[modeller_usage] Modeling a larger protein with multiple templates

[nornik <>]

Hello
I have sent this query before, but noone replied so I will send it again, hoping for some assistance.
I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this:
MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model
AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template
----BBBBSBBBBBBB--------------------------------------------------- template2
----------CCCCCCCCCSCCCCC------------------------------------------ template3
----------------------------------DDDDDSDDDDDDDSDDDDDD------------- template4
----------------------------------------------------------EEEESEEEE template5
        sulfur bridge               sulfur bridge     sulfur bridge

Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "inserts" with the other four templates and still maintain the sulfur bridges.

Any other suggestions are of course also welcome in trying to solve this problem.

Thank you