From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Jun 23 2007 - 09:23:20 CDT

On 6/22/07, Arneh Babakhani <ababakha_at_mccammon.ucsd.edu> wrote:
> Thanks John,
>
> I thought about doing it that way. But ultimately, I'd also like to
> animate these coordinates, and make a movie. So I thought about loading
> up these fake pdb files (each pdb file corresponding to a frame), and
> just hitting play.
>
> Is there a better way to do this?

arneh,
there might be an interesting alternative. i agree, it is indeed
more convenient to generate frames and render your speheres
as atoms.

however, if you want to determine the bonding pattern, the best
file type would be a .psf file, and then - depending on how large
the computational effort - you could do your whole generation of
coordinates within VMD (creating a selection for all atoms, then
use animate dup to generate a new frame, and using $sel set {x y z} $some_list
to set the coordinates. if you generate your coordinate output from a
c/c++ code, you can even wrap it into a tcl command and dynaload
and execute it from within VMD.

i have used each of the techniques separately (and can provide examples).

cheers,
    axel.

> Arneh
>
> John Stone wrote:
> > Hi,
> > For drawing your own non-atomic geometry, I'd suggest using the "draw"
> > commands rather than making fake PDB files. Try something like this:
> > draw sphere { 0 0 0 } radius 1.0
> > draw sphere { 0 1.18 0 } radius 1.0
> > draw sphere { -1.13 1.18 0 } radius 1.0
> > draw sphere { 1.13 1.18 0 } radius 1.0
> >
> > You can write those commands to files and have VMD read them with
> > a command like: source mystuff.tcl
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Fri, Jun 22, 2007 at 03:51:35PM -0700, Arneh Babakhani wrote:
> >
> >> Hi, Ok, I have the following pdb of four hydrogen atoms:
> >> HETATM 1 H XXX 1 0 0 0.00 H
> >> HETATM 2 H XXX 1 0 1.18 0.00 H
> >> HETATM 3 H XXX 1 -1.13 -0.34 0.00 H
> >> HETATM 4 H XXX 1 1.13 -0.34 0.00 H
> >> END
> >>
> >> I've also attached this as a file, if you'd like to play with it. When
> >> you load this up into VMD, it plots the 4 hydrogen atoms correctly and
> >> bonds them together (the one at the origin is bonded to the other three,
> >> forming a triangle shape in CPK rep).
> >>
> >> My question is: Can I put something in the PDB file that'll tell VMD to
> >> NOT make any bonds? In other words, the only thing I want to see (in
> >> CPK mode) are 4 spheres at the above coords, not connected to each
> >> other. I know there's an 'add/remove bonds' feature in VMD, but I'd
> >> really like to have something inherent in the PDB file that'll tell VMD
> >> not to make bonds (if that's possible).
> >>
> >> If you're wondering what the hell I'm doing, I'm trying to use VMD as a
> >> graphical interface for a mathematical/geometrical model, having nothing
> >> to do with chemistry. I love the GUI of VMD, so I'm trying to use it,
> >> instead of re-inventing the wheel and writing something new in OpenGL.
> >> So I'm creating a 'fake' pdb file, trying to plot these coordinates and
> >> connect them later in a manner that I wish (not in a manner that VMD
> >> thinks is chemically correct). If you have any better suggestions
> >> regarding this endeavor, please let me know!
> >>
> >> Thanks,
> >>
> >> Arneh
> >>
> >
> >
> >
> >
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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If you make something idiot-proof, the universe creates a better idiot.