[modeller_usage] helix alignment with gap

[Guillaume LETELLIER <>]

Hi all

I am new to modeller and i'm currently trying to build a model of a GPCR 
using the bovine rhodopsin structure as template.
I have notice that in the middle of one of a region corresponding to a 
transmembrane segment, there is a very unambiguous gap of two residue in 
the sequence alignment.

Two model of this receptor have already been published and in both 
cases, authors have used sequence alignment without gaps, which means 
that half the residues of this TM are clearly not correctly aligned with 
the template.

I am confuse of how I should handle this gap to build my model.
Using a 2 residues helix-gapped alignment in modeller would result in a 
model with
   - ugly coil in the middle of the helix
   - a switch from one helix face to the opposite of amino acids
   - a longer loop next to the TM (or maybe a longer helix ?)
On the contrary, ignoring the gap and using a wrong alignment result in 
a  much better looking helix.

Should I deliberately ignore the sequence similarity to provide modeller 
an alignment with no gap in the TM ?


Best regards,
Guillaume LETELLIER

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