Visualizing molecular motion can be challenging when the part of interest moves rapidly or unpredictably. Adjusting the camera manually to keep focus can be tedious, especially during long animations like molecular dynamics simulations or docking sequences. That’s where the Look at atoms animation in SAMSON becomes especially helpful.
This animation automatically adjusts the camera’s target point to follow the center of selected atoms, without changing the camera’s position. This means the world appears to shift around the molecule of interest, while your viewpoint remains fixed—simplifying analysis and storytelling alike.
Why It Matters
Imagine you’re studying a ligand entering a binding pocket during a molecular dynamics trajectory. If you want to keep watching this process closely, you could:
- Manually reposition the camera every few frames (painful and imprecise)
- Use complex trajectory-following scripts (time-consuming)
- Or, use the Look at atoms animation to have SAMSON track the action for you (easy and consistent 🎯)
How to Use It
- Select the atoms you want to track—these can be part of a residue, a molecule, or even the entire complex.
- Set the camera view where you’d like to observe from.
- In the Animator, go to the desired start frame in the Track View.
- Double-click on the Look at atoms animation in the Animation panel.
- Specify the end frame to determine how long the animation should follow the atoms.
The result: The camera maintains its fixed position, while the view direction is continuously updated to look at the moving center of your selected atoms.
Customization Options
You can fine-tune this behavior using the animation’s properties. Click on the animation in the Track View and then:
- Apply to active camera: Use this if you’re working with multiple cameras.
- Keep camera upwards: Ensures the camera stays aligned with the grid orientation, which can affect how the scene appears depending on your use of the grid.
You can also manually adjust the camera’s position using animation controllers, while the focus stays locked onto the selected atoms’ center.
When to Use It
This animation works especially well for:
- Ligand tracking during docking simulations
- Visualizing the motion of small domains or subunits in molecular complexes
- Creating educational videos where the subject of interest remains in view while surrounding context shifts naturally
Learn more in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.