Molecular modelers often spend a considerable amount of time simulating ligand unbinding pathways in protein-ligand systems. However, after the hard work of generating results, exporting and visualizing the actual ligand motions can still be confusing or time-consuming. If you’ve been wondering how to quickly convert those paths into something visual and shareable, this post is for you.
After running unbinding pathway simulations in the Ligand Path Finder extension in SAMSON, you can not only store and view the pathways but also export them to visualize ligand motions directly in 3D. Here’s how to do it.
From Results to Motion: Why Exporting Matters
Once the planner finds possible unbinding paths, each becomes a series of conformational states. These offer insight into how the ligand exits the binding pocket — a process essential for drug design, selectivity studies, or understanding protein mechanics.
Viewing these results in a static table isn’t enough if you want to examine ligand dynamics or share them with collaborators. Instead, you can export the entire motion as a trajectory directly into your SAMSON document.
Exporting Paths as Trajectories
After your run is complete and paths have been found, go to the Results tab in the Ligand Path Finder app. Each row corresponds to one path, with metrics like maximum energy and time taken.
To export paths:
- Select one or more paths from the table.
- Click the Export paths button at the bottom of the Results tab.
This creates a trajectory object in the SAMSON Document, allowing you to play back the motion or include it in structural visualizations and animations.
Exporting Conformations Along a Path
If you prefer exporting individual snapshots rather than a full trajectory, the app also allows for exporting selected conformations from paths:
- Select one or more paths.
- Choose the interval (e.g., every frame, every nth frame).
- Click Export to add the conformations as separate states in SAMSON.
This enables frame-by-frame analysis and makes it easier to inspect energy landscapes along the way.
Copying the Path Table and Energies
The table in the Results tab holds useful statistics for each path. You can copy selected rows or the full table simply by right-clicking and choosing Copy table content. This is helpful for sharing results or archiving data outside of SAMSON.
Want to compare energy profiles programmatically? Right-click and choose Copy path energy to export energy values across conformations. This makes plotting and comparison easy using external tools like Python or Excel.
Optional: Control Paths Like Animations
Once you’ve exported a trajectory, you can double-click it in your document to play or pause the motion. For more granular control, select the path and use the Inspector panel to change playback speed, cycle mode, and more.
Why This Matters
Visualizing and exporting ligand unbinding pathways makes it easier to communicate insights, validate results, or generate figures for publications. Whether you’re running multiple paths or just analyzing one, SAMSON makes it straightforward to move from simulation to visualization.
💡 Tip: If you’re only interested in exporting the motion of certain atoms rather than the whole ligand, check out the Export Along Paths SAMSON Extension for more control.
To learn more, visit the full documentation for the Ligand Path Finder: https://documentation.samson-connect.net/tutorials/ligand-path-finder/ligand-path-finder/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.