VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 13 2004 - 16:44:44 CDT

Hi,
  The top of the tcl script has some brief example instructions.
In your case, do something like this:
  mol new fixed.xyz
  source deleteallbonds.tcl
  deleteallbonds top all
 
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 13, 2004 at 04:21:16PM -0500, Jayendra Balasubramanian wrote:
> Hi John,
>
> Thanks for the help. I don't know much about tcl
> scripts...how do I run this in vmd to make it delete the bonds?
>
> Thanks,
> Jayendra.
>
>
>
>
>
>
>
>
> >
> > Hi,
> > Looking at your files, the first file is malformatted, because it
> > begins with a blank line and ends with a header for a missing
> > dataset.
> > Correcting those two problems allows the first file to load
> > correctly.
> > The second file is also malformatted, because it lacks the headers
> > that belong in each data set.
> >
> > I've attached the fixed version of your first file.
> > You'll note that even with the fixed version, you'll get bonds that
> > probably aren't what you want since VMD does a distance-based bond
> > determination on files (such as XYZ files) that don't provide bond
> > information.
> >
> > You can't hide the bonds via the labels menu, if you need to remove
> > bonds, you must do that with a script such as the one I've attached
> > to this email. The hide option in the labels menu is only for
> > hiding
> > distance measurement (aka bonds) labels that were added to the scene
> > and has no effect on bonds between atoms.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Apr 13, 2004 at 03:35:46PM -0500, Jayendra Balasubramanian
> > wrote:
> > > Hi,
> > >
> > > I'm attaching two files formatted differently...the first
> > > one 'ArOPT.xyz' vmd doesn't read.....the second one 'ArOPT1.xyz'
> > vmd
> > > does read but like I said it draws bonds between atoms and when I
> > go
> > > to the Labels menu to try to hide the bonds it doesn't show any
> > atoms
> > > in the list.
> > >
> > > Thanks,
> > > Jayendra.
> >
> > --
> > 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