VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jun 22 2007 - 20:04:40 CDT

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
>>
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