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new user and domain movements

Dear Modellers,
	I am a new user of modeller having just completed my PHD in X-ray crystallography. I have two questions about modeller.
	1) Do the template positions of domains in space, for multidomain proteins, have to always be pre-arranged/aligned by me to the approximate postions of the putative model before running modeller ? 

	I ask this because I tried to model a diabody using two identical Fv fragments (VH/VL), I input two copies  of the same template pdb coordinate file for both Fvs in the diabody, aligning the respective domains to a sequence that ran: VH-linker-VL(chain break)VH-linker-VL where the linker is any thing from 0-15 residues, the linkers were loop modelled.

                                ___________________        ___________________
                               |                                |        |                                 |N
                               |              VL              |--------|          VH                  |
                            C |__________________|        |___________________|
                            N |                                |        |                                |
                               |          VH                  |--------|           VL                  |
                               |__________________|        |___________________|C

	The result was that Modeller returned some ridiculous models where the two Fvs were basically occupying the same space. I repeated this excercise by arbitrarily aligning the two Fv domains such that the C-terminal of the VH was close to the N-terminal of the VL for each linker region. This time modeller returned results that were much more sensible but the Fv domains had not moved far from the original positions in which I placed them, I would like to influence the result less !

	2) In a way this is similar to the first question. How can I model the possible linker flexibility in a diabody ?
I would need to fix the atom positions in each Fv with respect to each other but not thier actual coordinates, whilst allowing a variety of linker models to be built.

	There are few diabody template structures available and the flexible linkers point to the potentiality of a large number of possible conformers for these molecules, I suppose what I really want to know is "Is modeller the program for this type of modelling ?"

	Thanks for your patience