From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 20 2012 - 14:05:58 CST

Hi Elia,
  The way VMD assigns atomic properties (e.g. radii, masses, etc) depends
greatly upon what file formats you used when you loaded the structure into
VMD. Some file formats provide VMD with explicit values for all of the
key atomic properties, other file formats provide nothing but the atom
name and coordinates. In the cases where the files loaded do not contain
an atomic property such as the radius, VMD has to "guess" this information
using some combination of the atomic properties that the file does specify.
Some VMD molecule file reader plugins also contain their own atomic
property lookup tables because they are able to do a better job at guessing
than VMD can because they have access to file-format-specific details that
VMD doesn't know about. So, the particular strategy that is used for a given
structure depends directly on the details of what files you loaded, what
file formats they were stored in, and what information was contained therein.

If you me us more about what files you're loading, I can tell you how the
radii are getting assigned.

Axel's suggestion is a simple way to address the immediate problem by
overriding the auto-assigned radii with an atom selection command.

Cheers,
  John

On Fri, Jan 20, 2012 at 11:57:19AM -0500, Zumot, Elia Nabil wrote:
> Thank you Axel.
>
> Could you direct me to the file that contains the atomic radii that are displayed in VMD?
>
> (I have found the PeriodicTable.C file but it contains the correct ionic radii)
>
> Best
>
> Elia
>
>
>
>
> 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
> ________________________________________
> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Thursday, January 19, 2012 10:12 PM
> To: Zumot, Elia Nabil
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ionic radii of sodium and chloride
>
> 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

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078