From: John Stone (
Date: Fri Jun 22 2007 - 13:24:30 CDT

  I'm not sure what you're asking here. VMD preserves the original
coordinates of the structures after they are loaded. The viewing
transformations applied for graphical scaling/rotation/translation
are completely independent from the atom coordinates. You can
query the atom coordinates using a selection to verify this for
  set sel [atomselect top all]
  $sel get {x y z}

If you're writing PDB files by hand, you need to make absolutely
sure that you've got the PDB columns lined up since it is a column
based format. If you write the coordinates into the wrong columns,
you'll get gibberish from VMD (and any other program....)

  John Stone

On Fri, Jun 22, 2007 at 11:10:06AM -0700, Arneh Babakhani wrote:
> Hello,
> I have a brief question about loading up pdb files in VMD. I noticed
> that when I load up a pdb file, one of the atoms is placed at the origin
> {0 0 0} and the rest are plotted around that. For instance, for the
> simple pdb file:
> ATOM 1 H XXX A 1 2.00 2.00 0.00 H
> ATOM 2 H XXX A 1 0.00 2.00 0.00 H
> the fist hydrogen atom is placed at {0 0 2}, the second is placed at {0
> 0 0}. So the distance between the two atoms is correct, but they're
> coordinates are different from what actually appears in the pdb file.
> So my question is, how can I load up the pdb file such that the atoms
> are placed in the 'absolute' coordinates of file? And how can I do that
> from the TCL command line, is there an option to 'mol load pdb
> whatever.pdb' ?
> Thanks,
> Arneh

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