Re: [modeller_usage] Homology Modelling homodimer - alignment

[Modeller Caretaker <modeller-care@ucsf.edu>]

Christopher Mohr wrote:
> In the resulting alignment there is a separation ("/") between the two
> chains of the template sequence. But in the sequence of the target there
> isn't a separation of course. Do i have to put a separation in the
> sequence of the target in the alignment file or in the input file for
> the alignment script? Or whats the best way to handle this problem ?

I don't think I quite understand your question, but the usage of chain
breaks ("/") in your alignment is simple - if you have a chain break in
the target sequence, Modeller will not link the backbone between the
residues either side of the break. If this is what you want, put in a
chain break, and if not, don't.

Since a chain break is not a "real" residue, you should always align it
with another chain break, or a gap, in the template structure(s).

	Ben Webb, Modeller Caretaker
-- 
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