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Dear Modellers.

I am trying to model a GPCR and I have a doubt about the transmembrane
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 :


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.