From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 14 2006 - 00:18:33 CST

Hi,
  You can't change the built-in automatic bond determination behavior,
but you can redefine what bonds exist via scripting or with the mouse if
you wish. I'm curious what sort of structure you're having trouble with
such that you want to change the default bond distance heuristic?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 07, 2006 at 01:12:42PM -0800, Weiqiang Wang wrote:
> Hi, John:
>
> Thanks for your reply!
> I think I mispresented my question. :0
> I was more interested in knowing how VMD calculate the number of bonds for each atom (from a given PDB file).
> The reason I'm asking is that I saw in the selection menu, there is an option "numbonds". So, it seems that VMD uses a default cutoff distance (~1.6A ?) to calculate if one atom is bonded to another. And I think it would be nice for me to be able to change the default cutoff distance value, which will result a different value for "numbonds".
> thank you for your time.
>
> Weiqiang Wang
>
>
> ----- Original Message -----
> From: John Stone <johns_at_ks.uiuc.edu>
> Date: Tuesday, March 7, 2006 11:59 am
> Subject: Re: vmd-l: change default bond cutoff distance
> To: Weiqiang Wang <wangweiq_at_usc.edu>
> Cc: vmd-l_at_ks.uiuc.edu
>
> >
> > Hi,
> > At present, VMD doesn't calculate the bond order, it either gets
> > thisinformation from a loaded file which contains bond order
> > information(such as Biograf, MOL2, etc..) or it sets the bond
> > order to a default value
> > of 1.0 if VMD's automatic bond determination code ends up being
> > invoked.
> > You can set the bond orders yourself using atom selections if you
> > have
> > a way of calculating them. The automatic bond calculation code in VMD
> > is just a relatively simple heuristic which can potentially be
> > tricked by
> > unusual atom names, bad VDW radii, or other bad parameters, so if
> > you really
> > need accurate bond information, the best thing to do is to provide
> > it to
> > VMD in the structure files you load. That said however, you can
> > changethe bond information in VMD on the fly as you wish, either
> > by manually
> > correcting any incorrect bonds with the mouse, or by writing scripts.
> > Let us know if you need more help with this.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Mar 07, 2006 at 01:25:53AM -0800, Weiqiang Wang wrote:
> > > Hi
> > >
> > > Is there a way of changing the default cutoff distance used in
> > calculating the bond order in VMD?
> > > This way, I wish VMD would be able to give me a different
> > numbond value other than the one calculated from the default
> > cutoff distance.
> > >
> > > Thanks.
> > >
> > > Weiqiang Wang
> >
> > --
> > 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
> >

-- 
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