VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 22 2007 - 15:01:26 CDT

Hi,
  Well, in some cases yes, the PDB plugin will determine that
something is terribly wrong and abort. One of the difficulties
of colummn-based file formats is that you can chop off several digits
of a number and still end up getting a valid read call on that field,
even though the value has been completely mangled. Anyway, now you've
seen the dark musty corners of the PDB file format :-)

  John

On Fri, Jun 22, 2007 at 01:04:24PM -0700, Arneh Babakhani wrote:
> Ok thanks. I guess I was confused because I thought if there was
> something wrong with my pdb file to begin with, it wouldn't be read in
> at all.
>
> Thanks,
>
> Arneh
>
> John Stone wrote:
> >Yes, the whitespace in a PDB file MUST BE EXACT, that's what I meant
> >when I said it was a column-based file format. Please see the PDB
> >file format specifications for more details:
> > http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
> >
> >Note the specific columns that deliniate the fields within an ATOM record.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Jun 22, 2007 at 12:38:42PM -0700, Arneh Babakhani wrote:
> >
> >>Yes, you're right, thanks. So the amount of whitespace in a pdb file
> >>must be exact? I thought most readers can parse that out? That's a
> >>very important lesson! Thanks for your help,
> >>
> >>Arneh
> >>
> >>Giovanni Bellesia wrote:
> >>
> >>>looks like your pdb is not formatted correctly:
> >>>Try this:
> >>>
> >>>ATOM 1 H XXX 1 2.00 2.00 0.00 H
> >>>ATOM 2 H XXX 1 0.00 2.00 0.00 H
> >>>END
> >>>
> >>>it worked for me.
> >>>
> >>>You also might want to take a look at this:
> >>>
> >>>http://www2.cs.uh.edu/~chandler/chem/PDBSpec.html
> >>>(9. Coordinate Section)
> >>>
> >>>
> >>>>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