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1.10. What are XYZ Files?#

The XYZ file format is a text-file format. Unlike PDB files, there is no formal standard and several variations exist. However, a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines.

Typically, we use these files to store molecular geometries in Quantum Mechanical (QM) calculations. These files generally contain up to a few hundred atoms. For example, let’s build the small molecule alanine dipeptide, and store this data in .xyz.

1.10.1. Example with Alanine Dipeptide#

1.10.2. :::{figure} ../../static/images/ala.png#

1.10.3. align: center figwidth: 75%#

:::

Alanine dipeptide is the amino acid, Alanine, with the N-/C-terminal capped by an N-acetyl and N′-methylamide to neutralize the charges. First we will build alanine dipeptide via IQmol, then save the structure as ala.xyz:

  1. Open up the software, IQmol

  2. Use your mouse/trackpad and click any area on the screen

  3. Starting with the first Carbon atom, add the rest of the atoms, ignoring hydrogen

  4. Click on the ‘C’ to get the periodic table

  5. Click on Nitrogen, and replace the appropriate Carbons

  6. Repeat step 5. but with Oxygen

  7. Click on the add hydrogens button

  8. Click on the minimize energy button

  9. Save the structure as ala.xyz to your desired location (I saved them to my ~/Desktop/)

1.10.4. :::{figure} ../../static/videos/iqmol_ala.mov#

1.10.5. align: center figwidth: 75%#

:::

1.10.6. Open the ala.xyz File#

First, open your terminal, and then change directories to where you saved the ala.xyz. Since I saved them to my ~/Desktop/, I will cd there, and use less to view ala.xyz:

cd ~/Desktop/
less ala.xyz

You should see something like this:

:::{code-block} bash :lineno-start: 1

22

C -4.63266 -0.12314 -0.02867 C -3.47843 0.78724 -0.33464 N -2.20323 0.42630 -0.00959 C -1.04137 1.27430 -0.28628 C 0.27575 0.55742 0.00041 N 1.45796 1.17048 -0.29496 C 2.75416 0.56631 -0.05757 O 0.27431 -0.56825 0.48031 O -3.70495 1.85032 -0.89391 C -1.11255 2.56299 0.55432 H -4.29553 -1.05515 0.47169 H -5.15086 -0.39580 -0.97185 H -5.34808 0.39806 0.64145 H -2.06950 -0.49744 0.42698 H -1.04318 1.52892 -1.36918 H 1.44851 2.11097 -0.71632 H 2.67618 -0.44502 0.39384 H 3.33886 1.21183 0.63059 H 3.30037 0.47916 -1.01990 H -2.03263 3.14107 0.33971 H -0.25509 3.23182 0.33529 H -1.10019 2.31238 1.63679 :::

Explanations:

  • The first line of ala.xyz is the total number of atoms.

  • The second line is reserved for comments, so you can include details about the structure here

  • The rest of the file contains the elemental symbol, followed by x-,y-z- coodinates

Simple yeah?

1.10.7. Additional Resources#

For more information, please refer to the following resource:

RCSB: Guide to Understanding PDB data

“The primary information stored in the PDB archive consists of coordinate files for biological molecules. These files list the atoms in each protein, and their 3D location in space. These files are available in several formats (PDB, mmCIF, XML). A typical PDB formatted file includes a large “header” section of text that summarizes the protein, citation information, and the details of the structure solution, followed by the sequence and a long list of the atoms and their coordinates. The archive also contains the experimental observations that are used to determine these atomic coordinates.”

UCSF: Introduction to PDB Format

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