Akansha Saxena wrote: > I used modeller to build a model for transmembrane > protein (its an ion channel). The model is fine but > has variations from the template structure. I wanted > to know does modeller uses some different constraints > for a transmembrane protein or it is similar to all > other proteins.

Modeller does not do anything special for transmembrane proteins; it simply extracts restraints from the template structures. Note, however, that Modeller's internal database of protein alignments, used to derive statistics, include no transmembrane proteins, so it may not behave as well as for globular systems.

Ben Webb, Modeller Caretaker