From: Axel Kohlmeyer (
Date: Sun Sep 07 2008 - 13:41:30 CDT

On Sat, 6 Sep 2008, Alfred Shaohui Zheng wrote:

ASZ> Dear all,
ASZ> I have molecular dynamics trajectory file. It is XYZ coordination
ASZ> file.
ASZ> Due to VMD default setting, my complex shows no bonding between
ASZ> metal center atom and ligand. Could anyone tell me how to drawing bonds
ASZ> between two atoms using VMD command window or console?

have a look at the subcommands "getbonds" and "setbonds" to
atomselection functions/variables generated by the atomselect

you can also manipulate bonds manually using the mouse (see mouse menu)
and then save the result in a (visualization only) .psf file with

animate write psf with-bonds.pdf

in the command window. other than that, you can study the mailing
list archives for additional hints, optrions and trickt. this kind
of question comes up regularly.


ASZ> Thanks a lot.
ASZ> With best regards,
ASZ> Shaohui Zheng

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.