VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 27 2011 - 12:42:54 CDT

Hi,
  You can do this with some scripting. Here is a simple example
that creates labels for all of the atoms. Doing this for all of
the bonds would be similar:
  
proc label_atoms { molid seltext } {
  set sel [atomselect $molid $seltext]
  set atomlist [$sel list]
  foreach {atom} $atomlist {
    set atomlabel [format "%d/%d" $molid $atom]
    label add Atoms $atomlabel
  }
  $sel delete
}

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 27, 2011 at 05:43:18PM +0100, Mike Wykes wrote:
> Hi there,
>
> I am a VMD novice and would greatly appreciate some help.
>
> Could someone tell me if it is possible to label all the
> covalent/coordinate bonds in a system (i.e. bonds shown by VMD when
> using the lines/bonds drawing method) without having to manually click
> every pair of bonded atoms ?
>
> I imagine this must somehow be possible via the tcl command line, but
> I have no idea where to start.
>
> Could someone possibly point me in the right direction on how to go
> about generating the required command?
>
> Many thanks,
>
> Mike 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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