When working with molecular dynamics simulations, one of the common challenges is maintaining a clear view of specific parts of a system as they evolve over time. Whether you’re following a ligand binding to a receptor, monitoring a conformational change, or exploring diffusion processes, the camera often drifts away from your region of interest. 👀
If this sounds familiar, there’s good news: SAMSON offers a simple yet powerful feature called Follow atoms to help you keep your perspective.
What is ‘Follow atoms’?
The Follow atoms animation in SAMSON makes your virtual camera follow selected atoms along their path during a simulation or an animation. The camera’s position and target move continuously, preserving a constant viewing angle and distance relative to these atoms. This ensures you don’t lose sight of the exact region you’re interested in.
This can be particularly helpful when visualizing mechanisms such as:
- Ligand migration through a protein
- Active site reorganization
- Subunit movement in a large molecular assembly
How to use it effectively
1. Select the atoms you want to track. This selection defines the focus of your animation.
2. Orient the camera to your preferred view. This sets the initial point of view for the animation.
3. In the Animator’s Track view, select the start frame and double-click the Follow atoms animation in the Animation panel.
4. Define the end frame. Between these frames, the camera will follow the selected atoms and rotate automatically to maintain a consistent relative view.
You can also adjust the start and end frames later as needed, giving you flexibility in synchronizing the camera tracking with important events in your simulation.
Advanced settings
By default, the animation applies to the active camera. You can modify this by inspecting the animation and deselecting Apply to active camera if necessary. Moreover, options like Keep camera upwards can ensure more stable rotations of the viewpoint, depending on whether the grid is turned on.
Additionally, although the camera’s target is locked to the geometric center of your atoms, you can fine-tune the camera’s position using animation controllers, giving you nuanced control over what part of the system is emphasized in your view.
Why it matters
Sometimes the simplest additions can make a huge difference in interpreting complex molecular behaviors. Instead of manually following atoms frame by frame or constantly readjusting your view, the Follow atoms functionality makes it easy to produce smooth animations that focus on the molecular events that matter most in your research or presentations.
You can learn more about this feature, including additional tips and properties, by visiting the official SAMSON documentation: Follow atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.