From: Norman Geist (
Date: Thu Sep 24 2015 - 02:31:36 CDT

Nonsense, changing the box makes everything wrong.


Use the periodic feature of representation. You might need several
representations. You can hide the original image using the periodic tab and
use selections like:


x > 25 and y > 25 and z > 25


to restrict your „non integer“ area of the box.

You might want to enable “update selection every frame” on the trajectory


Norman Geist


Von: [] Im Auftrag von
Morgan, Brittany
Gesendet: Mittwoch, 23. September 2015 15:36
An: Francesca Lønstad Bleken <>;
Betreff: vmd-l: RE: visualising unit cell "plus a little more"


You could try redefining the size of the periodic cell to be a little bit
bigger using "pbc set {X Y Z} -all".



From: <>
[] on behalf of Francesca Lønstad Bleken
Sent: Wednesday, September 23, 2015 5:34 AM
To: <>
Subject: vmd-l: visualising unit cell "plus a little more"



I would like to visualize the unit cell "plus a little more" in each
direction in order to see all the atoms at the cell edges. I have found that
you can extend the unit cell by multiple images in the graphical
representations box under periodic, but is there a way to do this in
non-integers? I imagine it should be possible in the console, but have not
found it.


What I want is to show all atoms within -0.1 and 1.1 of the unit cell in all


I think I can do this by making a 3x3x3 periodic structure and manually
choose which atoms to be shown and not, but it would be great if there was a
less cumbersome method to do this.


Best regards,



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