## VMD-L Mailing List

**From:** John Stone (*johns_at_ks.uiuc.edu*)

**Date:** Fri Jun 22 2007 - 17:51:59 CDT

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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

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