From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Sat Jun 23 2007 - 10:29:11 CDT

That was an excellent suggestions. I made the following psf file, and I
can connect the spheres any way I wish. Thanks!

PSF

       1 !NTITLE
 REMARKS VMD generated structure x-plor psf file

       4 !NATOM
       1 1 XXX H H 0.000000 1.0080 0
       2 1 XXX H H 0.000000 1.0080 0
       3 1 XXX H H 0.000000 1.0080 0
       4 1 XXX H H 0.000000 1.0080 0

       3 !NBOND: bonds
       2 4 4 3 2 3

       0 !NTHETA: angles

       0 !NPHI: dihedrals

       0 !NIMPHI: impropers

       0 !NDON: donors

       0 !NACC: acceptors

       0 !NNB

       0 0 0 0

       1 0 !NGRP
       0 0 0

Axel Kohlmeyer wrote:
> On 6/22/07, Arneh Babakhani <ababakha_at_mccammon.ucsd.edu> wrote:
>> 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,
> there might be an interesting alternative. i agree, it is indeed
> more convenient to generate frames and render your speheres
> as atoms.
>
> however, if you want to determine the bonding pattern, the best
> file type would be a .psf file, and then - depending on how large
> the computational effort - you could do your whole generation of
> coordinates within VMD (creating a selection for all atoms, then
> use animate dup to generate a new frame, and using $sel set {x y z}
> $some_list
> to set the coordinates. if you generate your coordinate output from a
> c/c++ code, you can even wrap it into a tcl command and dynaload
> and execute it from within VMD.
>
> i have used each of the techniques separately (and can provide examples).
>
> cheers,
> axel.
>
>> 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
>> >>
>> >
>> >
>> >
>> >
>>
>>
>
>