VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 15 2006 - 18:35:02 CST

Since there's not a built-in way to do this sort of thing, I don't have a
good short-term solution other than hacking the source code. One possibility
which I came up with but have not looked at closely yet would be to add a
new command to force VMD to recalculate all bonds with a user-specified
cutoff etc, but I don't yet know if this is practical or will cause
other problems. I may see about adding such a command as that would
give you an easy solution. Other than that, the best way to get correct
bonding is to specify it yourself, either by scripting or by loading a file
format like PSF, that fully specifies connectivity.

  John Stone
  vmd_at_ks.uiuc.edu
  

On Tue, Mar 14, 2006 at 12:11:22AM -0800, Weiqiang Wang wrote:
> 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
> > 

-- 
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