XYZ Format

XYZ files contain atomic coordinates. While variants of the format exist, Chimera reads XYZ files that conform to the following:

First line: total number of atoms (optional)
Second line: molecule name or comment (optional)
All other lines: element symbol or atomic number, x, y, and z coordinates, separated by spaces, tabs, or commas

Example:

12
glucose from 2gbp
C  35.884  30.895  49.120
C  36.177  29.853  50.124 
C  37.296  30.296  51.074 
C  38.553  30.400  50.259  
C  38.357  31.290  49.044  
C  39.559  31.209  48.082  
O  34.968  30.340  48.234  
O  34.923  29.775  50.910  
O  37.441  29.265  52.113  
O  39.572  30.954  51.086  
O  37.155  30.858  48.364  
O  39.261  32.018  46.920

XYZ files can be opened in many ways, like other registered file types. The file type can be indicated with a suffix (.xyz, part of the filename) or a prefix (xyz:, not part of the filename).

MD Movie can read a trajectory from multiple XYZ files, one per frame.

UCSF Computer Graphics Laboratory / December 2009