Understanding how a protein transitions between conformations is a key goal in structural biology. While computational tools for finding these paths exist, researchers frequently struggle with an important practical question: how can we export and visualize these conformational transitions in a way that integrates with downstream workflows?
If you’ve used the Protein Path Finder app in SAMSON to compute conformational pathways, you may want to extract those paths or generate informative visual outputs. In this post, we’ll explain how to export trajectories of atoms along computed conformational paths so that you can better analyze or communicate your results.
Why export conformational paths?
Once a path between two conformations is computed (e.g., from protein open to closed states), the data is stored in the SAMSON document, where it can be explored interactively. However, for many users, there’s value in connecting these results with external analysis pipelines, generating custom visuals, or saving specific atom movements. This is where exporting comes in.
Exporting from the Protein Path Finder window
To export conformations along one or more paths:
- Open the Results tab in the Protein Path Finder app.
- Select the path(s) you want to export by clicking them in the table (you can use Ctrl/Cmd to multi-select).
- To export paths as smooth trajectories into your document, click the Export paths button.
- To export individual conformations along a path (e.g., every 5th conformation), choose an export interval and click the Export button.
These exports are then available in your document and can be used for animations, further analyses, or visualization with external tools by saving in formats like .sam or .samx.
Exporting specific atom trajectories
If you don’t need full conformations but want to track the motion of specific atoms (e.g., C-alpha carbons or residues of interest), use the dedicated Export Along Paths app:
This tool allows you to select specific atoms and export their positions along the path as coordinate trajectories—ideal for custom analysis or plotting atomic movements over time.
Useful tips
- You can copy contents of the path table (energies, states, etc.) using Ctrl/Cmd+C.
- Right-click a path to copy energy values or access path options (like deleting or renaming).
- Double-clicking a path in the document will let you play or pause the trajectory for visualization.
Choose the right export method
Depending on your use case, you may prefer exporting full structures for visualization or only atomic positions for analysis. SAMSON supports both, giving you flexibility without the need for scripting.
Whether you’re preparing data for a presentation, creating publication figures, or integrating into a larger workflow, knowing how to export transition paths is a valuable skill.
To explore all the details or see more export options, check the full tutorial on the Protein Path Finder app: Protein Path Finder Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.