When working with molecular simulations or visualizations, there are times when you want part of the system to remain fixed—structurally intact—while the rest evolves or moves. For instance, you may want to animate the binding of a ligand while keeping the protein backbone stable. This is where the Hold atoms animation in SAMSON becomes especially useful.
Molecular modelers often need more than just a movie; they need precision and control over what moves and what doesn’t. Holding atoms static between certain frames of your animation helps you:
- Highlight specific interactions without distractions.
- Ensure structural components maintain relative placement during transitions.
- Create more controlled and understandable visuals for presentations or publications.
How does it work?
The Hold atoms tool in SAMSON lets you select a group of particles and lock their positions between two frames of an animation. Between these two keyframes, the selected atoms remain static regardless of other motion around them. This is particularly helpful when combining with effects like Move atoms, where you want to depict changes around a core or scaffold structure.
Adding a Hold atoms animation
Step-by-step:
- First, use SAMSON’s Selection tool to choose atoms or molecules whose positions you want to lock.
- Then, open the Animator (use Ctrl+7 or Cmd+7 depending on your OS).
- In the Animator’s Animation panel, double-click on Hold atoms.
- This will insert an animation that locks your selected atoms between the current two keyframes. You can move these keyframes as needed to adjust the timeframe where atoms are held in place.
Tip: The Hold atoms animation is most powerful when used in combination. For example, you can lock a molecular scaffold using Hold atoms while applying motion effects to ligands or atoms of interest. This approach creates clean and compelling presentation animations that clearly demonstrate molecular mechanisms.
Practical applications
If you’re building animations that illustrate conformational changes, ligand docking, or assembling biomolecular structures, holding part of the system static can make your visual much easier to interpret. Here are a few examples from SAMSON Connect presentations that used this method:
Whether you’re preparing content for teaching, research, or communication, mastering this simple technique can make your work more effective and easier to follow.
For more details, visit the official Hold atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.