[modeller_usage] Re: I don't want to use one region of a *target* for construction of my model.

[Modeller Caretaker <>]

On 3/12/24 11:14 AM, hmad3--- via modeller_usage wrote:
> If I remove "iiiii" from the sequence before aligning with the above
> template sequence (without the disordered region), "h" and "j" will
> be interpreted as continuous in the .pdb file of the target
> generated, affecting the structure of the protein. How would I make
> PDB interpret a gap between "h" and "j" that aligns with the gap
> between "b" and "d" in the template?

I think by "gap" here you mean "chain break", i.e. you don't want a 
peptide bond between the last residue in "h" and the first residue in 
"j". This is straightforward: add a chain break character ("/") between 
h and j in your target sequence. This simply tells Modeller to not 
construct that peptide bond. Normally one would align a chain break in 
the target with a chain break or a gap ("-") in the template.

> Another note: both the template and target sequences are single chains.

Perhaps you mean all residues have the same chain ID. The target will be 
two chains if you add a chain break. (Modeller will by default label 
them A and B, but you can call them both A if you like.)

	Ben Webb, Modeller Caretaker
-- 
             https://salilab.org/modeller/
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