Exporting Protein Conformation Paths and Energies with SAMSON

When studying protein conformational changes, modeling how a protein transitions from one conformation to another is just the beginning. Molecular modelers often need to analyze and share results: extract key conformations, view transition energies, or export trajectories for visualization and further simulation. If you’ve found yourself wondering how to efficiently turn your computed paths into reusable data, this article will help you do just that using the Protein Path Finder app in SAMSON.

Once you’ve used the Protein Path Finder to identify transition pathways between two conformations, the Results tab becomes your central hub for working with the data. This tab shows a handy path table with energy statistics, such as minimum and maximum energies along a conformation path, transition time, and barriers. But the power lies in what you can do next.

Visualizing Transition Path Energies

Clicking on a path in the results table will let you investigate the energy landscape of transitions. You’ll see conformation states mapped along an energy curve, with the current conformation displayed in the main viewport. Use the slider below the energy graph to browse conformational snapshots along the selected path.

Results path

Exporting Data: A Quick Overview

Here’s how you can export useful outputs depending on what you’re trying to do:

  • Copy the path summary table: Simply select one or more rows in the path table and use Ctrl+C (or Cmd+C on macOS), or right-click and choose Copy table content to paste into a spreadsheet or text editor.
  • Export energy values: For detailed analysis, right-click and choose Copy path energy to get all per-conformation energy values along the path.
  • Save trajectories: Clicking the Export paths button inserts selected trajectories into the SAMSON document as path nodes—these can be animated, visualized, or analyzed further.
  • Export selected conformations: Sometimes you don’t need every frame—select a path, specify an export interval, and click Export to insert conformations directly into your document as static structures.

Fine-tuning Paths and Viewing in Context

All exported elements integrate directly into SAMSON’s versatile document view. You can right-click on path nodes for more options (e.g., edit remarks, visualize individual states), or open the Inspector to control animations. Conformations are automatically aligned with your interaction model settings and energy updates are available in real time.

Export path

This export functionality is especially useful if you’re preparing figures for publications, collaborating with colleagues, or moving into additional refinement stages using other apps like P-NEB or Export Along Paths.

In practice, you can go from raw transition simulation to cleaned, structured output with just a few clicks—no scripting needed, and no data lost in transfer.

To learn more and explore detailed steps including animation or path refinement, visit the original tutorial page: Protein Path Finder in SAMSON documentation.

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

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