VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 26 2007 - 15:19:17 CDT

Hi,
  You can avoid having VMD calculate bonds by adding
"autobonds off filebonds off" to the "mol new" command
to load your fake PDB (same works for other formats).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 22, 2007 at 06:04:40PM -0700, Arneh Babakhani 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
>
> 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
> >>
> >
> >
> >
> > 

-- 
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