I noticed that the alignment made no sense at all so I resend the message with a new one with mono space characters and hope it will be easier:

Hello 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 "deletions" 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