XYZ file format

From Wikipedia, the free encyclopedia
Jump to: navigation, search
".xyz" redirects here. For a top-level domain, see .xyz (top-level domain).
XYZ format
Filename extension .xyz
Internet media type chemical/x-xyz
Type of format chemical file format

The XYZ file format is a chemical file format. There is no formal standard and several variations exist, but 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.[1] The file format is used in computational chemistry programs for importing and exporting geometries. The units are generally in ångströms. Some variations include using atomic numbers instead of atomic symbols, or skipping the comment line. Files using the XYZ format conventionally have the .xyz extension.

Format[edit]

The formatting of the .xyz file format is as follows:

<number of atoms>
comment line

XYz

Example[edit]

The methane molecule can be described in the XYZ format by the followings:

5
methane molecule (in ångströms)
C        0.000000        0.000000        0.000000
H        0.000000        0.000000        1.089000
H        1.026719        0.000000       -0.363000
H       -0.513360       -0.889165       -0.363000
H       -0.513360        0.889165       -0.363000

Animation[edit]

Most molecule viewers such as Jmol and VMD can show animations using .xyz files. The following is an example xyz format for m successive snapshot which can be rendered as an animation:

<number of atoms>
comment line
atom_symbol11 x-coord11 y-coord11 z-coord11
atom_symbol12 x-coord12 y-coord11 z-coord12
...
atom_symbol1n x-coord1n y-coord1n z-coord1n
<number of atoms>
comment line
atom_symbol21 x-coord21 y-coord21 z-coord21
atom_symbol22 x-coord22 y-coord21 z-coord22
...
atom_symbol2n x-coord2n y-coord2n z-coord2n
.
.
.
<number of atoms>
comment line
atom_symbolm1 x-coordm1 y-coordm1 z-coordm1
atom_symbolm2 x-coordm2 y-coordm1 z-coordm2
...
atom_symbolmn x-coordmn y-coordmn z-coordmn

Note that the xyz standard does not require that the number or chemical nature of atoms should be the same at subsequent snapshots, which allows for atoms disappearing from or coming into the field of view during the animation.

References[edit]

  1. ^ "The XYZ file specification". OpenBabel.