VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 22 2007 - 17:51:59 CDT

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