From: Stéphane Teletchéa (
Date: Thu Dec 15 2005 - 03:54:08 CST

John Stone a écrit :
> Stephane,
> 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

Well, here is my detailed procedure :
1 - load as New Molecule 1F88.pdb
2 - load as New Molecule 1GZM.pdb
3 - Change both molecules as 'NewCartoon' (nice by the way :-) and color
by molecule (easier to identify them)
4 - Launch Tools->Analysis->RMSD calculator (use default residue
selection 5 to 85 and 'Top')

--> You'll get an alignmment of chains A but not chain B :-(

Do the same, do one alignment then move one molecule relatively to the
other one (e.g. move the 1GZM with the 1F88 fixed). Unfix all molecule
then try again to aligne them. No movement is now happening, no error
message in the vmd console.

For what it worths, i'm on othographic perspective ...


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