When preparing molecular animations, it’s common to focus on what moves — conformational changes, ligand binding, structural transitions. But sometimes, equally important is making sure some parts stay still.
That’s where the “Hold atoms” animation in SAMSON becomes very helpful. If you’re building an animation and certain atoms start drifting when they shouldn’t — residues in a protein, non-interacting parts of a molecular complex, or even just a visual anchor point for your audience — this feature saves time and confusion.
When stability matters: the problem
Let’s say you’re creating a molecular animation where a ligand docks into a rigid active site. You want only the ligand to move. Even if your initial frames are static for the protein, there’s often slight movement or interpolated transitions that can look misleading if the atoms aren’t explicitly constrained.
This can misrepresent mechanisms — especially in presentations or teaching situations — if a viewer interprets motion where none exists. Beyond aesthetics, it’s about accuracy.
The fix: using “Hold atoms”
With SAMSON’s “Hold atoms” animation, you can straightforwardly freeze a selected group of atoms between two frames — ensuring no unwanted shifts.
Here’s how:
- Select the atoms or groups whose positions you want fixed. You can use SAMSON’s selection tools to easily grab residues, fragments or entire molecules.
- Open the Animation panel (via the Animator): this replaces the now-deprecated Animation menu.
- Double-click on the “Hold atoms” animation effect. This adds an effect between two keyframes.
- Adjust the keyframes if needed: for example, you might want the atoms held still during only part of the animation timeline.
That’s it — during the segment between the two frames, selected atoms won’t budge 📌.
Practical example: docking animations
In docking animations (e.g., ligand binding), applying “Move atoms” for mobile molecules and “Hold atoms” for the receptor is a clean strategy. The protein stays anchored visually and geometrically, while the ligand approaches and docks. This technique provides clarity and avoids the visual noise of unintended movement.
Here’s an example from the SAMSON documentation where the feature is used effectively:
Tips
- You can always move keyframes later to fine-tune the start and end of the static segment.
- Used in combination with other effects like “Move atoms” or “Fade atoms,” this enables precise control over both motion and focus.
Explore working animations
Need inspiration? These documents on SAMSON Connect use hold/move combos to great effect:
To learn more about the “Hold atoms” animation, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.