When studying the dynamics of complex molecular systems, one of the challenges modelers often face is visual clarity: how to keep visual focus on specific atoms or molecular fragments as they move throughout a simulation. If you’ve ever found yourself manually adjusting the camera to follow a ligand, ion, or protein loop of interest across a trajectory, you know it can be both tedious and imprecise.
Fortunately, SAMSON provides an elegant solution: the Follow Atoms animation. This feature allows the camera to dynamically track a group of atoms during an animation, automatically updating both the target and position of the camera to keep the selected atoms centered while maintaining a consistent viewpoint.
Why It Matters
Instead of static viewpoints that lose track of molecular motion, using Follow Atoms makes visualizations more insightful. For example, if you are analyzing the translocation of an ion through a membrane, or the path of a small molecule inside a protein tunnel, having the camera follow the atom(s) of interest helps maintain contextual continuity. It also makes sharing animations easier to understand for colleagues or students who may not be familiar with manual 3D navigation in molecular viewers.
How It Works
To use the Follow Atoms animation in SAMSON:
- First, select the atom(s) you want the camera to follow.
- Then, orient the camera the way you want it at the starting point of the animation.
- Go to the desired start frame in the Animator’s Track view, and double-click on Follow Atoms in the Animation panel.
- The camera will then move in sync with the atoms between the start and end frames while maintaining a fixed vector between the camera and the atoms’ geometric center.
- Don’t forget to set the end frame to define the duration of the animation.
You can fine-tune the behavior through several properties: whether to apply the animation to the active camera, and whether to use the Keep camera upwards option—useful when working with or without the grid active.
Adjusting Positions
If needed, you can manually adjust the camera position using animation controllers, but the target will stay locked to the selected atoms. This is helpful when you want to visualize from a specific angle or maintain a particular framing as the molecule moves.
When to Use This
This feature is particularly useful for:
- Demonstrating ligand binding and exit pathways
- Tracking conformational changes of flexible regions
- Following ions through channels or pores
- Creating presentations for teaching molecular movement
By combining dynamic atom-tracking with precise camera control, Follow Atoms helps you ensure that viewers stay focused on what’s important in your molecular animation.
Learn more in the official SAMSON documentation: Follow Atoms animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.