VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 16 2014 - 17:01:41 CST

Hi,
  If the bond is defined in the structure file you loaded (e.g. PSF file),
then VMD will draw it. To hide those bonds, you would need to delete
them. When showing ball-stick type representations, VMD draws the bonds
exactly as they are defined by the structure, so you'd need to delete the
bonds to get VMD to avoid showing them. If you loaded a file format that
doesn't define bonds, and VMD guessed the bonds, then it may be an issue
with the assignment of atoms types, VDW radii, and the default bond
guessing scheme VMD uses. If you provide more information about your
specific case, someone can undoubtably suggest ways to get what you want.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 16, 2014 at 05:53:54PM -0500, Sanjib Chowdhury wrote:
> Hi,
>
>
>
> When I visualize my water model in VMD using cpk or bond drawing method,
> it shows bonding between H in the water
>
> molecule. How I can avoid this? I guess I need to change the bond order
> cut-off value. How can I change it in VMD?
>
>
>
> I will appreciate your suggestion.
>
>
>
> Thanks,
>
> Sanjib
>
> 

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