VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 10 2005 - 22:44:16 CDT

Nicolas,
  I took another look at your BigConfig.pdb file, the source of
your problems is that you've got a large number of atoms that are
only a fraction of an Angstrom apart, particularly in the rod structure
that passes through your protein. This is the cause of the problems you
were having loading that structure. It seems likely that your coordinates
were in nanometers rather than Angstroms? That'd explain the problems
you were having with VMD. The bond determination code gets unhappy when
the atom density is 1000 times what it ought to be. ;-) I'll see if I can
make VMD more resistant to bad behavior with structures that have incorrect
units like this one.

  John

On Mon, Apr 04, 2005 at 12:31:31PM +0200, Nicolas CHARVIN wrote:
>
> >To load it, get the files in that directory, then execute VMD with:
> > vmd -e virus-simple.vmd
> >
> >Does VMD successfully render the structure on your machine?
>
> yes, it loads very smoothly. I get 2.8 fps in VDW mode, and 62 fps
> (maximum) in lines mode.
> By the way, the "Determining bond structure from distance search" seems to
> perform very quickly for a 395250 atoms molecule.
>
> When I try to load my "test" big molecule ( 640,000 atoms, grab it at
> http://www.univ-savoie.fr/labos/lmops/people/ncharvin/bazar/BigConfig.zip)
> , I get a "MolAtom #### : Exceeded maximum number of bonds (8)" error
> during "Determining bond structure from distance search" phase, and it
> seems to loop forever on Molatom number, which is new (vmd 1.8.2 crashed).
> By the way, Qmol can read and render it fairly smoothly.
>
> I do not know much about this big molecule, and about bonds and structure,
> stuff like that, so maybe theres are more than 8 bonds. That may explain
> why VMD refuse to load it.
>
> [...]
>
> Heyy ??? I've just generated a solvation box of 1.3 Million atoms, with
> "Solvate Plugin".
> I try to load solvate.pdb
> (http://www.univ-savoie.fr/labos/lmops/people/ncharvin/bazar/solvate.zip) ,
> WITHOUT using solvate.psf file, and it works perfectly, with the
> "Determining bond structure from distance search" phase.
>
> It seems something is wrong with my BigConfig.pdb...
>
> Any ideas ?
>
> Thanks in advance
>
> nicolas
>
> --
> Nicolas.Charvin_at_univ-savoie.fr
> LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
> Bât IUT - Université de Savoie
> 73376 LE BOURGET DU LAC CEDEX
> Tel: 04-79-75-86-53
>
> http://www.univ-savoie.fr/labos/lmops
> 

-- 
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