From: Ahmet Bakan (
Date: Fri Mar 12 2004 - 13:43:41 CST

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 Bakan
Chemistry, Junior
Koc University
ICQ #86167698
-----Original Message-----
From: John Stone []
Sent: Friday, March 12, 2004 8:47 PM
To: Ahmet Bakan
Subject: Re: vmd-l: Rotatind a chainn
  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
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
> ICQ #86167698

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