When analyzing protein conformational transitions, visualizing the path is just one step in the process. For publication, presentation, or further computational treatment, you often need to export the results, including the series of conformations along a transition path and key characteristics like energy profiles. If you’re using the Protein Path Finder extension in SAMSON, here’s a practical guide to exporting your data efficiently.
Why export?
Once you’ve identified a transition path between two conformations, you may want to:
- Analyze the energies of each intermediate conformation
- Use the path in a different tool (e.g., for further refinement with NEB or for visualizations)
- Share results with collaborators
- Document your findings for reproducibility
Export options in Protein Path Finder
In the Results tab of the Protein Path Finder app, once paths have been identified, you will see them listed in a table. This is your hub for exporting different types of data.
1. Copy table contents
You can copy details of one or more selected paths (such as the number of conformations, energy barriers, elapsed time) using:
- Ctrl + C or
- Right-click > Copy table content
This is particularly useful if you want to paste data into a spreadsheet or a report.
2. Copy energy profiles
To export energy values along the conformational path:
- Right-click on a selected path
- Select Copy path energy
You can then paste the result into a text editor or import it into external plotting tools.
3. Export paths to SAMSON document
For visualization and further manipulations within SAMSON:
- Select your desired paths from the path table
- Click the Export paths button
This will add trajectory representations of the paths directly into your working document.
4. Export conformations
You can also export the conformations along selected paths. After selecting paths:
- Specify the export interval (e.g., every N conformations)
- Click Export to add the conformations to the document
This is helpful for frame-by-frame visualization or for creating animations.
Bonus: Play and inspect exported paths
Double-click an exported path in the document tree to start or stop its animation. To fine-tune frames or playback settings, you can open the Inspector (Ctrl + 2) while the path is selected.
With these options, you can customize what gets exported and in what format, making it easier to reuse your results in other contexts.
For more on generating protein paths and exporting results, visit the original tutorial:
Protein Path Finder tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started at www.samson-connect.net.