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).

Chimera will assign unique atom names based on element and order of occurrence in the file. For example, the first carbon will be C1 and the first oxygen will be O1.

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

UCSF Computer Graphics Laboratory / June 2014