[modeller_usage] Rigid bodies on the backbone only.

[Gregoire Depret <gdepret@ulb.ac.be>]

Hello,
I would like to apply rigid bodies only on the mainchain of my model in order 
to run molecular dynamics and conjuguate gradients. I have already tried to 
do it with :

mdl.restraints.rigid_bodies.append(rigid_body(mdl.residue_range('56:A', 
'48:A')))

and just before the optimization start :

atmselall = selection(mdl)
atmsel = selection.only_mainchain(atmselall)

and then :

cg.optimize(atmsel, max_iterations=50, actions=actions.trace(5, trcfil))

But my model is destroyed by CG and MD which is not the case when rigid body 
is applied on the whole chain.

Maybe I can define "rigid_body" with "atom_range" in place of "residue_range" 
and selecting all the atoms of the backbone (Ca, CO, N) for my residue range, 
but I think there must be a better way to achieve this.
Many Thanks for any suggestion.

Depret Grégoire
Graduate Student

gdepret@ulb.ac.be
Service de Structure et Fonction des Membranes Biologiques
Centre de Biologie Structurale et de Bioinformatique
Université Libre de Bruxelles
Boulevard du Triomphe CP 206/2
B-1050 Bruxelles
Belgium