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Pathlines: visualize motion of the center of mass of an atomic system#

Use the Pathlines visual model to display the center-of-mass (COM) trajectory of selected atoms along a path. This is ideal for visualizing ligand unbinding, macromolecular conformational changes, or tracking atomic motion across simulations.

Why Use Pathlines?#

  • Track motion of ligands, residues, or atom groups over a path.
  • Visualize center-of-mass displacement in complex systems.
  • Analyze unbinding, diffusion, or domain movement.

Getting Started#

  1. Log into SAMSON Connect.
  2. Visit the Pathlines Extension page and click Add.
  3. Restart SAMSON - your extension will be ready to use.

Step 1 - Load the Sample System#

Load the sample system:

  1. Click Home > Download.
  2. Paste https://www.samson-connect.net/documents/046f1acd-c799-40f6-8185-cb4847eff795 ().
  3. Click Download.

Download the sample document

This will load a document with this tutorial's sample from SAMSON Connect.

The sample document contains a structural model of Lactose permease (1PV7) with its ligand Thiodigalactosid (TDG) and the unbinding paths generated with Ligand Path Finder (see the Ligand Path Finder tutorial). In the Document view (1), you can see the protein under the name Protein_chain_A, the ligand under the name TDG, and two paths.

  1. Interface menu > Document view or
    , : Ctrl+1,
    : Cmd+1

Step 2 - Select Atoms and Paths#

To create pathlines, select in the Document view a group of atoms for which you want to visualize the motion of their center of mass and one or more paths (to select more than one node, hold the Ctrl / Cmd key).

If no atoms are selected, the entire system is used. If no paths are selected, all paths in the document are used.

Select a group of atoms

Step 3 - Create a Pathline Visual Model#

To create a visual model:

  1. Go to Visualization > Visual model > More... (shortcut: Ctrl/Cmd + Shift+V).
  2. In the dialog, choose Pathline of the center of mass and click OK.

Add visual model

This creates a visual pathline showing the COM motion of the selected atoms along the selected path(s).

Pathlines - first frame

Step 4 - Explore and Customize#

  • Double-click a path in the Document view to start/stop it.
  • Right-click a path to access Path > ... options in its context menu.
  • To access the path controllers, select the path and open the Inspector (Ctrl/Cmd + 2).

Pathlines - last frame

  • Adjust the visual model properties (color, thickness) in the Inspector by selecting the pathline visual model.

Pathline attributes in the Inspector

Note

If you delete a path, the associated pathline will also be removed. Deleting atoms used for a pathline will modify the visualization.

Use Cases#

  • Display ligand unbinding/rebinding routes.
  • Analyze collective domain motions in protein complexes.
  • Visualize center-of-mass movement in reaction coordinate workflows.

Next Steps#

Now that you know how to visualize paths, you might want to use the P-NEB app to optimize them - see the tutorial on how to optimize transition paths with the Parallel Nudged Elastic Band (P-NEB) method.

Need Help?#

Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.