From: Leonardo Trabuco (
Date: Fri Jul 06 2007 - 10:10:10 CDT


Just to add to what Peter said, you can use a measure of structural
similarity called Qres. It works on a set of aligned structures and does
not require a 1:1 correspondence as the RMSD; it is implemented in
MultiSeq (Extension->Analysis->Multiseq). For a definition of the Qres
measure, please refer to the following paper:

Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey-Schulten
MultiSeq: Unifying sequence and structure data for evolutionary analysis
BMC Bioinformatics, 2006, 7:382


On Fri, Jul 06, 2007 at 01:50:49AM -0500, Peter Freddolino wrote:
> Hi,
> yes, it can -- you just need to define which atoms are equivalent in
> each case (for example, all atoms in some highly conserved region of the
> protein). Making an atom selection for equivalent atoms in each protein
> will allow you to calculate an RMSD. The whole concept is rather
> ill-defined if you don't have a 1:1 correlation between some subset of
> residues in each protein... if you have some other sort of measure in
> mind, you should be able to write a tcl script to calculate it.
> Peter
> hori koshii wrote:
> > Hi everybody.
> >
> > Just wonder if VMD allows calculation of RMSD for several molecules
> > with different numbers of amino acids. Very appreciated.
> >
> >
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Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign