[modeller_usage] Rigid bodies on the backbone only.

[Gregoire Depret <>]

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


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