VMD-L Mailing List

From: Jayendra Balasubramanian (balas002_at_bama.ua.edu)
Date: Tue Apr 13 2004 - 16:21:16 CDT

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
> 

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