When animating molecular systems, one recurring challenge is showcasing a specific motion—say, a ligand docking or a protein conformational change—while keeping a subset of atoms still. If some atoms move when they shouldn’t, it can confuse viewers and diminish the clarity of your presentation.
This is where the Hold atoms animation effect in SAMSON comes in handy. It allows you to fix the positions of selected atoms between two keyframes. Whether you’re comparing conformations or isolating motion to a specific domain of a molecule, this is a simple but powerful effect to clarify visual storytelling in molecular animations.
What does it do?
Hold atoms ensures that selected particles (e.g., atoms, residues, molecules) do not interpolate between keyframes. From the viewer’s perspective, these atoms remain stationary as the animation progresses, no matter what other structural changes occur around them.
This tool is especially useful when:
- You want to isolate the motion of a flexible loop while keeping the rest of the protein fixed.
- You are animating a ligand docking trajectory and wish to highlight only the motion of the ligand, while keeping the binding site static.
- You are aligning and comparing two conformations frame by frame and need to avoid unintended shifts in unrelated parts of the system.
How to use it
- Select the atoms you want to keep fixed. This can be any group—backbone atoms, binding site residues, or an entire chain. Selection tools in SAMSON are flexible, and you can combine different selections easily.
- Open the Animation panel in the Animator interface and double-click on the Hold atoms animation effect.
- SAMSON will insert keyframes and ensure your selected atoms are held still between them. You can then adjust the timeline by sliding the keyframes to define the exact time interval during which the atoms remain fixed.
In the example shown above, both Move atoms and Hold atoms effects are used. This enables isolating motion in one part of the system while keeping another part perfectly still.
Common questions
Can I move the keyframes later?
Yes, you can always reposition the keyframes in the timeline to change when the Hold effect starts and ends.
What if I want to modify the selection?
You can delete the animation effect and reapply it with a new selection. SAMSON’s interface makes it easy to iterate.
Want to see this in action?
Several example documents on SAMSON Connect demonstrate the use of Hold atoms to isolate important molecular motions:
These can give you a real sense of how Hold atoms can clean up movement and spotlight processes that matter.
To learn more, read the full documentation for Hold atoms.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.