From: Weiqiang Wang (wangweiq_at_usc.edu)
Date: Tue Mar 07 2006 - 15:12:42 CST

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
>
> --
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> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
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>