From: Samuel Jobbins (
Date: Mon Mar 30 2015 - 11:28:54 CDT

Hi Josh and Axel,

Thanks a lot guys - you've both been very helpful and I've got enough information now to fix the problem. Apologies once again for my ignorance!


From: Josh Vermaas <>
Sent: 30 March 2015 17:14
To: Samuel Jobbins;
Subject: Re: Fw: vmd-l: Colour coordinating atoms in a trajectory by Coordination Number

Definitely making it too complicated. :D If you have the labels in what sounds like an xyz or pdb format, you could load each frame individually into VMD, copy over the label pieces into user, and then color by user. Labels are supposed to be static and unchanging throughout the simulation, so this is why you are having some difficulties, as VMD will read the labels/atomnames from the first frame and not let them change. The file formats just weren't designed with this in mind, since for most applications, the names of atoms don't change, and it saves storage space. Basically you'd need to get around this limitation by reading in one frame at a time, and copying the label over to a field that is allowed to change with time.


On 03/30/2015 10:13 AM, Samuel Jobbins wrote:

Hi both,

Thanks for your prompt responses and the help you've posted so far.

Sadly I'm still struggling to get VMD to do what I want. I don't need to compute the first coordination sphere as I already have that data in a separate file. I've used that data to generate a trajectory of 3200 frames, each with 2400 atoms, where the atom label has an integer after it denoting its CN. For example, Zn3 would correspond to a zinc atom coordinates to three other atoms.

As this is a trajectory of a phase transition, the coordination of each atomic site changes through the trajectory, such that Zn3 might be Zn6 in the final frame. I just want to be able to colour coordinate each atom in my xyz by its label - i.e. for the label to be read each frame, rather than just from the initial frame. This way, I can observe how the coordination changes in local parts of the structure during the transition.

Is this possible in this way, or do I have to calculate the CN in VMD? I am really sorry if this is a silly question, but I am relatively inexperienced with the finer workings of VMD. I may very well be over simplifying (or over complicating!) the problem.

Thanks so much,


From: Josh Vermaas <><>
Sent: 26 March 2015 17:12
To: Samuel Jobbins;<>
Subject: Re: vmd-l: Colour coordinating atoms in a trajectory by Coordination Number

Hi Sam,

Set the per frame user field. For instance, if your coordination numbers for 5 atoms never changed, here is what you might do:

set CN [list 1 2 3 4 5]
set sel [atomselect top "index 0 to 4"]
for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
$sel frame $f
$sel set user $CN

There are also 3 more per-atom user fields if you need them (user2, user3, and user4). Naturally you'd want to calculate the coordination number within the loop.

-Josh Vermaas

On 3/26/15 9:57 AM, Samuel Jobbins wrote:

Hello everyone,

I have a trajectory of a phase transition in XYZ format, along with coordination sphere data for each atom in each frame of the trajectory.

I am trying to visualise the trajectory on VMD and I would like to colour coordinate the atoms by their coordination number. I was planning to do this by changing the labels of the atoms in each frame corresponding to their CN, such that one could interactively see the evolution of each atom's CN. However, I've noticed that VMD seems to only take the labels from the first frame of the trajectory, and keep them constant throughout the simulation.

I have tried using different 'real' atomic labels (such as replacing Zn with Cu, Fe, Co etc, depending on CN) as well as dummy labels (eg Zn3, Zn4, Zn5 to indicate CN). I've also tried using different file types (e.g. pdb). However, every time VMD only takes the label from the first frame.

Does anyone know a way around this?

Sorry if this is a very mundane question, but I cannot find a solution to this problem!

Thanks for your time,