VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Mar 26 2015 - 12:12:29 CDT

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,
>
> Sam
>