jinlian05@lzu.cn wrote: > I use multiple templates to model target protein, those templates have no overlap, > how does MODELLER to determine the orientation of multiple templates? There is no > information about orientation restraint on target or template.

It doesn't - the restraints are distance restraints, and as such are independent of orientation. You can certainly orient your templates by any method you so desire (e.g. manually; see http://salilab.org/modeller/9v2/manual/node26.html), or by setting initial_malign3d (see http://salilab.org/modeller/9v2/manual/node53.html), but that won't affect the restraints generated - only the initial model (.ini file). A reasonable initial model is, however, desirable, as the optimizer will have a much easier time generating your final models from it.

Ben Webb, Modeller Caretaker