From: John Stone (
Date: Fri May 11 2007 - 11:06:17 CDT

  If I understand your question correctly, you wish to display the text labels
for all atoms?

If so, you can use a simple script like this one, to add labels
for any selection you like:

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

You'd call this with something like:
  set molid [molinfo top]
  label_atoms $molid "name CA"

If you want to draw your own text labels for each of the atoms
(rather than using the built-in labeling feature) you can also
devise a script that does this, for example:

proc show_partial_charge { selection } {
  set sel [atomselect top $selection]
  foreach q [$sel get charge] pos [$sel get {x y z}] {
    set qstr [format %4.3f $q]
    graphics 0 text $pos $qstr

You'd call this with something like:
  show_partial_charge "residue 0"

You can of course modify this to do anything you like.

  John Stone
On Fri, May 11, 2007 at 01:49:10PM +0200, Petrica GASCA wrote:
> Hello,
> I am a new user of VMD and I am trying to get used to it on a Linux machine.
> What is really important for my work is to see atom numbers (the index field
> from the Labels window).
> Is there any possibility to show them as atom labels the same way that we
> can see the name of the atom when we select them manually?
> Thanks in advance.

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