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 noinformation 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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage