Working with protein conformational transitions often leads to a fundamental question after the paths are computed: How do I get the motion of specific atoms along a transition path?
Whether you’re interested in backbone atoms, catalytic residues, or specific side chains moving during a function-critical transition, being able to extract atom trajectories is essential for further analysis or visualization outside of SAMSON (e.g., in analysis tools, videos, or machine learning pipelines).
Exporting specific atom trajectories along a protein path
If you’re using the Protein Path Finder app in SAMSON to calculate conformational transition pathways between two states of a protein, you can easily export only the trajectories of atoms you care about — without exporting the entire structure at every frame. Here’s how.
1. Compute or load a path
This assumes you’ve already run or loaded a path using the Protein Path Finder app, and paths are visible in the document.
2. Install the appropriate extension
To export atom trajectories, you’ll need to install the Export Along Paths app. Once installed, you’ll find it under Apps > Export Along Paths.
3. Select atoms of interest
Select the atoms you’d like to track in your export. You can do this manually in the Document view, or efficiently using the Node Specification Language (NSL).
For example, to select alpha carbon atoms in residues GLY 12 and ARG 123, you would use:
|
1 |
("CA" in "GLY 12") or ("CA" in "ARG 123") |
4. Open Export Along Paths
With your atoms selected, launch the Export Along Paths app. Choose:
- The path(s) along which to export the trajectories
- The export format (e.g., CSV, XYZ, etc.)
- The export interval (e.g., export every frame, every nth state)
5. Export and analyze
The resulting file will contain the positions of the selected atoms at each conformation along the path. This is particularly useful if you want:
- To analyze correlations between atom movement
- To feed trajectories into custom scripts or software
- To visualize atom motion with external tools
Here’s an example of a visual output from a documented path:
Why this is helpful
Sometimes, full trajectories with all atoms are unnecessarily heavy or simply overwhelming when all you want is to look at residue side chain shifts, binding site rearrangements, or pivot points in the protein backbone. This export method is efficient and focused — allowing users to streamline post-processing.
Things to keep in mind
- The atoms must exist in all conformations of the path.
- The exported coordinates use the same spatial coordinates as SAMSON.
- The Export Along Paths app complements visualization by allowing exports directly useful for scripting or numerical post-processing.
To learn more about this functionality, visit the Protein Path Finder documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.