A molecular path can be easy to inspect in a 3D workspace and awkward to use in a downstream workflow. If you need coordinate files for a reaction-coordinate analysis, a free-energy calculation, or simply to examine how a ligand moves, exporting the entire system may include far more atoms than you need. Exporting only a relevant group—such as the ligand—can make the resulting files easier to work with.
SAMSON’s Export Along Paths extension lets you export coordinates from selected paths as PDB files. You can export all atoms represented by a path, or define one or more atom groups to export. You can also choose whether all frames go into one PDB file or each frame is written to a separate PDB file.
First, know what the path contains
In SAMSON, a path is a node that stores atomic trajectories for a group of atoms. Double-clicking a path in the Document view starts or stops moving those atoms along it. Exporting the path turns those stored coordinates into files you can use outside that interactive view.
This distinction matters when planning an export: the path is the changing structural information, while your export choice determines which atoms and frames are written out. Before exporting, decide whether your next step needs the whole system or only a specific group, and whether you prefer one file containing all frames or a separate file for each frame.
Export the whole path, or focus on a subset
For a straightforward export, select one or more paths in the Document view, choose a PDB output mode, and click Export atoms along paths to PDB files. The app will prompt you to choose a destination folder and file prefix. If you need to adjust how frequently frames are exported, expand the Advanced section and change the frame export interval.
If the analysis concerns a ligand’s motion, exporting every atom may make the output harder to inspect than necessary. Instead, expand Advanced, select the desired atoms in the Document view, and click Add to define them as a model for export. For example, the sample system includes the ligand TDG; selecting it creates a focused export group.
The export list can contain multiple atom groups. You can rename a model by double-clicking its name, and use Select or Unselect to highlight the atoms included in a model. If you need to redefine a group, use Reset for its row. These controls are useful when you want to keep separate groups—such as a ligand and another selected region—organized as distinct export models.
A small checklist before exporting
- Choose the path: select the relevant path or paths in the Document view.
- Choose the atoms: export all atoms, or add the specific group or groups your workflow needs.
- Choose the organization: decide between all frames in one PDB file and one PDB file per frame.
- Check the frame interval: use the Advanced section if you want to change the export interval.
- Choose a destination: when prompted, select a folder and file prefix that will make the output easy to identify.
For instance, when preparing ligand coordinates for later analysis, a practical sequence is to select the ligand, add it as a model, select the path, choose the desired PDB organization, and export. This keeps the export focused on the atoms relevant to that task, without changing the path itself.
To see the complete interface and sample-system workflow, read the Export atom trajectories along paths documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.