Hi,
May be you would like to have a look to MODELLER's ALPHA restraints. They take the helical gaps into consideration very nicely. Prevents kinking and keeps the faces nicely.
Hope it helps.
br,
Vivek Sharma
On 2/2/06, Guillaume LETELLIER guillaume.letellier@cea.fr wrote: > > 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 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > >