Visualizing a molecular structure using an XYZ file
An XYZ file is used for storing a molecule’s geometry based on the coordinates of its atoms. To make an XYZ file, follow these steps.
Open a text editor program such as Notepad or TextEdit.
On line 1 of your file, enter the total number of atoms in your molecule.
On line 2 of your file, enter a description or leave this line blank.
The coordinates of your molecule begin on line 3. Each line will contain information for a single atom based on four entries:
atomic symbol x coordinate y coordinate z coordinate
These entries should be separated by tabs or space.
Save your file with the extension .xyz
Using a molecular visualizer program such as Jmol, open your .xyz file
Download an example for pentane (C5H12) here
