VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 20 2012 - 11:03:06 CST

On Fri, Jan 20, 2012 at 11:57 AM, Zumot, Elia Nabil <enz1_at_pitt.edu> 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)

there is none. just re-read my last e-mail.

the main problem is not the radii itself, but
that apparently VMD doesn't know from the
data that you provide which radius to use.

and - again - like i wrote before you can easily
reset those to anything you like using VMD scripting.
no need at all to mess with any VMD internals.

axel

>
> 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 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.