VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 15 2004 - 13:49:01 CST

Ahmet,
  Here's a simple page explaining how to do rotations about an
arbitrary normalized vector. Google is a useful tool even for things
like this:
  http://www.cprogramming.com/tutorial/3d/rotation.html

The OpenGL book has the same thing in a less boiled down form
but I thought this is a common enough question to merit finding
a useful link for people rolling their own scripts etc.

  John

On Fri, Mar 12, 2004 at 09:43:41PM +0200, Ahmet Bakan wrote:
> Dear John and All,
>
> I have some further questions on rotation around some vector:
>
> I want to simulate two chains and find the surface with maximum free
> energy possible. I will think two chains as two spheres next to each
> other. I plan to write a script which will take the larger sphere and
> locate its geometric center to zerovector and will move the smaller
> sphere around the large sphere and occationally rotate the small sphere
> around a vector. For each different alignment the loop will make some
> equilibration dynamics. To write this script I need a command or any
> idea to perform rotation around some vector.
>
> Thanks so far John, your instructions will be useful.
> Ahmet
>
> ==============ABC==============
> Ahmet Bakan
> Chemistry, Junior
> Koc University
> abakan_at_ku.edu.tr
> MSN ahmetbakan_at_msn.com
> ICQ #86167698
> http://home.ku.edu.tr/~abakan
>
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Friday, March 12, 2004 8:47 PM
> To: Ahmet Bakan
> Cc: VMD-L
> Subject: Re: vmd-l: Rotatind a chainn
>
>
> Hi,
> Use the Mouse->Move->Rep mode, press and hold shift, and then click on
>
> a representation set to the chain you want to rotate, and you should be
> able to modify the atom coordinates (rather than just rotating the
> scene). You can also use the atomselect 'move' subcommand to apply a
> transformation to an atom selection. Once you've done all this, you can
> save out a new coordinate file by selecting the molecule in the molecule
> browser of the main VMD window, then use File->Save Coordinates to save
> a new coordinate or trajectory file.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 12, 2004 at 04:59:09PM +0200, Ahmet Bakan wrote:
> > Dear VMD Fellows,
> >
> > I have two binding chains. Using TkCon console I can rotate scene.
> > What I want to do is altering coordinates of one of the two chains
> > with respect to the other by rotation and then starting a simulation
> > with this alignment. How can I perform this?
> >
> > Thanks in advance,
> > Ahmet Bakan
> >
> > ==============ABC==============
> > Ahmet Bakan
> > Chemistry, Junior
> > Koc University
> > abakan_at_ku.edu.tr
> > MSN ahmetbakan_at_msn.com
> > ICQ #86167698
> > http://home.ku.edu.tr/~abakan
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> Institute for Advanced Science and Technology University of Illinois,
> 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078