From: Samuel Bowerman (
Date: Wed Jan 20 2016 - 16:54:23 CST

Hi Reza,

You can change the "atom" label to display indices the following way:

In the Main window, pull down the "Graphics" tab and choose "Labels..."
Click on the "Properties" tab, then change "Format" to be "%i".

If you turn on Tcl logging "File -> Log TCL commands to Console", then you
can learn all the text commands for this to streamline the process to all
your atoms of interest by some sort of list iteration or for loop. I'll
leave that to your own discretion, though.

Take care,

On Wed, Jan 20, 2016 at 4:28 PM, reza vatan <> wrote:

> Dear all,
> I tried a lot to find a way to ask VMD to label the all atoms in my loaded
> xyz structure by their own indexes (numbers), but without success. Could
> anyone please help me with that problem?
> Best,
> Reza