VMD-L Mailing List

From: Weiqiang Wang (wangweiq_at_usc.edu)
Date: Tue Mar 14 2006 - 02:11:22 CST

Thanks for the reply.
And the structure I'm studying is a simple a-SiO2 system. Because it's amorphous, the first peak position of the Si-O bond pair distribution is broadened to a range of 1.50-1.80A. So, when I want to look at the Si atoms (which normally has 4 bonded Oxygen atoms) by using selection "name Si and numbonds=4", VMD then couldn't give me a correct display result, because VMD calculates the bond using the default cutoff distance 1.6A.
The "dynamic bond" is a good feature of VMD, but when I want to look at those defects (i.e. when I want to show only the Si atoms having 3 bonded oxygen atoms), I can't find a way out.

Weiqiang Wang

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Monday, March 13, 2006 10:18 pm
Subject: Re: vmd-l: change default bond cutoff distance
To: Weiqiang Wang <wangweiq_at_usc.edu>
Cc: vmd-l_at_ks.uiuc.edu

>
> 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
> withsuch 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
>