When preparing molecular animations, one common challenge is visual clutter. Especially in complex systems, it’s easy to lose focus on the region of interest when atoms all around are shifting, vibrating, or drifting across frames. This can be distracting and sometimes misleading in presentations, tutorials, or publications.
A straightforward solution to this is to temporarily “freeze” parts of your system—keeping certain atoms fixed between frames so the viewer can better focus on the changes that do matter. In SAMSON, this is made possible using the Hold atoms animation effect. This tutorial explains how this function works, who can benefit from it, and how to apply it efficiently in your next molecular animation.
Why freeze atoms?
Molecular modelers often need to highlight a specific event: a ligand binding to a protein, a structural rearrangement, or the movement of a domain. If every atom is moving, it becomes harder to spot these key events. By holding certain atoms in place, the animation becomes easier to follow and often more visually compelling.
Examples include:
- Docking animations where the protein remains fixed and only the ligand moves.
- Assembly of macromolecular complexes, where some subunits stay stationary while others attach or rotate.
- Focus on a local conformational change without distraction from solvent or distant atoms.
Using the “Hold atoms” effect in SAMSON
Hold atoms allows you to fix the position of selected atoms between two keyframes in the animation timeline. Here’s how to use it:
- Select the atoms or group of particles that you want to hold steady during the animation.
- Open the Animation panel in the Animator.
- Double-click on the Hold atoms animation effect to activate it.
- This will lock the selected atoms’ positions between the two keyframes. You can then move the keyframes as needed to define when the atoms should stop and resume motion.
Tips for effective usage
- Combine Hold atoms with Move atoms animations to create clean sequential effects—keeping one group immobilized while another moves.
- Use keyframes creatively: you can change the timing to align with specific molecular events (e.g., before or after docking).
- You can always adjust the keyframes later if you change the duration or flow of the animation.
See it in action
SAMSON Connect offers online documents that already use this feature effectively. For example:
These examples demonstrate how freezing certain parts of a complex system can dramatically enhance clarity and viewer comprehension.
To learn more, visit the full documentation page on Hold atoms.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.