VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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
commands.

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.

cheers,
    axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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If you make something idiot-proof, the universe creates a better idiot.