From: Toni Giorgino (toni.giorgino_at_gmail.com)
Date: Thu Jun 23 2011 - 14:50:14 CDT

Dears,

I was wondering - would it be appropriate to use the "measure inertia"
function now built in VMD, like this?

# Return the matrix which reorients the principal axes of inertia with
# x, y, z. The largest inertia axis will be aligned along z.
proc transinertia {sel} {
    set m [lindex [measure inertia $sel] 1]
    set v0 "[lindex $m 0] 0"
    set v1 "[lindex $m 1] 0"
    set v2 "[lindex $m 2] 0"
    set v3 "0 0 0 1"
    set m4 [list $v0 $v1 $v2 $v3]
    return $m4
}

set a [atomselect top all]
$a move [transinertia $a]

Best,
Toni Giorgino

On Thu, Jun 23, 2011 at 8:42 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Jun 22, 2011 at 3:17 PM, Adrian Roitberg <roitberg_at_qtp.ufl.edu>
> wrote:
> > Hi,
> >
> > Is there a simple way to align the moments of inertia of a selection of
> > atoms to the nominal x,y,z axes vmd uses ?
>
> hi adrian,
>
> could this be what you are looking for?
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
>
> cheers,
> axel.
>
> >
> > Thanks !
> >
> > --
> > Dr. Adrian E. Roitberg
> > Full Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg_at_ufl.edu
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>

-- 
Toni Giorgino, PhD - toni.giorgino_at_gmail.com - fax +39 0382 1850209
Post-doctoral research fellow - Computational Biochemistry and Biophysics
Lab
Universitat Pompeu Fabra - Barcelona Biomedical Research Park (PRBB)
C/ Doctor Aiguader 88, 08003 Barcelona, Spain