structures temporarily.
- Compare two states of a system without visual clutter, by hiding one as the other appears.
- Create introductory scenes in presentations or teaching materials where parts of a molecule are gradually introduced.
How it works
The Hidden animation works by toggling the visibility of selected nodes (atoms, residues, molecules, etc.) between a start and an end keyframe in an animation timeline. This is fundamentally different from using transparency—which can still leave objects visible and distracting.
Adding a Hidden animation step-by-step
- Select the nodes you want to hide during an animation interval.
- In the Animation panel of the Animator, double-click on the “Hidden” effect. This places a starting keyframe at the current timeline frame.
- Move the end keyframe to set the duration of the hidden effect. SAMSON will interpolate the visibility off/on between the two.
- You can always reposition keyframes later for fine-tuning.
This effect is particularly helpful in combination with the Shown, Appear, or Flash animations, which offer complementary visibility controls.
Adjusting animation smoothness
You can fine-tune the way visibility changes over time by modifying the Easing curve. This lets you control whether the transition is sudden or gradual, which can add clarity and emotion to your visual narrative.
Remember
Use “Hidden” when you want true invisibility and sharp visual focus. Use transparency when you want to keep context while minimizing visual impact. The two approaches serve different but complementary purposes.
To learn more, visit the full documentation page 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.