Whether you’re visualizing protein docking, showcasing a molecular simulation, or animating custom atom movements, path recording can drastically enhance molecular presentations. But what happens once the movement is complete? Many molecular modelers face the challenge of capturing and exporting atom trajectories for further data analysis, publication, or visualization. In SAMSON, the “Record path” animation provides a structured way to do exactly that.
This blog post focuses on a specific and practical solution: how to export atom trajectories from animations in SAMSON. This is especially useful when you want to retain and reuse molecule movement paths or convert animation motion into reusable data structures.
Why export a path?
Imagine you’ve spent time fine-tuning an animation showing how a ligand navigates toward a protein pocket. You’ve adjusted frames, atom positions, and maybe combined several effects. The full presentation plays beautifully—but what if you want to extract that movement for later editing, data reporting, or reusing part of it in another project?
This is where exporting the path becomes a critical step in your workflow.
Recording the path in SAMSON
Before a path can be exported, it first needs to be recorded using the Record path animation. This animation acts as a recorder that tracks atom positions over time during the presentation. It’s particularly useful when used in combination with animations that actually create motion, such as:
While the recording is running, track segments appear green (positions recorded) or red (positions missing or invalid). You can always enable or disable recording for performance reasons. For example, you might want to disable recording while still working on other animations.
Exporting the recorded path
Once your presentation has been played and the path animation shows only green segments (indicating that all frames have been recorded), you can officially export the path. This involves creating a Path node in your document:
- Open the Inspector for the Record path animation and click on Create path; or
- Right-click on the animation in the Animator and select Create path.
This creates a permanent object that stores the trajectory and can be used in further manipulation, analysis, or exporting to external formats. It’s great for turning dynamic presentations into reusable data streams, for example:
- As input for simulations starting from specific conformations
- To visualize and communicate molecular movement in educational contexts
- For publishing supplementary materials showing transition pathways
Tips to improve your workflow
- Order matters: In SAMSON’s Animator panel, animations are executed top-down. So always place the Record path animation after movement-inducing effects.
- Editable keyframes: You can move animation keyframes at any time, even after having recorded parts of the path.
Conclusion
If you’re frequently animating atom movements in SAMSON, exporting those movements as reusable paths can help you create higher-quality models, improve collaboration, and gain deeper insights from molecular motion. It’s not just about flashy visuals—recorded paths make your animations useful far beyond presentation time.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/record-path/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.