Dear Modellers.

I am trying to model a GPCR and I have a doubt about the transmembrane helices. It is known that they contain Pro residues which produce a kink in the helix, so I am not interesting in modelling the seven helices as an ideal helix .

My cuestions are:

1) If I do :

MAKE_RESTRAINTS RETRAINT_TYPE ='alpha'

Can MODELLER take account for these proline kinks ? (I mean if it has specific backbone dihedarl angles for modelling them or should I introduce them as constraints ?)

2) If not, is it a good option to divide the whole helix in segments, excluding the prolines, and to force them to be an ideal alpha helix?

Thanks in advance.