VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 29 2007 - 00:11:02 CDT

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