VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 13 2004 - 15:59:32 CDT

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
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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