For molecular modelers and researchers looking to create clear, dynamic, and focused visualizations of molecular data, the ability to control how atoms and bonds appear and disappear is invaluable. SAMSON’s Conceal Atoms animation offers a straightforward way to progressively hide selected atoms and their bonds, providing a smooth transition that can enhance your presentations or analyses.
What Problem Does “Conceal Atoms” Solve?
Efficiently communicating structure-function relationships in molecules can be challenging, especially when working with complex models. Sometimes, you’d like to guide your audience or yourself by focusing on specific regions of a molecule and “hiding” others dynamically. Instead of suddenly making atoms invisible or playing with their transparency, the Conceal Atoms animation uses a smooth, progressive hiding mechanism, based on ordered visibility, to gradually declutter the molecular scene. This method ensures the visual focus flows naturally from one region of interest to another.
How to Use the Conceal Atoms Animation
The Conceal Atoms animation works via 4 keyframes, which give you precise control over the transitions:
- Keyframes 1 and 2: All selected atoms and the bonds between them are fully visible.
- Keyframes 2 to 3: The progressive concealment begins, hiding parts of the selection in a determined order (based on their position in the selection).
- Keyframes 3 and 4: All selected atoms and bonds are entirely hidden, ensuring a clean transition.
To add this animation:
- Select the atoms and bonds you want to hide progressively.
- Double-click on the Conceal Atoms animation in the Animation panel of the Animator.
- Adjust the keyframes as needed to fit your presentation or analysis timeline. For instance, you can drag the keyframes closer or further apart to control the speed of concealment.
Fine-Tuning with Easing Curves
To make your animations feel more natural, you can adjust how the concealment progresses over time using Easing curves. Whether you want a steady concealment or a more dramatic effect (such as starting slow and speeding up), this tweak ensures your presentation aligns with your storytelling needs.
An Example in Action
The following animation captures how Conceal Atoms, when combined with its counterpart Reveal Atoms, enhances molecular presentations. Observe how atoms smoothly transition between visible and hidden states:
Where Can You Apply This?
The Conceal Atoms animation isn’t limited to flashy presentations. It’s useful in:
- Highlighting critical areas in large molecular systems such as binding pockets or functional groups.
- Creating stepwise tutorials for students or colleagues to intuitively learn how parts of a molecule interact.
- Focusing attention during molecular dynamics or structural property explanations in academic or industrial research.
For examples of this animation in use, check out presentations like 1AF6 – Fly around or 1AF6 – Fly around – 2.
Learn More
To dig deeper, refer to the complete Conceal Atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it today at https://www.samson-connect.net.