From: Peter Freddolino (
Date: Sun Jul 01 2007 - 13:40:52 CDT

Hi Francesco,
you can use a script like the following to label all of the atoms with
their serial number:

set sel [atomselect top all]
set graphicsmol [mol new]
foreach xyz [$sel get {x y z}] serial [$sel get serial] {
    graphics $graphicsmol text $xyz $serial
display resetview

You can then delete the numbers with
mol delete $graphicsmol

Note that when you are in mouse mode 1 (atom pick), simply clicking on
an atom will print its index, name, and some other information to the
vmd console.

You should be able to modify the atom selection listed above to suit
your purposes.


Francesco Pietra wrote:
> The "small" organic molecule is at the forefront of my problems with MD, and I
> need to locate the atoms in space with respect to the "atom serial number" in
> pdb files.
> I have loaded into VMD 1.8.6 the molecule in attachment (which makes part of
> amber tutorials), I have printed the pdb file, noticed that it it is an
> abridged form of pdb file and that, even in this restricted form, it digresses
> from pdb rules (atom Cl, for chlorine, should be left-justified at column 13).
> This is no criticism, it is only to learn how to refine pdb files for my
> unpublished organic molecules in view of MD.
> As taking into account stereochemistry is a must in my studies, may I ask
> advice in locating the atoms in space through VMD 1.8.6? Though it is
> irrelevant to the case in attachment, this one will teach me how to deal with
> cases where stereochemical assignments are relevant.
> I have read about the "atom select" command of VMD. Is that the way? Is any
> possibility of graphical output on the VMD screen of the "atom serial number",
> or anything that can be related to that? In practice, I want to know which is
> which for H3/H4, F1/F2/F3, and so on.
> Thanks
> francesco pietra
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