Molecular simulations often involve tracking complex atomic rearrangements: docking events, folding pathways, or drug interactions. But replaying those subtle moves isn’t always straightforward. If you’ve ever needed a clean, visual representation of how atoms moved throughout a simulation for presentations or further analysis, then recording their trajectory as a path might be the solution you’re looking for.
SAMSON provides a simple yet effective animation—Record path—that does exactly that: it captures the positional history of atoms during a molecular presentation and stores it as a path. This path can then be reused, analyzed, or exported. If you’re working with simulations, assembling systems, or manually positioning atoms, this tool can help you document and reuse the results of your work.
Why Record Paths?
Let’s say you run a simulation showing a ligand docking into a protein. You play the animation, the atoms shift places, and the molecule settles in. But if you want to compare that motion or replay it even after adjusting the structure, you’ll need a way to preserve the trajectory. That’s where Record path comes in. It adds a track that captures each frame’s atomic positions and keeps them accessible.
Getting Started
To use the Record path animation:
- Go to the Animation panel in the Animator.
- Double-click on Record path to add it to your animation sequence.
- A keyframe will appear at your current frame. If you need it elsewhere, you can move it later.
The paths are partially displayed with color-coded segments:
- Green: Positions have been successfully recorded.
- Red: No valid position data—either not yet recorded or outdated.
When to Place It
One subtle point: the Record path animation must appear after the animations that move atoms (such as Simulate or Move atoms) in the Animator. SAMSON processes these from the top down, so order matters.
Optimizing Performance
If your system becomes slow during editing or playback, that might be due to continuous recording. You can disable the Record path temporarily:
- In the animation’s Inspector, toggle Enable recording.
- Or right-click on the animation in the timeline and make the same change.
When disabled, controllers associated with the animation will appear darkened, indicating that changes won’t be tracked.
Exporting the Trajectory
After recording the full animation (confirmed when the entire animation line turns green), you can convert the recorded track into a Path node. This step allows you to reuse the movement:
- In the Inspector, click Create path, or
- Right-click the track in the Animator and choose Create path.
Summary
Whether you’re illustrating a mechanism, capturing a simulation trajectory, or visualizing docking events, Record path offers a simple visual record of atomic motion. Try using it in your next presentation or collaboration—it might just make those molecular movies easier to understand and share.
To learn more, visit the full documentation page on Record path.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.