VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 14 2002 - 15:25:53 CST

Hi,
  You could use a forged "PSF" file with your PDB so that VMD
reads the connectivity information (or lack thereof) from the fake
PSF file, then it will not attempt to do the bond determination for
itself. If these aren't really atoms, then perhaps you'd be better
off just using the "draw" commands in VMD to render spheres or points?
If they are atoms, but not meant to be a normal structure, then forging
a fake PSF file is definitely the way to go at the present time.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 14, 2002 at 12:31:17PM -0800, Christophe Guilbert wrote:
> Dear VMD users,
>
> I create a big PDB file which contains only "dummy" atoms.
>
> Many of those atoms overlap and it take hours to VMD to download them
> since VMD tries to redefine the atoms connectivities and generate a
> lot's of error message: "ERROR) MolAtom 3057: Exceeded maximum number of
> bonds (8)."
>
> Is there a way to avoid that ?
>
> Thanks
>
> Chris
>
> --
> --------------------------------------------------------------------------
> Christophe Guilbert, Ph.D.
> Dept. of Pharmaceutical Chemistry, box:0446
> University of California
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> office phone: 415-476-0707
> office fax : 415-476-0688
> email: cguilbert_at_picasso.nmr.ucsf.edu
> http://picasso.nmr.ucsf.edu/~cguilbert/
> --------------------------------------------------------------------------
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> who needs Windows and Gates?
> - Sun Microsystems 

-- 
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              
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