Molecular modelers often spend a great deal of time analyzing ligand unbinding pathways. Once paths are identified, it’s not uncommon to want to export the atomic coordinates corresponding to a subset of atoms moving along these paths—for example, to investigate specific residue-ligand interactions, generate animations, or run follow-up simulations.
If you’re using SAMSON’s Ligand Path Finder, there’s a streamlined way to export atomic trajectories from computed pathways using the Export Along Paths app. This lets you extract just the information you need, efficiently and flexibly.
Why export atom trajectories?
After identifying viable unbinding paths, researchers often want to:
- Study the ligand’s movement in specific regions of the protein
- Track conformational changes of nearby residues
- Use selected atomic trajectories in umbrella sampling or machine learning workflows
- Export animations for presentations or publications
The ability to export just a subset of atomic trajectories—rather than the entire system—can help reduce data size, focus analysis, and improve clarity.
How it works in SAMSON
After a ligand path is found using the Ligand Path Finder, follow these general steps to export atomic trajectories:
- Select the path(s) from the Results tab of the Ligand Path Finder window.
- Choose the atoms you want to export. These can be defined in either the Viewport or the Document View using standard selection tools.
- Use the Export Along Paths app from SAMSON Connect to export the trajectories.
This app specializes in exporting per-atom trajectory data along paths. You can save the trajectories in compatible formats for analysis or visualization in SAMSON or external tools.
Export options and flexibility
When exporting, you can typically choose:
- The export format (.sam, .samx)
- The interval between conformations (e.g., every frame or every nth frame)
- Specific atom subsets, allowing more focused data sets
This modular setup makes it easy to collect the exact data needed for your analysis or visualization pipeline.
Where to find the tools
The Export Along Paths app can be downloaded from SAMSON Connect. Once installed, and after paths are generated with the Ligand Path Finder tool, you can access export features via the path table and right-click menu options.
For developers and power users, exported data can be used to generate custom plots or serve as input for other molecular modeling workflows.
Final thoughts
The ability to focus on just the atoms you care about and export their trajectories—cleanly and on demand—is a small but incredibly useful feature when working with complex systems in SAMSON. It keeps workflows streamlined and helps molecular modelers spend more time analyzing, and less time converting data.
To learn more and see this feature in context, visit the original documentation page: Ligand Path Finder Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.