Pathlines: show a path of the center of mass of an atomic system

In this tutorial, we will show you how to create pathlines thanks to the Pathlines visual model. Pathlines are visual models which represent the trajectory of the center of mass of the selected atoms along selected trajecotories (paths). Pathlines may be used to understand the motion of a group of atoms (or a single atom) along a path/trajectory.

In SAMSON, go to Home > Download and insert https://www.samson-connect.net/documents/046f1acd-c799-40f6-8185-cb4847eff795 - this will load a document with this tutorial's sample from SAMSON Connect.

The sample document contains a structural model of Lactose permease 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

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 select one or more paths (to select more than one node, use the Ctrl / Cmd key). If no path is chosen, all the paths from the active document will be used. If no atoms are selected, all atoms from the active document will be used. Select the ligand named TDG.

Go to Visualization > Visual model > More... (1) to create a visual model. In the pop-up window, choose "Pathline of the center of mass" and press OK.

1. , : ++ctrl+shiftv++, : Cmd+Shift+V

The new pathline will show how the center of mass of the TDG ligand moves alongside the chosen path.

Tip

You can double-click on a path in the document to start/stop it.

To access the path controllers, select the path and open the Inspector (1).

If you right-click on a path, you can also access some of its options via Path > ....

1. Interface > Inspector, , : Ctrl+2, : Cmd+2"""

You can modify the thickness and color of a pathline in the Inspector by selecting a pathline.

Note

If you delete a Path, the corresponding pathline will be deleted too. If you delete some of the atoms for which a pathline was created, the pathline will be modified.

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.

If you have any questions or feedback, please use the SAMSON Connect Forum.