From a Moving Path to Coordinates You Can Analyze

A path can be easy to understand on screen and surprisingly awkward to use in a simulation workflow. You may see a ligand move through a protein, but downstream analysis often needs the coordinates at each step—not just an animation. Exporting a path turns that motion into PDB data you can inspect, visualize, or prepare for further calculations.

This is especially useful when you need a ligand’s exit trajectory for enhanced sampling, want intermediate structures for comparison, or need coordinates for a reaction-coordinate workflow. The key is deciding what to export: every atom in the path, or only a meaningful subset such as the ligand.

First, know what a path contains

In SAMSON, a path is a node that stores atomic trajectories for a group of atoms. Double-clicking a path in the Document view starts or stops its motion. Export Along Paths lets you write the coordinates along selected paths to PDB files, either with all atoms or with explicitly defined atom groups.

The distinction matters: exporting a path gives you coordinate snapshots. It does not, by itself, provide energies or define a complete free-energy calculation. Treat the files as structural input for the next stage of your workflow.

Choose a useful export scope

If you need the complete structural context, select one or more paths in the Document view and export all atoms. This is a straightforward choice when you want to preserve the full moving system for inspection. You can save all frames in a single PDB file or write each frame as a separate PDB file. The Advanced section also lets you change the frame export interval, which can help when you do not need every stored frame.

If your analysis focuses on a particular molecule, define that subset instead. Expand the app’s Advanced panel, select the atoms in the Document view—for example, the ligand—and click Add. The selected group appears in the export list as a named model. You can rename it by double-clicking its name, add additional atom groups, and use the Select or Unselect controls to highlight the atoms included in each model.

Selecting the TDG ligand in the Document view
Select the molecular group you want to export before adding it as a model.

For example, the tutorial sample contains lactose permease (1PV7), the ligand thiodigalactosid (TDG), and two unbinding paths. Exporting TDG alone can give you a focused ligand trajectory; exporting additional groups lets you include other selected atoms as separate models.

A practical sequence

  1. Open the sample or your own SAMSON document, and identify the path or paths you need in the Document view.
  2. Open Home > Apps > All > Export Along Paths. You can also find the app using Find everything… with Shift+E.
  3. For all atoms, select the paths and choose whether frames go into one PDB file or separate PDB files.
  4. For a subset, expand Advanced, select the atoms, and click Add. Repeat for other groups if needed.
  5. Choose the relevant paths and export. When prompted, choose a destination folder and file prefix.
Advanced Export Along Paths interface showing model export controls
The Advanced panel is where you define named atom groups for a focused export.

Before you run downstream analysis

Check that the intended path is selected and that the model list contains the atom groups you mean to export. Decide whether a single file or separate frame files better fits the next tool in your workflow, and consider the frame interval if exporting every frame is unnecessary. After export, inspect the resulting structures in your preferred viewer or analysis tool before using them as simulation input.

For a full walkthrough, see the Export atom trajectories along paths tutorial.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.

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