VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 07 2012 - 15:11:19 CDT

Hi,
  Here is an old ellipsoid drawing script that Chris Forman (cjf41_at_cam.ac.uk)
wrote for VMD a while back. This is a good starting point for someone that
needs to draw ellipsoids and doesn't want to wait for a built-in feature
to be implemented. This is a simple Tcl script that draws ellipsoids
given the appropriate axes and rotation information. See attached script.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 31, 2012 at 10:14:54PM -0400, Axel Kohlmeyer wrote:
> On Thu, May 31, 2012 at 5:03 PM, bsnmrem-obj_at_yahoo.com
> <bsnmrem-obj_at_yahoo.com> wrote:
> > Dear Alex:
> >
> > Here is the post I was referring to:
> >
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/1820.html
>
> this is a very old post. i am not aware of what VMD
> command john is referring to. i know that there is
> an OpenGL primitive that can be used to turn a sphere
> into an ellipsoid and john and i have been discussing
> on occasion to have this implemented in VMD, but
> right now. the only option would be to approximate
> the ellipsoid through a set of triangles writing a custom
> command as john mentions. you might be able to
> make those smooth and look more like an ellipsoid
> using the trinorm primitive instead.
>
> axel.
>
> > I would like to draw many ellipsoids and be able to visualize
> > them. The result could be something just like this:
> >
> > mol new
> > draw material Opaque
> > draw color 1
> > draw sphere {0.1 0.7 0.2} radius 0.3 resolution 100
> > draw color 2
> > draw sphere {1.0 2.0 1.0} radius 1.2 resolution 100
> > mol new
> > draw material Transparent
> > draw color 3
> > draw sphere {0.0 0.0 0.0} radius 1 resolution 100
> >
> > Except that the spheres should be ellipsoids.
> >
> > Each ellipsoid would be given by the length of its semi-principal
> > axes. Also, the ellipsoid could be translated and rotated. The
> > translation would be given by a three dimensional vector. The
> > rotation could be given either by a rotation matrix in three
> > dimensions or three angles, whichever is easier to work with.
> >
> > Thank you for your attention.
> >
> >
> >
> > ----- Original Message -----
> > From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> > To: "bsnmrem-obj_at_yahoo.com" <bsnmrem-obj_at_yahoo.com>
> > Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> > Sent: Thursday, May 31, 2012 12:35 PM
> > Subject: Re: vmd-l: Drawing an ellipsoid
> >
> > On Thu, May 31, 2012 at 9:44 AM, bsnmrem-obj_at_yahoo.com
> > <bsnmrem-obj_at_yahoo.com> wrote:
> >> Hi!
> >>
> >> I would like to draw an ellipsoid. I have read other posts about it and
> >> someone said that it could be done by scaling a sphere
> >
> > "someone" is a horribly bad source of information.
> > almost as bad as the "friend of a friend".
> >
> >> non-uniformly. However, I could not find out how to scale a sphere
> >> non-uniformly. Can someone please give me an example?
> >
> > there is too little information here to give a reasonable answer.
> > what is it exactly that you want to do with that ellipsoid in VMD?
> >
> > axel.
> >
> >> Thanks,
> >> Brian
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com  http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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