Hello,
It is right. Or as good as it gets, for two reasons, because Modeller does not account for the environment explicitly anyway and loop modeling will effect only the loop regions while keeping the rest of the structure intact, irrespectively of how properly the rest was built.
You will find a web interface to loop modeling in Modeller at http://alto.compbio.ucsf.edu/modloop//modloop.html that may help.
best wishes,Andras
On Wed, 2003-08-27 at 02:32, Moshe Amitay wrote: > Hi all, > I whuld like your advice: > I build a model of a membrane protein and I want now to do "loop modeling" > to few extra cellular and intra-cellular loops. > I wonder if this protocol of modeller is the right > choice since the model doesn't contain the membrane and I actually ignore > the influence of the polar heads. > thank's > Moshe Amity. > > > > > -------------------------------------- > Moshe Amity amitaym@mail.biu.ac.il > Dep. of Chemistry > Bar Ilan University > Israel.