Creating molecular animations is a cornerstone of molecular modeling and visualization. Often, molecular modelers need a way to showcase atoms and bonds gradually within a structure, either to demonstrate assembly processes, highlight key features, or make presentations smoother. The Reveal atoms animation in SAMSON is designed to do just that. This blog post explores how to use this feature to make atoms and bonds progressively appear between frames, offering an essential tool for crafting dynamic and engaging visualizations.
What Does the ‘Reveal Atoms’ Animation Do?
The Reveal atoms animation makes atoms (and the bonds between them) progressively appear over time. Unlike techniques based on transparency, this animation relies on the visibility of nodes, effectively creating a “fade-in” effect by showing specific atoms and bonds step-by-step.
Whether you’re designing molecular models for educational purposes, presentations, or research analysis, this feature provides a clean and efficient way to bring your molecular structures to life, all while maintaining focus on the key elements of your model.
How to Add and Use the ‘Reveal Atoms’ Animation
Here’s a step-by-step guide to using this feature effectively:
- Choose your elements: Select the atoms and bonds that you want to progressively reveal. This can be done via SAMSON’s selection tools.
- Add the animation: Double-click on the Reveal atoms animation effect in the Animation panel of SAMSON’s Animator.
- Understand the keyframes: This animation includes four keyframes:
- Between keyframes 1 and 2, all the selected atoms and bonds will be hidden.
- Between keyframes 2 and 3, the selected atoms and bonds will progressively appear based on their order in the selection.
- Between keyframes 3 and 4, all selected atoms and bonds will be fully visible.
- Customize your timeline: Adjust the positions of the keyframes to control the timing and duration of the animation. Moving the keyframes allows you to adapt the animation to the exact needs of your project.
Advanced Tip: Modifying the Easing Curve
To take your animations further, you can adjust how the parameters are interpolated between frames by modifying the Easing curve. This allows you to control the acceleration and deceleration of the animation, creating smoother or more dramatic reveal effects as needed for your presentation.
Examples and Inspiration
The Reveal atoms feature is particularly useful when demonstrating how a molecular structure builds up or becomes visible during a process. For instance, educators might use it to explain chemical bonds step-by-step, while researchers can utilize it to illustrate specific regions of interest in a complex biological pathway.
Below is an example GIF that demonstrates how the Conceal and Reveal animations can work together for dynamic effects:
Conclusion
The Reveal atoms animation is a simple yet powerful tool that gives molecular modelers precise control over their visualizations. By progressively showing atoms and bonds, it ensures that molecular animations are not only engaging but also informative and clear.
To learn more about this feature, visit the official documentation page: Reveal Atoms Documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.