Spotlight on Pathlines: Tracking Center-of-Mass Motion in Molecular Models.

For molecular modelers, visualization is frequently the bridge between complex data and meaningful insights. Tracking the motion of molecules, ligands, or atom groups can be critical for studying ligand unbinding, diffusion, or macromolecular conformational changes. To address this need, SAMSON provides the Pathlines visual model, a powerful tool that simplifies the analysis of center-of-mass trajectories.

Why Pathlines Are Worth Your Attention

The Pathlines feature offers a targeted solution: it displays the trajectory of the center-of-mass (COM) of chosen atom groups along pre-defined paths. This makes it especially useful for molecular modelers interested in:

  • Visualizing ligand unbinding paths or binding site explorations.
  • Understanding collective domain motions in protein complexes.
  • Analyzing atomic motion across simulation data.

The tool’s beauty lies in bringing motion to life, as it graphically showcases how molecules move and interact.

How to Get Started

Using Pathlines starts with incorporating the necessary extension. Here’s a quick guide:

  1. Log into SAMSON Connect.
  2. Visit the Pathlines extension page and click the Add button.
  3. After restarting SAMSON, the extension will be ready to use.

Creating Your First Pathline

Once the extension is installed, follow these steps to visualize a molecule’s center-of-mass motion:

  1. Load a sample system, like the structural model of Lactose permease (1PV7) with its ligand Thiodigalactosid (TDG), by downloading it from this link. The sample system includes unbinding paths that can be analyzed.
  2. In the Document view, select the atom groups and paths you want to analyze. If needed, use the Ctrl/Cmd key for multi-selection. (If you skip this step, the entire system and all paths will be selected by default.)
  3. Create the pathline by navigating to Visualization > Visual model > More… (shortcut: Ctrl/Cmd + Shift + V). Choose Pathline of the center of mass from the dialog and confirm.

You will immediately see the pathline visual representation of the center-of-mass motion.

Customizing and Exploring Pathlines

Once your pathline is created, there is plenty you can do to customize and analyze it:

  • Double-click on a path in the Document view to start or stop it.
  • Use the Inspector panel (Ctrl/Cmd + 2) to adjust properties such as color and thickness for better visualization.
  • Experiment with right-click context options for paths to discover additional settings.

The Larger Picture

Pathlines are more than just neat visualizations—they serve practical purposes. Molecular modelers can use them to track ligand unbinding, study how proteins transition between conformations, or gain insights into reaction coordinate workflows. These functionalities make Pathlines an indispensable tool in simulation-driven research workflows.

Want to dive deeper? Visit the full Pathlines documentation for additional tips and related tutorials.

*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can access SAMSON at https://www.samson-connect.net.*

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