Understanding ligand unbinding pathways can be a complex process, but once you’ve spent time simulating this motion with SAMSON’s Ligand Path Finder, the next step is often just as important: exporting the results. If you’re a molecular modeler trying to analyze or share your simulation findings, clear export options are essential—but not always obvious.
This post walks you through the main ways to export the results of ligand pathway planning using the Ligand Path Finder in SAMSON.
Why export results?
Once you’ve used the planner to find unbinding pathways, exporting the data allows you to:
- Analyze energy profiles along a path
- Compare conformations over time
- Share pathway data with collaborators
- Use the results for publication figures or further validation (e.g., with P-NEB)
Export options available
After running the planner and navigating to the Results tab, you’ll see the list of paths with energy and structural information. SAMSON provides several export options that are easy to use once you know where to find them.
1. Copying Path Table Content
You can copy the entire table or selected rows using:
- Ctrl/Cmd + C
- Right-click > Copy table content
This provides you with a spreadsheet-friendly format for saving pathway energies, time elapsed, saddle energy, and more.
2. Exporting Path Energy Values
Select one or more rows, right-click, and choose Copy path energy. This exports only the energy values along the pathway, useful for plotting or external analyses.
3. Exporting Path Trajectories
You can generate trajectory documents from the path data:
- Select one or more paths
- Click Export paths
This embeds the calculated conformations into your SAMSON document as visible trajectory nodes.
4. Exporting Conformations
To extract specific conformations along the path:
- Select paths of interest
- Set the export interval
- Click the Export button
This is particularly helpful when you need to perform additional analysis on structural intermediates or share specific conformations with collaborators.
5. Playing Back Pathways
To interact with your exported data directly in SAMSON:
- Double-click on a path in the document to start or stop it
- Use the inspector for playback options and frame control
- Right-click for additional options under Path > …
This gives you immediate feedback on ligand motion and helps you validate whether export results match expectations.
Before You Share
Once results are exported, be sure to verify conformations and select meaningful time points if integrating the outputs into presentations, publications, or downstream apps (e.g., export to P-NEB for pathway refinement).
Summary
If you’ve gone through the process of identifying ligand unbinding pathways, knowing how to export results efficiently lets you take full advantage of your simulations. Whether you’re plotting energies, sharing with colleagues, or preparing visuals, SAMSON’s export options make it easier to work with your data.
To learn more about all the steps involved in using Ligand Path Finder in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/tutorials/ligand-path-finder/ligand-path-finder/