Re: [modeller_usage] help--orient multiple template

[Modeller Caretaker <>]

 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
--
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