VMD-L Mailing List

From: Germain Vallverdu (germain_vallverdu_at_yahoo.fr)
Date: Sun May 02 2010 - 15:29:22 CDT

Axel,

Thanks you.

If I well understand you advice me to plot the vector who gives the orientation of my ellipsoid insteed of the ellipsoid ? Or is it a way with the licorice rep to give to a 2 atoms molecules a shape who looks like elliptic ?

You said that you looked into it a while ago, did you find a solution ? Did you wrote a script I could eventually use ?

In my model, each particle is define with a position of the center of mass and a vector orthogonal to the plane of the molecule (this is disklike molecules). Thus that is all information I have to represent my system.

In order to represent the shape of my molecule I first use numerous dummy atoms placed on the external surface of the particle. But if I have about one million of particles and I need thousound atoms to reprensent one particles, I think it will be hard to visualize that !

Thanks for your help

Germain

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Germain Salvato-Vallverdu
post-doctorant CEA/DAM/DPTA/SPMC/LDDM
01 69 26 48 01
PagePerso : http://germain.salvato-vallverdu.perso.sfr.fr

----- Message d'origine ----
De : Axel Kohlmeyer <akohlmey_at_gmail.com>
À : Germain Vallverdu <germain_vallverdu_at_yahoo.fr>
Cc : vmd-l_at_ks.uiuc.edu
Envoyé le : Dim 2 mai 2010, 22 h 08 min 54 s
Objet : Re: vmd-l: ellipsoidal particles

On Sun, May 2, 2010 at 3:10 PM, Germain Vallverdu
<germain_vallverdu_at_yahoo.fr> wrote:
> Dear VMD users

dear germain,

> I am using anisotropic potential for ellipsoidal particles and I would
> like to find a way to vizualise configurations extrated from a dynamics
> with pymol. I would like to know if is it a way to do so with VMD ?

not directly. it would require some work in the internals of VMD.
not impossible (i've looked into it a while ago), but not trivial either.

a workaround would be to convert your ellipsoids into two atoms
with a bond and then use the licorice representation.

salut,
    axel.

>
> Thank you for your help
>
> Germain
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Germain Salvato-Vallverdu
> post-doctorant CEA/DAM/DPTA/SPMC/LDDM
> 01 69 26 48 01
> PagePerso : http://germain.salvato-vallverdu.perso.sfr.fr
>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.