VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 06 2003 - 11:04:57 CDT

Ramesh,
  There's currently no way to override the automatic bond-determination
heuristic with your own values. However, you can use the "dynamic bonds"
representation in VMD to get what you want in 95% of the cases.
A superior alternative would be to build a PSF structure file which
contains explicit bond information, as well as atom radii and other info
that VMD is forced to guess for itself when it is only provided with a
PDB file. Let me know if you need more help getting what you want out of
the dynamic bonds representation.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 06, 2003 at 01:24:34PM +0530, Ramesh K. Sistla wrote:
> Hello List!
>
> I am using VMD to plot some configurations of inorganic glasses. They
> contain atoms Li, P and O. When I load the pdb, it connects the P and O
> as per its own default value. How can I change this default value? I
> read somewhere that, vmd takes R1*R2*0.6 as the default bond length
> where R1 and R2 are radii of the two atoms. Hope my query is clear.
> Thanks in advance for any help.
> regards
> --
> :-)
> ramesh k. sistla
>
> The Prayer of India:
> --------------------
> lOkAh samastAh suKhinO bhavantu -- Let the entire world be in peace!
>
> If we can go above our own personal hardships and see the problems of
> others and decide to work for a larger cause, then there is natural
> elevation of our mind.
> - President A.P.J.Abdul Kalam 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078