VMD-L Mailing List

From: Stéphane Teletchéa (steletch_at_jouy.inra.fr)
Date: Thu Dec 15 2005 - 11:59:52 CST

Dow Hurst DPHURST a écrit :
> You can't align chain A and B simultaneously as they come from different
> space groups. I'd recommend using 1GZM chain A for your rhodopsin inactive
> starting template for any GPCR modelling. You get undistorted loops from
> that crystal structure. Chain A is considered in both 1F88 and 1GZM to be
> the better structure.
> Dow
>

Hum, you're right, i should have thought about this before.
Since, the problem still stands :

If you move one molecule relatively to another one, the rmsd align does
not work any more (on any chain). As i'm using the alpha version to help
improving it, i thought this report could help tracking the bug.

By the way, thanks for the space group recommendation.

Stéphane 

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 121 / 3086
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901