If you’ve ever tried to create a molecular animation and found yourself repeatedly frustrated by parts of the molecule moving when you wish they wouldn’t, you’re not alone. Whether you’re demonstrating a docking mechanism, visualizing a conformational change, or assembling molecular complexes, there are often scenarios where some atoms should remain fixed while others move.
Visual clarity in animations can be crucial for communicating molecular mechanisms effectively. Unintended motion or drifting in parts of your structure can mislead your audience or obscure the key points you want to emphasize. Fortunately, SAMSON offers an intuitive solution with the Hold atoms animation effect.
Fixing atom positions with the Hold atoms animation
The Hold atoms animation in SAMSON allows you to lock the positions of specific atoms between two frames of an animation. It’s particularly helpful when you want part of the molecule to act as a stationary reference or prevent it from moving while other components undergo transformations.
How to apply this effect
- Select the atoms you want to keep fixed. You can do this manually or by using any selection tool in SAMSON.
- Open the Animator interface and locate the Animation panel.
- Double-click on the Hold atoms animation.
- Adjust the keyframes as necessary along the timeline. The selected atoms will remain static between those frames.
This functionality is especially useful in structuring complex animations. For example, you might show one region of a protein holding steady while another domain binds a ligand. Holding atoms in place reduces visual noise and enhances clarity.
Real-world examples
Want to see it in action? Here are some example animations built using this feature:
Each of these examples takes advantage of the Hold atoms feature to add stability and coherence to animations of molecular assembly or docking processes.
Tip: Use it with other animation effects
The Hold atoms animation pairs well with other animation types like Move atoms. A typical use case involves moving one fragment of a molecule toward a receptor site while holding the receptor steady. Combined, these tools offer greater control over motion and focus in your animations.
Note: If you’ve used older versions of SAMSON, you may remember an “Animation” menu. This has been replaced—animations are now all accessed through the Animation panel in the Animator interface, which you can invoke via Ctrl + 7 or Cmd + 7 depending on your operating system.
By leveraging Hold atoms, you can make animations not only more accurate but also more intelligible for colleagues, students, or viewers of a scientific presentation.
Learn more about using Hold atoms in SAMSON’s documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.