Molecular modeling often involves presenting complex structures and processes to convey molecular dynamics or chemical behaviors. For modelers striving to visually simplify such presentations, making certain atoms or connections fade out progressively can effectively capture attention and highlight key aspects of the molecular system. The ‘Conceal Atoms’ animation in the SAMSON integrative molecular design platform provides a solution to this need.
What is the ‘Conceal Atoms’ Animation?
The ‘Conceal Atoms’ animation gradually makes selected atoms and bonds disappear between frames. Unlike transparency adjustments, this effect manipulates the visibility of nodes, creating smooth transitions for specific atom groups. This precise control can be leveraged to emphasize particular regions of the structure while de-emphasizing others, allowing researchers to tailor their presentations.
How to Use ‘Conceal Atoms’
To apply this animation, follow these simple steps:
- Select the atoms and bonds you wish to progressively hide.
- Open the Animation panel in SAMSON’s Animator tool.
- Double-click on the ‘Conceal Atoms’ animation effect to activate it.
This animation works with four keyframes:
- Keyframe 1 to 2: All selected atoms and bonds are fully visible.
- Keyframe 2 to 3: Atoms and bonds are progressively concealed. The order of concealment depends on the selection order.
- Keyframe 3 to 4: All selected atoms and bonds are fully hidden.
You can adjust the positioning of keyframes in the timeline to control the speed and timing of this effect, ensuring it fits seamlessly into your animation sequence.
Going Deeper: Fine-Tuning Visibility Transitions
The ‘Conceal Atoms’ animation comes with additional customization. You can modify the Easing curve to adjust how parameters are interpolated between the frames. This enables you to control whether the conceal effect occurs linearly or with an acceleration/deceleration feel, providing greater flexibility for your animation style.
Applications of ‘Conceal Atoms’
This animation can be used in presentations where subtle de-emphasis of certain molecular components is required. Some examples include:
- Preparing educational content where the focus transitions from one functional group to another within a larger molecule.
- Demonstrating the relevance of specific bonds in an active site by concealing irrelevant parts of the structure.
- Creating cleaner visuals to highlight the core trajectory or conformational change in dynamic simulations.
For inspiration, check out examples of SAMSON presentations that use this animation, such as 1AF6 – Fly around and 1AF6 – Fly around – 2.
Get Started
The ‘Conceal Atoms’ animation simplifies your molecular visualization workflow, helping you achieve clean, impactful presentations that resonate with your audience. To learn more details about this feature, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at SAMSON Connect.