From: John Stone (
Date: Wed Dec 14 2005 - 12:48:00 CST

  Can you tell me exactly what atom selections you're using when you're
aligning the molecules? They have a different number of atoms and residues,
so you must be selecting a subset of atoms even to get as far as you're
describing. In order to get correct behavior, you must make an atom selection
which yields a 1-to-1 mapping of atoms in the one molecule to atoms in the
other. If you can't do this with a single atom selection, then the graphical
RMSD tool won't be able to do what you need, and you'll have to do it using
the 'measure fit' command instead. There's a simple example of how to do
this with the scripting interface in the VMD tutorial:

  John Stone

On Wed, Dec 14, 2005 at 01:05:11PM +0100, Stéphane Teletchéa wrote:
> Hello,
> I'm encountering a problem while trying to align two molecules (1F88.pdb
> and 1GZM.pdb) :
> - they contains two chains and while i align one of them, i get only
> chain A aligned, both chain B are opposite.
> - if i want ot manually move the molecule 2 relative to the molecule 1
> (molecule 1 is fixed in that case), when i press align, or rmsd after
> this manual translation and rotation, there's nothing happening.
> I htink this behaviour is lagging for some time (at least since 1.8.1)
> but i'm not sure i've already reported it. Done :-)
> Any clue about the alignment ?
> More information needed ?
> Thanks a lot in advance for suggestion/help,
> Stéphane
> --
> Stéphane Téletchéa, PhD.
> Unité Mathématique Informatique et Génome
> INRA, Domaine de Vilvert Tél : (33) 134 652 121 / 3086
> 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901

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