.XYZ File Extension

Molecule Specification File

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Category	Data Files
Format	.XYZ
Cross Platform	Update Soon

What is an XYZ file?

.XYZ files are plain text files used for representing molecular structures in three-dimensional space.

They consist of atomic coordinates and optional additional information, such as atomic symbols, connectivity, and molecular properties.

Each line typically corresponds to a single atom, with its coordinates specified in Cartesian space.

More Information.

The XYZ file format was first introduced by Charles M. Breneman and Joshua A. Herron in the late 1980s.

Initially, it was designed as a lightweight and platform-independent format for storing molecular coordinates generated by the molecular mechanics program GAMESS (General Atomic and Molecular Electronic Structure System).

Over time, its usage expanded beyond GAMESS to encompass various other computational chemistry software packages.

Origin Of This File.

The .XYZ file format traces its roots back to the early days of computational chemistry. It emerged as a simple and versatile means of exchanging molecular structure data between different software packages.

The format’s simplicity and human-readable nature contributed to its widespread adoption across the scientific community.

File Structure Technical Specification.

XYZ files follow a straightforward structure, making them easy to parse and manipulate programmatically. Each line in the file represents an atom and consists of three main components:

Atomic Symbol: The elemental symbol of the atom.
X, Y, Z Coordinates: The Cartesian coordinates of the atom in space.

Additional information such as atomic connectivity or molecular properties may be included. However, the core structure remains consistent across all XYZ files, facilitating interoperability between different software tools.

How to Convert the File?

Converting .XYZ files to other formats or vice versa is relatively straightforward. Numerous software tools and libraries support conversion between XYZ and formats such as PDB (Protein Data Bank) or SDF (Structure Data File).

Users can utilize command-line utilities or graphical interfaces provided by these tools to perform the conversion.

For instance, Open Babel, a versatile chemical toolbox, offers command-line functionality for converting between various chemical file formats, including XYZ. Users can use commands like babel input.xyz output.pdb to convert XYZ files to PDB format.

Advantages And Disadvantages.

Advantages:

Simplicity: The plain text format is easy to create, read, and modify using basic text editors.
Portability: XYZ files can be exchanged between different software programs and platforms without loss of information.
Versatility: They can store not only atomic coordinates but also additional data, providing flexibility for various applications.

Disadvantages:

Lack of Standardization: While the format itself is well-defined, there is no standardized convention for additional information beyond atomic coordinates.
Limited Metadata: XYZ files primarily focus on geometry and lack robust support for metadata such as molecular symmetry or electronic structure.

How to Open XYZ?

Open In Windows

Use Notepad or any other text editor:

Right-click on the .XYZ file.
Select “Open with” and choose Notepad or another text editor from the list.
The .XYZ file will open, displaying its contents in plain text format.

Open In Linux

Use gedit or any other text editor:

Open a terminal.
Navigate to the directory containing the .XYZ file.
Use the command gedit filename.xyz to open the file in gedit.
Alternatively, use any text editor of your choice to open and view the .XYZ file.