From: Arneh Babakhani (
Date: Fri Jun 22 2007 - 17:51:35 CDT

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

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!