VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 11 2007 - 11:06:17 CDT

Hi,
  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
  vmd_at_ks.uiuc.edu
 
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. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078