VMD-L Mailing List

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Aug 30 2007 - 08:49:25 CDT

I did re-index my pdb file already.

You don't have to hurry to send me the test version.
Take your time.

Thank you.

Have a nice day.

On 8/29/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> The "measure rmsd" command doesn't support an order parameter yet, as
> you've discovered. I'll see about adding one, but in the mean time you
> may find it more time-efficient to reorder the atom indices in your file
> or possibly to select different atoms to use in computing the RMSD.
> If you like, I could possibly provide a test version of VMD with
> an rmsd order parameter, perhaps by next week.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 28, 2007 at 05:35:49PM -0400, Myunggi Yi wrote:
> > I meant the order parameter could be applied
> > ONLY to "measure fit"
> > NOT to "measure rmsd"
> >
> > Even after right fitting, you can't measure right RMSD.
> >
> >
> >
> > On 8/28/07, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
> > > On Tue, Aug 28, 2007 at 10:22:35AM -0400, Myunggi Yi wrote:
> > > > 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.
> > >
> > > Yes, the order parameter applies to the second selection.
> > >
> > > 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
>
> --
> 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
> 

-- 
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