Extracting Atom Trajectories from Protein Transition Paths in SAMSON

For molecular modelers analyzing protein conformational changes, it’s often not enough to just visualize start and end structures. Understanding the atomic-level movements along the transition path is key to gaining insights into protein mechanisms, identifying stable regions, and preparing for enhanced sampling or refinement using techniques like Molecular Dynamics.

If you’ve used the Protein Path Finder App in SAMSON to generate conformational transition paths, you may now want to extract atom trajectories along those paths—for selected atoms or groups—for further analysis or to share results clearly with collaborators. Fortunately, there’s an efficient way to do that in SAMSON using the Export Along Paths Extension.

Why export atom trajectories?

Researchers often need to:

  • Visualize movement of specific residues or atoms involved in function.
  • Use exported coordinates as input to further simulations or analysis pipelines.
  • Generate figures or animations showing how selected atoms travel during transitions.

Instead of manually tracking conformations and saving frames one by one, the Export Along Paths App automates this process—providing a clean and fast export of positional data.

What you’ll need

Before exporting trajectories, ensure you’ve already run a path search using the Protein Path Finder app and obtained some results. You’ll also need the Export Along Paths App, which is freely available via SAMSON Connect.

Step-by-step overview

  1. Load your document with a computed transition path.
  2. Select the path(s) you want to export from the Results tab of the Protein Path Finder App.
  3. Install and launch the Export Along Paths App.
  4. Select the atoms you want to track—this could be individual atoms (e.g., CA in GLY 12) or groups defined via the Node Specification Language (NSL).
  5. Specify output format (e.g., CSV, text) and whether you want relative or absolute coordinates.
  6. Define the export resolution (e.g., every conformation or every 5th).
  7. Run the export and retrieve time-stamped spatial data ready for use.

Each entry includes:

  • The step or time point along the path.
  • Atom ID and coordinates (x, y, z).
  • Optionally, energy values or residue identifiers.

When to use this:

This functionality is especially useful in situations where:

  • You want to generate plots of atom displacement over time.
  • You’re comparing different paths or conformational behaviors.
  • You want to export data for scripting, ML models, or further simulation software.

Here’s an example from the Protein Path Finder workflow, where atoms from GLY 12 and ARG 123 are selected as active and their motion is tracked across conformations:

Add active atoms

This same group could be tracked with the Export Along Paths App to get rich coordinate data capturing their movement through transition space.

Tips

  • Use intuitive group names in the Document View to streamline selection.
  • Always review your exported data visually in SAMSON before exporting.
  • Combine this workflow with P-NEB refinement to export higher quality transition paths.

To learn more and see the full tutorial, visit the Protein Path Finder documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and explore available apps at https://www.samson-connect.net.

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