VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 22 2007 - 13:52:21 CDT

Hi,
  I think you must have a misformatted file if you're getting a different
coordinate from the atom selection than what you see in the file.
The viewing transformations only affect the _display_ of the molecule,
and do not affect the atom selections, coordinates, or measuring parts
of the program at all. Please check that your PDB file is correctly
formatted, or else send me a copy and I'll check it for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 22, 2007 at 11:50:59AM -0700, Arneh Babakhani wrote:
> Thanks, let me try to clarify.
>
> Assuming the pdb is formatted correctly, when I load it up and query the
> coordinates of say the first atom, I get this:
> >Main< (PracticeVMD) 67 % [atomselect top "index 0"] get {x y z}
> {2.0 0.0 0.0}
>
> But this does not match up with the coordinates in the actual pdb file,
> where the coordinates for the first atom are {2.0 2.0 0.0}, b/c of what
> you stated below (the viewing transformation is independent of the atom
> coordinates).
>
> My question is, how can I load up the pdb without such a viewing
> transformation? In other words, when I do 'get {x y z}', I want the
> result to be the exact coordinates found in the pdb file.
>
> Thanks,
>
> Arneh
>
>
>
> John Stone wrote:
> >Hi,
> > 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
> >yourself:
> > 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....)
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >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
> >>END
> >>
> >>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
> >>
> >
> > 

-- 
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