From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 19 2012 - 21:12:49 CST

On Jan 19, 2012, at 10:03 PM, "Zumot, Elia Nabil" <enz1_at_pitt.edu> wrote:

> Dear VMDers,
>
> Any reason why VMD shows sodium ions to be bigger than chloride when it should be the other way around?
>
> In crystals the radius of Na+ is 0.095 nm and that of Cl- 0.181 nm.
>

That is because VMD cannot tell the difference between an element and
an ion or a chlorine or chloride and a carbon.

If you don't like VMD's choices you can always write a little script
that changes it or use a file format that does contain the radius
information in a way that VMD supports reading it.

VMD is very deliberately a very dumb and ignorant software that relies
on you to provide it with the proper information. It does not even try
to be smart (for the most part, that is).

Axel

>
> Thanks
>
> Elia Zomot
>
>
>
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 624 8699 - Fax: 412 648 3163
> enz1_at_pitt.edu