## VMD-L Mailing List

**From:** Arneh Babakhani (*ababakha_at_mccammon.ucsd.edu*)

**Date:** Fri Jun 22 2007 - 20:04:40 CDT

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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
*

*>>
*

*>
*

*>
*

*>
*

*>
*

**Next message:**Petrica GASCA: "Re: Text/Labels on ray tracing external renderer"**Previous message:**John Stone: "Re: Using VMD just to plot some coordinates from a mathematical/geometrical model"**In reply to:**John Stone: "Re: Using VMD just to plot some coordinates from a mathematical/geometrical model"**Next in thread:**Axel Kohlmeyer: "Re: Using VMD just to plot some coordinates from a mathematical/geometrical model"**Reply:**Axel Kohlmeyer: "Re: Using VMD just to plot some coordinates from a mathematical/geometrical model"**Reply:**John Stone: "Re: Using VMD just to plot some coordinates from a mathematical/geometrical model"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]