From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Aug 28 2007 - 09:22:35 CDT

I found another problem.

"measure fit $sel $ref order {3 4 5 6 0 1 2}"

This works, but the following doesn't.

"measure rmsd $sel $ref order {3 4 5 6 0 1 2}"

I think I have to reindex again.

On 8/28/07, Myunggi Yi <myunggi_at_gmail.com> wrote:
> I did reindex using editor. ^_^;
> Thank you.
>
>
> On 8/24/07, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
> > Hi,
> >
> > On Thu, Aug 23, 2007 at 11:19:35PM -0400, Myunggi Yi wrote:
> > > I want to select two atom sets to superimpose two molecules.
> > > However, VMD always ignore my selection order.
> > >
> > > set sel [atomselect 1 "index 6 7 8 1 2 3 4"]
> > > set ref [atomselect 0 "index 1 2 3 5 6 7 8"]
> > > $sel get index
> > > returns 1 2 3 4 6 7 8
> >
> > This is the expected behavior.
> >
> > > Then how can I do the right rms fitting?
> >
> > You can achieve this by passing an order parameter to 'measure fit'. The
> > order is a 0-based list that reorders the second selection. In your
> > case, you want something like (assuming I got the order right :-)):
> >
> > measure fit $sel $ref order {3 4 5 6 0 1 2}
> >
> > It seems though that this option to 'measure fit' is not docummented in
> > the user guide or the command usage yet.
> >
> > Cheers,
> > Leo
> >
> > --
> > Leonardo Trabuco, Ph.D. student
> > Theoretical and Computational Biophysics Group
> > University of Illinois at Urbana-Champaign
> >
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
>

-- 
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi