On Jan 13, 2016, at 9:58 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

(1) after reading in the XYZ file, add bonds manually yourself, for example, select two “atoms” (Ctrl-click, Shift-Ctrl-click) and then use command “bond sel”.  Repeat.  This could be tedious if you have a lot of bonds to add.  You could also use atom names instead of selecting, for example “bond @c1,c2”.  Although the XYZ file doesn’t contain atom names, “atoms” of the same “element” will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html>