[modeller_usage] clockwise pentamer to anticlockwise model

Dear colleagues,

       I want to model a pentamer. I have two templates. One of the templates is arranged anti-clockwise in the order ABCDE. The other template runs clockwise (AEDCB) and has identical chains. Thus if I overlap the two templates, subunit B overlaps with subunit E and so on.

I want to do modelling in 2 steps.

a. I want to get an initial anticlockwise model (ABCDE) from clockwise template (identical chains AEDCB).
b. The model obtained from step 1 will be overlapped with the anticlockwise template to build some missing residues.


I tried to get through step a by 
 
1. Changing the alignment file
2. by changing chain identification number in the template
3. by changing the order of subunits arranged in the template

Each time, I end up with the same clockwise model.

Thanks in advance for any kind of suggestion in this regard.

Prema,
Graduate student,
UOH.